Starting phenix.real_space_refine on Fri Aug 7 22:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.map" model { file = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2026/8v32_42941.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.034 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 103 5.49 5 Mg 7 5.21 5 S 80 5.16 5 C 15347 2.51 5 N 4309 2.21 5 O 4744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24592 Number of models: 1 Model: "" Number of chains: 20 Chain: "Q" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2440 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "J" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3707 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 434} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21784 SG CYS J 139 78.454 110.315 45.286 1.00 74.34 S ATOM 21805 SG CYS J 142 75.876 109.050 42.735 1.00 82.56 S ATOM 22019 SG CYS J 167 78.594 111.482 41.591 1.00 78.23 S ATOM 22108 SG CYS J 178 81.922 100.551 55.975 1.00 90.70 S ATOM 22131 SG CYS J 181 84.264 98.248 57.901 1.00 88.13 S ATOM 22266 SG CYS J 197 82.394 97.102 54.595 1.00 80.72 S ATOM 22287 SG CYS J 200 80.627 97.435 57.835 1.00 84.71 S Time building chain proxies: 5.24, per 1000 atoms: 0.21 Number of scatterers: 24592 At special positions: 0 Unit cell: (143.85, 151.248, 153.714, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 80 16.00 P 103 15.00 Mg 7 11.99 O 4744 8.00 N 4309 7.00 C 15347 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 - 3.00 Amino acid : True - 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: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS J 170 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 142 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 167 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 139 " pdb=" ZN J 502 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 200 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 178 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 197 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 181 " Number of angles added : 9 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 11 sheets defined 62.4% alpha, 5.2% beta 38 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.857A pdb=" N LEU Q 11 " --> pdb=" O PRO Q 8 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR Q 13 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 8 through 13' Processing helix chain 'Q' and resid 15 through 25 Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 79 Processing helix chain 'Q' and resid 80 through 82 No H-bonds generated for 'chain 'Q' and resid 80 through 82' Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.655A pdb=" N TYR Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 125 removed outlier: 3.567A pdb=" N LYS Q 125 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 164 Processing helix chain 'Q' and resid 172 through 178 Processing helix chain 'Q' and resid 181 through 186 removed outlier: 4.738A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 200 removed outlier: 3.530A pdb=" N THR Q 199 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.681A pdb=" N PHE Q 214 " --> pdb=" O LEU Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 removed outlier: 3.544A pdb=" N HIS Q 254 " --> pdb=" O THR Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 266 through 273 Processing helix chain 'Q' and resid 277 through 295 removed outlier: 3.551A pdb=" N LYS Q 282 " --> pdb=" O ILE Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.622A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 330 Processing helix chain 'R' and resid 8 through 13 Processing helix chain 'R' and resid 15 through 25 Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.648A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 removed outlier: 3.536A pdb=" N ARG R 67 " --> pdb=" O LYS R 63 " (cutoff:3.500A) Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 148 through 164 Processing helix chain 'R' and resid 173 through 178 Processing helix chain 'R' and resid 186 through 200 removed outlier: 4.284A pdb=" N CYS R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU R 192 " --> pdb=" O GLN R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.844A pdb=" N THR R 213 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.520A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 273 Processing helix chain 'R' and resid 277 through 295 Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.591A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 330 removed outlier: 3.964A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 343 removed outlier: 3.518A pdb=" N VAL R 336 " --> pdb=" O THR R 332 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 13 removed outlier: 3.541A pdb=" N LEU S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.519A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 Proline residue: S 80 - end of helix removed outlier: 3.915A pdb=" N GLU S 83 " --> pdb=" O LEU S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 173 through 178 Processing helix chain 'S' and resid 184 through 200 removed outlier: 4.007A pdb=" N GLN S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU S 192 " --> pdb=" O GLN S 188 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU S 195 " --> pdb=" O CYS S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 removed outlier: 3.524A pdb=" N THR S 213 " --> pdb=" O GLU S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 224 Processing helix chain 'S' and resid 237 through 254 Processing helix chain 'S' and resid 266 through 275 Processing helix chain 'S' and resid 277 through 296 Processing helix chain 'S' and resid 301 through 308 removed outlier: 3.788A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 344 removed outlier: 3.549A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 14 removed outlier: 3.584A pdb=" N LEU T 12 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 26 Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 83 Proline residue: T 80 - end of helix Processing helix chain 'T' and resid 105 through 118 Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 173 through 178 Processing helix chain 'T' and resid 184 through 200 removed outlier: 4.015A pdb=" N GLN T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 removed outlier: 3.595A pdb=" N LEU T 281 " --> pdb=" O CYS T 277 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 308 removed outlier: 3.566A pdb=" N ARG T 308 " --> pdb=" O ASP T 304 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 329 removed outlier: 3.664A pdb=" N LYS T 317 " --> pdb=" O ALA T 313 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN T 328 " --> pdb=" O GLU T 324 " (cutoff:3.500A) Processing helix chain 'T' and resid 332 through 344 Processing helix chain 'U' and resid 8 through 13 Processing helix chain 'U' and resid 15 through 26 removed outlier: 3.705A pdb=" N ARG U 19 " --> pdb=" O PRO U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 46 Processing helix chain 'U' and resid 62 through 85 Proline residue: U 80 - end of helix removed outlier: 3.978A pdb=" N SER U 84 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 118 Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 184 through 198 removed outlier: 4.141A pdb=" N GLN U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU U 189 " --> pdb=" O LEU U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 215 removed outlier: 3.602A pdb=" N THR U 213 " --> pdb=" O GLU U 210 " (cutoff:3.500A) Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 254 Processing helix chain 'U' and resid 266 through 275 removed outlier: 3.608A pdb=" N PHE U 270 " --> pdb=" O HIS U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 308 removed outlier: 3.585A pdb=" N ARG U 308 " --> pdb=" O ASP U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 329 removed outlier: 3.548A pdb=" N LYS U 317 " --> pdb=" O ALA U 313 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN U 328 " --> pdb=" O GLU U 324 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 344 removed outlier: 3.560A pdb=" N VAL U 336 " --> pdb=" O THR U 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 13 removed outlier: 3.602A pdb=" N LEU V 11 " --> pdb=" O PRO V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.525A pdb=" N ARG V 19 " --> pdb=" O PRO V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 46 Processing helix chain 'V' and resid 62 through 78 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 172 through 178 Processing helix chain 'V' and resid 184 through 199 removed outlier: 3.683A pdb=" N GLN V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU V 192 " --> pdb=" O GLN V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 removed outlier: 3.588A pdb=" N THR V 213 " --> pdb=" O GLU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 224 Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 266 through 274 Processing helix chain 'V' and resid 277 through 296 Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.506A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.512A pdb=" N GLU V 324 " --> pdb=" O LYS V 320 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 344 Processing helix chain 'W' and resid 8 through 13 removed outlier: 3.520A pdb=" N LEU W 11 " --> pdb=" O PRO W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 25 Processing helix chain 'W' and resid 30 through 46 Processing helix chain 'W' and resid 62 through 77 Processing helix chain 'W' and resid 78 through 83 removed outlier: 3.730A pdb=" N GLU W 83 " --> pdb=" O LEU W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 148 through 164 Processing helix chain 'W' and resid 173 through 178 removed outlier: 3.861A pdb=" N GLY W 177 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 200 removed outlier: 3.727A pdb=" N GLN W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 215 Processing helix chain 'W' and resid 218 through 224 Processing helix chain 'W' and resid 237 through 255 Processing helix chain 'W' and resid 263 through 265 No H-bonds generated for 'chain 'W' and resid 263 through 265' Processing helix chain 'W' and resid 266 through 275 Processing helix chain 'W' and resid 277 through 295 Processing helix chain 'W' and resid 301 through 308 removed outlier: 4.093A pdb=" N ARG W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 330 Processing helix chain 'W' and resid 332 through 344 Processing helix chain 'J' and resid 40 through 52 Processing helix chain 'J' and resid 55 through 64 Processing helix chain 'J' and resid 70 through 75 Processing helix chain 'J' and resid 76 through 78 No H-bonds generated for 'chain 'J' and resid 76 through 78' Processing helix chain 'J' and resid 81 through 87 removed outlier: 3.557A pdb=" N PHE J 85 " --> pdb=" O PHE J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 91 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 156 through 161 Processing helix chain 'J' and resid 219 through 244 removed outlier: 4.153A pdb=" N GLN J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 265 removed outlier: 3.508A pdb=" N ASP J 262 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 279 through 288 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 308 through 314 Processing helix chain 'J' and resid 324 through 329 removed outlier: 3.873A pdb=" N GLN J 328 " --> pdb=" O THR J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 359 Processing helix chain 'J' and resid 366 through 375 Processing helix chain 'J' and resid 377 through 385 removed outlier: 4.054A pdb=" N HIS J 384 " --> pdb=" O THR J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 425 removed outlier: 3.723A pdb=" N CYS J 389 " --> pdb=" O PHE J 385 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN J 425 " --> pdb=" O SER J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 436 Processing helix chain 'J' and resid 442 through 446 Processing helix chain 'J' and resid 448 through 461 Processing sheet with id=AA1, first strand: chain 'Q' and resid 91 through 95 Processing sheet with id=AA2, first strand: chain 'R' and resid 91 through 95 removed outlier: 5.953A pdb=" N ILE R 53 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY R 207 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL R 55 " --> pdb=" O GLY R 207 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE R 230 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR R 56 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 92 through 95 removed outlier: 3.608A pdb=" N VAL S 92 " --> pdb=" O VAL S 167 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE S 53 " --> pdb=" O LEU S 205 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE S 230 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR S 56 " --> pdb=" O PHE S 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 91 through 95 removed outlier: 6.827A pdb=" N VAL T 92 " --> pdb=" O PHE T 169 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP T 171 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE T 94 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY T 57 " --> pdb=" O GLY T 207 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE T 52 " --> pdb=" O VAL T 226 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 133 through 135 Processing sheet with id=AA6, first strand: chain 'U' and resid 91 through 95 removed outlier: 6.568A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE U 53 " --> pdb=" O LEU U 205 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'U' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'V' and resid 91 through 95 removed outlier: 6.843A pdb=" N VAL V 92 " --> pdb=" O PHE V 169 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASP V 171 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE V 94 " --> pdb=" O ASP V 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY V 57 " --> pdb=" O GLY V 207 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE V 52 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE V 228 " --> pdb=" O PHE V 52 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE V 54 " --> pdb=" O ILE V 228 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE V 230 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR V 56 " --> pdb=" O PHE V 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.756A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 92 through 94 removed outlier: 3.958A pdb=" N CYS W 204 " --> pdb=" O PHE W 168 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE W 53 " --> pdb=" O LEU W 205 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 134 through 135 1195 hydrogen bonds defined for protein. 3342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4448 1.33 - 1.45: 6689 1.45 - 1.57: 13828 1.57 - 1.70: 198 1.70 - 1.82: 109 Bond restraints: 25272 Sorted by residual: bond pdb=" CA GLN R 186 " pdb=" C GLN R 186 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA THR J 8 " pdb=" C THR J 8 " ideal model delta sigma weight residual 1.526 1.462 0.064 1.37e-02 5.33e+03 2.17e+01 bond pdb=" CA LEU T 195 " pdb=" C LEU T 195 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.27e-02 6.20e+03 1.80e+01 bond pdb=" N LEU J 6 " pdb=" CA LEU J 6 " ideal model delta sigma weight residual 1.463 1.409 0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" CA LEU J 6 " pdb=" C LEU J 6 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.21e-02 6.83e+03 1.44e+01 ... (remaining 25267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 34342 2.75 - 5.51: 236 5.51 - 8.26: 31 8.26 - 11.02: 5 11.02 - 13.77: 2 Bond angle restraints: 34616 Sorted by residual: angle pdb=" C GLU J 362 " pdb=" N PRO J 363 " pdb=" CA PRO J 363 " ideal model delta sigma weight residual 127.00 113.23 13.77 2.40e+00 1.74e-01 3.29e+01 angle pdb=" C GLU J 362 " pdb=" N PRO J 363 " pdb=" CD PRO J 363 " ideal model delta sigma weight residual 120.60 133.13 -12.53 2.20e+00 2.07e-01 3.24e+01 angle pdb=" N THR J 8 " pdb=" CA THR J 8 " pdb=" C THR J 8 " ideal model delta sigma weight residual 109.69 101.51 8.18 1.44e+00 4.82e-01 3.23e+01 angle pdb=" CA PRO V 90 " pdb=" N PRO V 90 " pdb=" CD PRO V 90 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" C PRO J 364 " pdb=" N PRO J 365 " pdb=" CA PRO J 365 " ideal model delta sigma weight residual 119.89 125.02 -5.13 1.02e+00 9.61e-01 2.53e+01 ... (remaining 34611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 12099 17.74 - 35.49: 1985 35.49 - 53.23: 834 53.23 - 70.97: 199 70.97 - 88.72: 45 Dihedral angle restraints: 15162 sinusoidal: 6905 harmonic: 8257 Sorted by residual: dihedral pdb=" CA LYS J 447 " pdb=" C LYS J 447 " pdb=" N GLN J 448 " pdb=" CA GLN J 448 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU J 362 " pdb=" C GLU J 362 " pdb=" N PRO J 363 " pdb=" CA PRO J 363 " ideal model delta harmonic sigma weight residual 0.00 -21.09 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP J 286 " pdb=" C TRP J 286 " pdb=" N GLN J 287 " pdb=" CA GLN J 287 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 15159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3125 0.050 - 0.099: 632 0.099 - 0.149: 114 0.149 - 0.199: 5 0.199 - 0.248: 3 Chirality restraints: 3879 Sorted by residual: chirality pdb=" CB ILE W 322 " pdb=" CA ILE W 322 " pdb=" CG1 ILE W 322 " pdb=" CG2 ILE W 322 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA TYR J 9 " pdb=" N TYR J 9 " pdb=" C TYR J 9 " pdb=" CB TYR J 9 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU S 263 " pdb=" CB LEU S 263 " pdb=" CD1 LEU S 263 " pdb=" CD2 LEU S 263 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3876 not shown) Planarity restraints: 4117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL V 89 " 0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO V 90 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO V 90 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO V 90 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 185 " 0.021 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU R 185 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU R 185 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN R 186 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 46 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" CD GLU R 46 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU R 46 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU R 46 " -0.017 2.00e-02 2.50e+03 ... (remaining 4114 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 189 2.55 - 3.14: 18463 3.14 - 3.72: 40420 3.72 - 4.31: 54455 4.31 - 4.90: 90627 Nonbonded interactions: 204154 Sorted by model distance: nonbonded pdb=" OG1 THR R 64 " pdb="MG MG R 601 " model vdw 1.959 2.170 nonbonded pdb=" O3G ATP R 600 " pdb="MG MG R 601 " model vdw 1.973 2.170 nonbonded pdb=" OG1 THR S 64 " pdb="MG MG S 601 " model vdw 1.995 2.170 nonbonded pdb=" OG1 THR U 64 " pdb="MG MG U 601 " model vdw 2.034 2.170 nonbonded pdb=" OG1 THR V 64 " pdb="MG MG V 601 " model vdw 2.043 2.170 ... (remaining 204149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'S' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'T' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'U' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'V' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'W' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) } 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: 2.910 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.099 25280 Z= 0.247 Angle : 0.633 13.771 34625 Z= 0.399 Chirality : 0.041 0.248 3879 Planarity : 0.005 0.124 4117 Dihedral : 20.854 88.718 9822 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.43 % Allowed : 32.98 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2802 helix: 1.13 (0.13), residues: 1650 sheet: -0.87 (0.42), residues: 187 loop : -0.41 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 231 TYR 0.027 0.001 TYR W 37 PHE 0.037 0.001 PHE W 169 TRP 0.022 0.001 TRP J 284 HIS 0.005 0.001 HIS T 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.25 (25272) covalent geometry : angle 0.63143 / 0.40 (34616) hydrogen bonds : bond 0.17321 / 11.68 ( 1289) hydrogen bonds : angle 5.27161 / 3.78 ( 3530) metal coordination : bond 0.00421 / 0.25 ( 8) metal coordination : angle 3.17570 / 1.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 580 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 210 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6745 (tm-30) REVERT: R 46 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7077 (tm-30) REVERT: R 100 GLU cc_start: 0.7741 (pm20) cc_final: 0.7509 (pm20) REVERT: R 316 GLN cc_start: 0.8070 (mt0) cc_final: 0.7839 (mt0) REVERT: S 145 SER cc_start: 0.8542 (p) cc_final: 0.8337 (p) REVERT: S 148 VAL cc_start: 0.8408 (m) cc_final: 0.8188 (t) REVERT: S 306 GLN cc_start: 0.8356 (mt0) cc_final: 0.8135 (mt0) REVERT: S 326 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7762 (mt-10) REVERT: S 332 THR cc_start: 0.8306 (p) cc_final: 0.8034 (t) REVERT: T 73 LYS cc_start: 0.8108 (tptp) cc_final: 0.7849 (tptp) REVERT: T 116 THR cc_start: 0.8393 (m) cc_final: 0.8146 (t) REVERT: T 268 GLU cc_start: 0.7937 (mp0) cc_final: 0.7719 (mt-10) REVERT: T 326 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7460 (mt-10) REVERT: T 340 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8012 (mtt-85) REVERT: U 17 THR cc_start: 0.7865 (m) cc_final: 0.7637 (t) REVERT: U 54 PHE cc_start: 0.8289 (m-80) cc_final: 0.7770 (m-80) REVERT: U 95 GLU cc_start: 0.7449 (tt0) cc_final: 0.7199 (tt0) REVERT: U 178 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8577 (mttm) REVERT: U 253 GLN cc_start: 0.8192 (mp10) cc_final: 0.7820 (mp10) REVERT: U 286 LYS cc_start: 0.7327 (tmtm) cc_final: 0.7049 (tttm) REVERT: V 38 GLU cc_start: 0.7651 (tp30) cc_final: 0.7332 (tp30) REVERT: V 68 LEU cc_start: 0.8876 (mt) cc_final: 0.8640 (mp) REVERT: V 90 PRO cc_start: 0.8398 (Cg_exo) cc_final: 0.8132 (Cg_endo) REVERT: V 130 VAL cc_start: 0.8441 (t) cc_final: 0.8228 (p) REVERT: V 327 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7543 (ttp80) REVERT: W 52 PHE cc_start: 0.7652 (m-10) cc_final: 0.7264 (m-80) REVERT: W 69 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7340 (ttp80) REVERT: W 106 TRP cc_start: 0.8189 (m100) cc_final: 0.7960 (m100) REVERT: W 119 GLU cc_start: 0.6707 (pp20) cc_final: 0.6359 (pp20) REVERT: W 153 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7605 (mtp180) REVERT: W 168 PHE cc_start: 0.8254 (t80) cc_final: 0.7753 (t80) REVERT: W 224 ARG cc_start: 0.7716 (mtp85) cc_final: 0.7393 (mtt-85) REVERT: J 69 ASN cc_start: 0.8160 (t0) cc_final: 0.7957 (m-40) REVERT: J 86 ASN cc_start: 0.7973 (m-40) cc_final: 0.7584 (m110) REVERT: J 172 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7659 (mmmm) REVERT: J 310 VAL cc_start: 0.8156 (m) cc_final: 0.7945 (p) REVERT: J 431 GLU cc_start: 0.6951 (tt0) cc_final: 0.6717 (tp30) outliers start: 35 outliers final: 28 residues processed: 606 average time/residue: 0.1878 time to fit residues: 171.3206 Evaluate side-chains 580 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 552 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain T residue 188 GLN Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 163 ARG Chi-restraints excluded: chain U residue 188 GLN Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 188 GLN Chi-restraints excluded: chain V residue 234 CYS Chi-restraints excluded: chain W residue 158 ASN Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 382 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 25 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 316 GLN S 337 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 188 GLN ** T 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 314 GLN V 186 GLN V 188 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118699 restraints weight = 36644.012| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.01 r_work: 0.3368 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25280 Z= 0.198 Angle : 0.592 8.275 34625 Z= 0.318 Chirality : 0.043 0.230 3879 Planarity : 0.005 0.064 4117 Dihedral : 17.634 84.721 4320 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.24 % Allowed : 27.43 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2802 helix: 1.21 (0.13), residues: 1645 sheet: -0.97 (0.41), residues: 186 loop : -0.18 (0.22), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 153 TYR 0.015 0.002 TYR R 183 PHE 0.020 0.002 PHE J 323 TRP 0.013 0.002 TRP J 284 HIS 0.008 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (25272) covalent geometry : angle 0.58940 / 0.32 (34616) hydrogen bonds : bond 0.04923 / 3.25 ( 1289) hydrogen bonds : angle 4.35770 / 3.12 ( 3530) metal coordination : bond 0.00646 / 0.38 ( 8) metal coordination : angle 3.59804 / 1.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 598 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 157 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7823 (mt-10) REVERT: R 307 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8132 (mtmt) REVERT: R 316 GLN cc_start: 0.8266 (mt0) cc_final: 0.8063 (mt0) REVERT: S 10 GLU cc_start: 0.7051 (pp20) cc_final: 0.6839 (pp20) REVERT: S 135 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7447 (ttp-170) REVERT: S 148 VAL cc_start: 0.8255 (m) cc_final: 0.8045 (t) REVERT: S 172 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7655 (mm-30) REVERT: S 186 GLN cc_start: 0.7760 (tt0) cc_final: 0.7446 (tt0) REVERT: S 320 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8133 (ttmm) REVERT: S 345 LEU cc_start: 0.8740 (mt) cc_final: 0.8483 (mm) REVERT: T 63 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7917 (mttm) REVERT: T 116 THR cc_start: 0.8418 (m) cc_final: 0.8198 (t) REVERT: T 268 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7736 (mt-10) REVERT: T 326 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7756 (mt-10) REVERT: T 338 ASN cc_start: 0.7316 (m-40) cc_final: 0.6970 (m-40) REVERT: T 340 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7959 (mtt180) REVERT: U 17 THR cc_start: 0.7906 (m) cc_final: 0.7669 (t) REVERT: U 54 PHE cc_start: 0.8231 (m-80) cc_final: 0.7744 (m-80) REVERT: U 69 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6958 (ttp-110) REVERT: U 95 GLU cc_start: 0.7728 (tt0) cc_final: 0.7480 (tt0) REVERT: U 178 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8583 (mttm) REVERT: U 198 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (mtt) REVERT: U 242 GLN cc_start: 0.8290 (mm110) cc_final: 0.7949 (mm110) REVERT: U 253 GLN cc_start: 0.8330 (mt0) cc_final: 0.7897 (mp10) REVERT: U 286 LYS cc_start: 0.7401 (tmtm) cc_final: 0.7030 (tttp) REVERT: U 324 GLU cc_start: 0.8001 (tp30) cc_final: 0.7745 (tp30) REVERT: V 38 GLU cc_start: 0.7935 (tp30) cc_final: 0.7691 (tp30) REVERT: V 68 LEU cc_start: 0.8816 (mt) cc_final: 0.8572 (mp) REVERT: V 130 VAL cc_start: 0.8486 (t) cc_final: 0.8232 (p) REVERT: V 157 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7720 (tt0) REVERT: V 190 ASP cc_start: 0.8320 (m-30) cc_final: 0.7921 (m-30) REVERT: W 41 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7541 (mpp) REVERT: W 44 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7698 (mp) REVERT: W 52 PHE cc_start: 0.7707 (m-10) cc_final: 0.7320 (m-80) REVERT: W 119 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6513 (pp20) REVERT: W 153 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7590 (mtp180) REVERT: W 158 ASN cc_start: 0.8067 (m-40) cc_final: 0.7813 (m-40) REVERT: W 168 PHE cc_start: 0.8306 (t80) cc_final: 0.7769 (t80) REVERT: W 327 ARG cc_start: 0.7386 (ptt-90) cc_final: 0.7120 (ptt-90) REVERT: W 336 VAL cc_start: 0.7538 (t) cc_final: 0.7276 (t) REVERT: J 86 ASN cc_start: 0.8029 (m-40) cc_final: 0.7615 (m110) REVERT: J 97 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7182 (mtp) REVERT: J 172 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7826 (mmmm) REVERT: J 366 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.7342 (p) REVERT: J 367 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7402 (tpp) REVERT: J 414 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: J 431 GLU cc_start: 0.6945 (tt0) cc_final: 0.6680 (tp30) REVERT: J 446 TYR cc_start: 0.7304 (m-80) cc_final: 0.7025 (m-10) outliers start: 104 outliers final: 48 residues processed: 652 average time/residue: 0.1826 time to fit residues: 178.4440 Evaluate side-chains 636 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 577 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 171 ASP Chi-restraints excluded: chain S residue 239 GLU Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 188 GLN Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 174 GLN Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 44 ILE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 119 GLU Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 326 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 337 GLN T 105 ASN T 323 GLN U 188 GLN U 328 GLN V 142 ASN J 75 ASN J 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118309 restraints weight = 36392.697| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.99 r_work: 0.3359 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25280 Z= 0.198 Angle : 0.572 8.146 34625 Z= 0.305 Chirality : 0.043 0.245 3879 Planarity : 0.005 0.053 4117 Dihedral : 17.547 86.911 4286 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.24 % Allowed : 26.82 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 2802 helix: 1.17 (0.13), residues: 1643 sheet: -1.04 (0.40), residues: 186 loop : -0.24 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 153 TYR 0.020 0.001 TYR J 399 PHE 0.035 0.002 PHE J 323 TRP 0.019 0.001 TRP J 284 HIS 0.007 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (25272) covalent geometry : angle 0.56865 / 0.30 (34616) hydrogen bonds : bond 0.04761 / 3.16 ( 1289) hydrogen bonds : angle 4.17762 / 2.99 ( 3530) metal coordination : bond 0.00397 / 0.27 ( 8) metal coordination : angle 3.90865 / 1.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 613 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 92 VAL cc_start: 0.8634 (p) cc_final: 0.8343 (t) REVERT: R 157 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7778 (mt-10) REVERT: R 307 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8096 (mtmt) REVERT: R 310 LEU cc_start: 0.8312 (mp) cc_final: 0.8072 (mt) REVERT: R 336 VAL cc_start: 0.7795 (t) cc_final: 0.7500 (m) REVERT: R 337 GLN cc_start: 0.7616 (mm110) cc_final: 0.7337 (mm110) REVERT: S 135 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7578 (ttp-170) REVERT: S 148 VAL cc_start: 0.8226 (m) cc_final: 0.8004 (t) REVERT: S 172 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7625 (mm-30) REVERT: S 246 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8177 (p) REVERT: S 318 MET cc_start: 0.8359 (mtp) cc_final: 0.8135 (mtm) REVERT: S 324 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7275 (mm-30) REVERT: S 327 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.7827 (ttp-110) REVERT: S 345 LEU cc_start: 0.8765 (mt) cc_final: 0.8483 (mm) REVERT: T 54 PHE cc_start: 0.8186 (m-80) cc_final: 0.7902 (m-80) REVERT: T 63 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7849 (mttm) REVERT: T 186 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: T 268 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7770 (mt-10) REVERT: T 326 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7766 (mt-10) REVERT: T 338 ASN cc_start: 0.7280 (m-40) cc_final: 0.6918 (m-40) REVERT: T 340 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7921 (mtt180) REVERT: U 17 THR cc_start: 0.7952 (m) cc_final: 0.7716 (t) REVERT: U 95 GLU cc_start: 0.7715 (tt0) cc_final: 0.7462 (tt0) REVERT: U 144 GLU cc_start: 0.6682 (tp30) cc_final: 0.6441 (tp30) REVERT: U 178 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8587 (mttm) REVERT: U 198 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8065 (mtt) REVERT: U 242 GLN cc_start: 0.8294 (mm110) cc_final: 0.7936 (mm110) REVERT: U 272 GLU cc_start: 0.7792 (tt0) cc_final: 0.7559 (tt0) REVERT: V 12 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7150 (mt) REVERT: V 38 GLU cc_start: 0.7925 (tp30) cc_final: 0.7702 (tp30) REVERT: V 39 ILE cc_start: 0.8181 (mt) cc_final: 0.7914 (mt) REVERT: V 130 VAL cc_start: 0.8540 (t) cc_final: 0.8249 (p) REVERT: V 144 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: V 190 ASP cc_start: 0.8351 (m-30) cc_final: 0.7887 (m-30) REVERT: W 41 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (mmp) REVERT: W 52 PHE cc_start: 0.7731 (m-10) cc_final: 0.7406 (m-80) REVERT: W 116 THR cc_start: 0.8040 (t) cc_final: 0.7685 (m) REVERT: W 118 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7239 (mm-30) REVERT: W 119 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6562 (pp20) REVERT: W 153 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7691 (mtp180) REVERT: W 158 ASN cc_start: 0.8071 (m-40) cc_final: 0.7807 (m-40) REVERT: W 168 PHE cc_start: 0.8327 (t80) cc_final: 0.7818 (t80) REVERT: W 172 GLU cc_start: 0.7770 (tt0) cc_final: 0.7207 (tm-30) REVERT: W 324 GLU cc_start: 0.7999 (tp30) cc_final: 0.7069 (tp30) REVERT: W 327 ARG cc_start: 0.7377 (ptt-90) cc_final: 0.7163 (ptt-90) REVERT: W 336 VAL cc_start: 0.7559 (t) cc_final: 0.7301 (t) REVERT: J 86 ASN cc_start: 0.8022 (m-40) cc_final: 0.7621 (m110) REVERT: J 87 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6846 (mtm-85) REVERT: J 172 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7861 (mmmm) REVERT: J 310 VAL cc_start: 0.8434 (m) cc_final: 0.8152 (p) REVERT: J 414 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: J 431 GLU cc_start: 0.6875 (tt0) cc_final: 0.6600 (tp30) REVERT: J 446 TYR cc_start: 0.7467 (m-80) cc_final: 0.7092 (m-80) outliers start: 104 outliers final: 57 residues processed: 669 average time/residue: 0.1936 time to fit residues: 194.6360 Evaluate side-chains 657 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 589 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 184 LYS Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 119 GLU Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 326 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 128 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN R 220 GLN R 328 GLN S 186 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN T 323 GLN U 328 GLN J 75 ASN J 106 GLN J 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118704 restraints weight = 36277.845| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.97 r_work: 0.3364 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25280 Z= 0.172 Angle : 0.553 8.329 34625 Z= 0.295 Chirality : 0.041 0.246 3879 Planarity : 0.005 0.050 4117 Dihedral : 17.449 88.741 4277 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.41 % Allowed : 26.82 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2802 helix: 1.19 (0.13), residues: 1657 sheet: -1.10 (0.40), residues: 186 loop : -0.25 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 224 TYR 0.013 0.001 TYR W 37 PHE 0.031 0.002 PHE J 323 TRP 0.020 0.001 TRP J 284 HIS 0.007 0.001 HIS S 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (25272) covalent geometry : angle 0.54989 / 0.29 (34616) hydrogen bonds : bond 0.04416 / 2.91 ( 1289) hydrogen bonds : angle 4.08197 / 2.92 ( 3530) metal coordination : bond 0.00367 / 0.24 ( 8) metal coordination : angle 3.66768 / 1.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 614 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 119 GLU cc_start: 0.7641 (tp30) cc_final: 0.7438 (tp30) REVERT: R 88 ARG cc_start: 0.6625 (tpt170) cc_final: 0.6074 (tpt170) REVERT: R 92 VAL cc_start: 0.8609 (p) cc_final: 0.8331 (t) REVERT: R 100 GLU cc_start: 0.7700 (pm20) cc_final: 0.7462 (pm20) REVERT: R 157 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7712 (mt-10) REVERT: R 307 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8088 (mtmt) REVERT: R 336 VAL cc_start: 0.7809 (t) cc_final: 0.7522 (m) REVERT: S 135 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7576 (ttp-170) REVERT: S 148 VAL cc_start: 0.8225 (m) cc_final: 0.8006 (t) REVERT: S 172 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7600 (mm-30) REVERT: S 246 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8202 (p) REVERT: S 324 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7138 (mm-30) REVERT: S 327 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7751 (ttp-110) REVERT: S 345 LEU cc_start: 0.8758 (mt) cc_final: 0.8480 (mm) REVERT: T 54 PHE cc_start: 0.8200 (m-80) cc_final: 0.7877 (m-80) REVERT: T 63 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7877 (mttm) REVERT: T 186 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: T 188 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7890 (mm-40) REVERT: T 338 ASN cc_start: 0.7275 (m-40) cc_final: 0.6914 (m-40) REVERT: T 340 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7931 (mtt180) REVERT: U 17 THR cc_start: 0.7977 (m) cc_final: 0.7740 (t) REVERT: U 95 GLU cc_start: 0.7710 (tt0) cc_final: 0.7460 (tt0) REVERT: U 108 GLU cc_start: 0.8263 (tp30) cc_final: 0.7968 (tp30) REVERT: U 142 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.7048 (t0) REVERT: U 178 LYS cc_start: 0.8855 (mmtm) cc_final: 0.8601 (mttm) REVERT: U 198 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (mtt) REVERT: U 242 GLN cc_start: 0.8294 (mm110) cc_final: 0.7942 (mm110) REVERT: U 272 GLU cc_start: 0.7781 (tt0) cc_final: 0.7558 (tt0) REVERT: U 282 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7373 (tttm) REVERT: V 12 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7184 (mt) REVERT: V 38 GLU cc_start: 0.7917 (tp30) cc_final: 0.7693 (tp30) REVERT: V 39 ILE cc_start: 0.8210 (mt) cc_final: 0.7827 (mt) REVERT: V 130 VAL cc_start: 0.8540 (t) cc_final: 0.8232 (p) REVERT: V 144 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: V 190 ASP cc_start: 0.8344 (m-30) cc_final: 0.7898 (m-30) REVERT: V 304 ASP cc_start: 0.6930 (m-30) cc_final: 0.6536 (m-30) REVERT: W 41 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7998 (mmm) REVERT: W 52 PHE cc_start: 0.7736 (m-10) cc_final: 0.7414 (m-80) REVERT: W 116 THR cc_start: 0.8092 (t) cc_final: 0.7728 (m) REVERT: W 118 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7204 (mm-30) REVERT: W 119 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: W 153 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7779 (mtp180) REVERT: W 158 ASN cc_start: 0.8078 (m-40) cc_final: 0.7818 (m-40) REVERT: W 168 PHE cc_start: 0.8321 (t80) cc_final: 0.7820 (t80) REVERT: W 172 GLU cc_start: 0.7719 (tt0) cc_final: 0.7099 (tm-30) REVERT: W 193 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7766 (ttpp) REVERT: W 198 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: W 220 GLN cc_start: 0.7568 (tp40) cc_final: 0.6779 (tp40) REVERT: W 227 ASP cc_start: 0.6375 (p0) cc_final: 0.6164 (p0) REVERT: W 317 LYS cc_start: 0.8342 (ptpp) cc_final: 0.7924 (ptpp) REVERT: W 324 GLU cc_start: 0.8012 (tp30) cc_final: 0.7125 (tp30) REVERT: W 327 ARG cc_start: 0.7351 (ptt-90) cc_final: 0.7129 (ptt-90) REVERT: W 336 VAL cc_start: 0.7527 (t) cc_final: 0.7280 (t) REVERT: J 86 ASN cc_start: 0.8000 (m-40) cc_final: 0.7621 (m110) REVERT: J 87 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6831 (mtm-85) REVERT: J 135 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7727 (mtp180) REVERT: J 172 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7850 (mmmm) REVERT: J 236 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: J 288 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (p) REVERT: J 310 VAL cc_start: 0.8438 (m) cc_final: 0.8016 (p) REVERT: J 368 GLU cc_start: 0.7093 (mp0) cc_final: 0.6299 (mp0) REVERT: J 398 ASN cc_start: 0.7352 (p0) cc_final: 0.7054 (p0) REVERT: J 405 LEU cc_start: 0.6854 (tt) cc_final: 0.6646 (tt) REVERT: J 411 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7225 (tp) REVERT: J 414 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: J 431 GLU cc_start: 0.6830 (tt0) cc_final: 0.6557 (tp30) REVERT: J 446 TYR cc_start: 0.7530 (m-80) cc_final: 0.7126 (m-80) outliers start: 108 outliers final: 65 residues processed: 673 average time/residue: 0.1809 time to fit residues: 183.2133 Evaluate side-chains 678 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 596 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 265 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 239 GLU Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 320 LYS Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 198 MET Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 119 GLU Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 276 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 106 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 248 optimal weight: 0.0970 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN T 197 ASN V 142 ASN J 106 GLN J 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119107 restraints weight = 36327.619| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.00 r_work: 0.3374 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25280 Z= 0.148 Angle : 0.540 11.981 34625 Z= 0.286 Chirality : 0.041 0.245 3879 Planarity : 0.004 0.049 4117 Dihedral : 17.378 89.709 4275 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.45 % Allowed : 26.61 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2802 helix: 1.26 (0.13), residues: 1658 sheet: -1.12 (0.41), residues: 186 loop : -0.19 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 224 TYR 0.014 0.001 TYR J 399 PHE 0.039 0.001 PHE J 323 TRP 0.023 0.001 TRP J 284 HIS 0.005 0.001 HIS U 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (25272) covalent geometry : angle 0.53618 / 0.29 (34616) hydrogen bonds : bond 0.04156 / 2.75 ( 1289) hydrogen bonds : angle 3.99478 / 2.86 ( 3530) metal coordination : bond 0.00397 / 0.26 ( 8) metal coordination : angle 3.89350 / 1.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 613 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 172 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7335 (mm-30) REVERT: Q 210 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6754 (tm-30) REVERT: R 92 VAL cc_start: 0.8570 (p) cc_final: 0.8305 (t) REVERT: R 100 GLU cc_start: 0.7768 (pm20) cc_final: 0.7550 (pm20) REVERT: R 102 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7683 (ttm170) REVERT: R 153 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7968 (ttt90) REVERT: R 157 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7555 (mt-10) REVERT: R 307 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: R 336 VAL cc_start: 0.7767 (t) cc_final: 0.7503 (m) REVERT: S 100 GLU cc_start: 0.7957 (pm20) cc_final: 0.7746 (pm20) REVERT: S 103 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: S 135 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7655 (ttp-170) REVERT: S 148 VAL cc_start: 0.8256 (m) cc_final: 0.8022 (t) REVERT: S 172 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7601 (mm-30) REVERT: S 201 ILE cc_start: 0.8762 (mm) cc_final: 0.8503 (mt) REVERT: S 246 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8181 (p) REVERT: S 295 ARG cc_start: 0.7855 (ptp-110) cc_final: 0.7390 (ptm-80) REVERT: S 306 GLN cc_start: 0.8392 (mt0) cc_final: 0.8149 (mt0) REVERT: S 324 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7135 (mm-30) REVERT: S 327 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7693 (ttp-110) REVERT: S 345 LEU cc_start: 0.8776 (mt) cc_final: 0.8505 (mm) REVERT: T 63 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7825 (mttm) REVERT: T 186 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: T 268 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7725 (mt-10) REVERT: T 326 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7720 (mt-10) REVERT: T 338 ASN cc_start: 0.7260 (m-40) cc_final: 0.6879 (m-40) REVERT: T 340 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7910 (mtt180) REVERT: U 17 THR cc_start: 0.8000 (m) cc_final: 0.7761 (t) REVERT: U 69 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7675 (ttt180) REVERT: U 95 GLU cc_start: 0.7693 (tt0) cc_final: 0.7444 (tt0) REVERT: U 242 GLN cc_start: 0.8268 (mm110) cc_final: 0.7906 (mm110) REVERT: U 272 GLU cc_start: 0.7821 (tt0) cc_final: 0.7591 (tt0) REVERT: U 282 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7380 (tttm) REVERT: V 12 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7188 (mt) REVERT: V 39 ILE cc_start: 0.8185 (mt) cc_final: 0.7891 (mt) REVERT: V 68 LEU cc_start: 0.8803 (mt) cc_final: 0.8548 (mp) REVERT: V 130 VAL cc_start: 0.8549 (t) cc_final: 0.8227 (p) REVERT: V 144 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: V 190 ASP cc_start: 0.8337 (m-30) cc_final: 0.7891 (m-30) REVERT: V 304 ASP cc_start: 0.7026 (m-30) cc_final: 0.6746 (m-30) REVERT: W 41 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: W 52 PHE cc_start: 0.7734 (m-10) cc_final: 0.7392 (m-80) REVERT: W 116 THR cc_start: 0.8127 (t) cc_final: 0.7766 (m) REVERT: W 118 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7221 (mm-30) REVERT: W 119 GLU cc_start: 0.6745 (pp20) cc_final: 0.6539 (pp20) REVERT: W 153 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7833 (mtp180) REVERT: W 158 ASN cc_start: 0.8064 (m-40) cc_final: 0.7787 (m-40) REVERT: W 168 PHE cc_start: 0.8226 (t80) cc_final: 0.7681 (t80) REVERT: W 172 GLU cc_start: 0.7744 (tt0) cc_final: 0.7052 (tm-30) REVERT: W 198 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: W 220 GLN cc_start: 0.7556 (tp40) cc_final: 0.6928 (tp40) REVERT: W 224 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7454 (mtt90) REVERT: W 227 ASP cc_start: 0.6381 (p0) cc_final: 0.6179 (p0) REVERT: W 244 PHE cc_start: 0.5124 (t80) cc_final: 0.4904 (t80) REVERT: W 317 LYS cc_start: 0.8352 (ptpp) cc_final: 0.7938 (ptpp) REVERT: W 324 GLU cc_start: 0.7953 (tp30) cc_final: 0.7043 (tp30) REVERT: W 327 ARG cc_start: 0.7335 (ptt-90) cc_final: 0.7100 (ptt-90) REVERT: W 336 VAL cc_start: 0.7501 (t) cc_final: 0.7251 (t) REVERT: J 39 GLU cc_start: 0.7413 (tt0) cc_final: 0.7156 (tt0) REVERT: J 86 ASN cc_start: 0.8015 (m-40) cc_final: 0.7614 (m110) REVERT: J 87 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6870 (mtm-85) REVERT: J 172 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7852 (mmmm) REVERT: J 236 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: J 288 SER cc_start: 0.8462 (m) cc_final: 0.8245 (p) REVERT: J 310 VAL cc_start: 0.8459 (m) cc_final: 0.8039 (p) REVERT: J 398 ASN cc_start: 0.7376 (p0) cc_final: 0.7081 (p0) REVERT: J 405 LEU cc_start: 0.6843 (tt) cc_final: 0.6514 (tt) REVERT: J 408 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6788 (tt) REVERT: J 411 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7199 (tp) REVERT: J 414 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6041 (mp0) REVERT: J 431 GLU cc_start: 0.6822 (tt0) cc_final: 0.6564 (tp30) REVERT: J 446 TYR cc_start: 0.7555 (m-80) cc_final: 0.7158 (m-80) outliers start: 109 outliers final: 64 residues processed: 666 average time/residue: 0.1940 time to fit residues: 192.8540 Evaluate side-chains 671 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 590 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 296 GLU Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN J 106 GLN J 148 GLN J 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118666 restraints weight = 36259.919| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.01 r_work: 0.3366 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25280 Z= 0.165 Angle : 0.544 9.411 34625 Z= 0.290 Chirality : 0.041 0.249 3879 Planarity : 0.004 0.050 4117 Dihedral : 17.359 89.966 4270 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.61 % Allowed : 26.65 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2802 helix: 1.26 (0.13), residues: 1653 sheet: -1.14 (0.41), residues: 186 loop : -0.17 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 153 TYR 0.013 0.001 TYR J 399 PHE 0.037 0.002 PHE J 323 TRP 0.027 0.001 TRP J 284 HIS 0.006 0.001 HIS J 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (25272) covalent geometry : angle 0.54106 / 0.29 (34616) hydrogen bonds : bond 0.04205 / 2.78 ( 1289) hydrogen bonds : angle 3.96824 / 2.83 ( 3530) metal coordination : bond 0.00408 / 0.28 ( 8) metal coordination : angle 3.68631 / 1.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 616 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8301 (mt) cc_final: 0.8040 (pt) REVERT: Q 172 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7328 (mm-30) REVERT: Q 210 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6760 (tm-30) REVERT: R 92 VAL cc_start: 0.8547 (p) cc_final: 0.8310 (t) REVERT: R 102 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7675 (ttm170) REVERT: R 153 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7996 (ttt90) REVERT: R 157 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7553 (mt-10) REVERT: R 307 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8055 (mtmt) REVERT: S 103 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: S 135 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7699 (ttp-170) REVERT: S 148 VAL cc_start: 0.8298 (m) cc_final: 0.8049 (t) REVERT: S 172 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7612 (mm-30) REVERT: S 201 ILE cc_start: 0.8761 (mm) cc_final: 0.8503 (mt) REVERT: S 246 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8181 (p) REVERT: S 295 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7400 (ptm-80) REVERT: S 324 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7162 (mm-30) REVERT: S 327 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7643 (ttp-110) REVERT: S 332 THR cc_start: 0.8344 (p) cc_final: 0.8066 (t) REVERT: T 17 THR cc_start: 0.8429 (m) cc_final: 0.8183 (p) REVERT: T 54 PHE cc_start: 0.8224 (m-80) cc_final: 0.7945 (m-80) REVERT: T 63 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7833 (mttm) REVERT: T 186 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: T 268 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7725 (mt-10) REVERT: T 326 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7734 (mt-10) REVERT: T 338 ASN cc_start: 0.7281 (m-40) cc_final: 0.6907 (m-40) REVERT: T 340 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7943 (mtt180) REVERT: U 17 THR cc_start: 0.8008 (m) cc_final: 0.7772 (t) REVERT: U 69 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7754 (ttt180) REVERT: U 95 GLU cc_start: 0.7703 (tt0) cc_final: 0.7458 (tt0) REVERT: U 127 ASP cc_start: 0.7830 (t0) cc_final: 0.7438 (t0) REVERT: U 142 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.7028 (t0) REVERT: U 242 GLN cc_start: 0.8253 (mm110) cc_final: 0.7885 (mm110) REVERT: U 282 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7399 (tttm) REVERT: V 12 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7196 (mt) REVERT: V 39 ILE cc_start: 0.8194 (mt) cc_final: 0.7825 (mt) REVERT: V 130 VAL cc_start: 0.8560 (t) cc_final: 0.8235 (p) REVERT: V 144 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: V 190 ASP cc_start: 0.8326 (m-30) cc_final: 0.7869 (m-30) REVERT: V 304 ASP cc_start: 0.7025 (m-30) cc_final: 0.6771 (m-30) REVERT: W 41 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: W 44 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7719 (mp) REVERT: W 52 PHE cc_start: 0.7755 (m-10) cc_final: 0.7419 (m-80) REVERT: W 116 THR cc_start: 0.8151 (t) cc_final: 0.7903 (m) REVERT: W 118 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7254 (mm-30) REVERT: W 158 ASN cc_start: 0.8077 (m-40) cc_final: 0.7813 (m-40) REVERT: W 168 PHE cc_start: 0.8221 (t80) cc_final: 0.7651 (t80) REVERT: W 172 GLU cc_start: 0.7797 (tt0) cc_final: 0.7106 (tm-30) REVERT: W 198 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: W 220 GLN cc_start: 0.7550 (tp40) cc_final: 0.7025 (tp40) REVERT: W 317 LYS cc_start: 0.8353 (ptpp) cc_final: 0.7961 (ptpp) REVERT: W 324 GLU cc_start: 0.7915 (tp30) cc_final: 0.7008 (tp30) REVERT: W 327 ARG cc_start: 0.7343 (ptt-90) cc_final: 0.7114 (ptt-90) REVERT: W 336 VAL cc_start: 0.7501 (t) cc_final: 0.7270 (t) REVERT: J 86 ASN cc_start: 0.8012 (m-40) cc_final: 0.7602 (m110) REVERT: J 87 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6876 (mtm-85) REVERT: J 115 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7945 (ptp90) REVERT: J 172 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7874 (mmmm) REVERT: J 236 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: J 310 VAL cc_start: 0.8470 (m) cc_final: 0.8038 (p) REVERT: J 398 ASN cc_start: 0.7379 (p0) cc_final: 0.7093 (p0) REVERT: J 405 LEU cc_start: 0.6838 (tt) cc_final: 0.6491 (tt) REVERT: J 408 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6837 (tt) REVERT: J 411 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7136 (tp) REVERT: J 414 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: J 431 GLU cc_start: 0.6839 (tt0) cc_final: 0.6567 (tp30) REVERT: J 446 TYR cc_start: 0.7642 (m-80) cc_final: 0.7172 (m-80) outliers start: 113 outliers final: 76 residues processed: 675 average time/residue: 0.1924 time to fit residues: 195.1536 Evaluate side-chains 697 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 601 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 320 LYS Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 44 ILE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 270 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 108 optimal weight: 0.0070 chunk 196 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 chunk 162 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN V 203 HIS J 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.146142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119494 restraints weight = 36333.594| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.02 r_work: 0.3384 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25280 Z= 0.127 Angle : 0.526 8.493 34625 Z= 0.282 Chirality : 0.040 0.242 3879 Planarity : 0.004 0.053 4117 Dihedral : 17.274 87.852 4270 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.12 % Allowed : 27.31 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2802 helix: 1.39 (0.13), residues: 1648 sheet: -1.11 (0.41), residues: 186 loop : -0.11 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 153 TYR 0.016 0.001 TYR R 22 PHE 0.028 0.001 PHE J 323 TRP 0.035 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (25272) covalent geometry : angle 0.52299 / 0.28 (34616) hydrogen bonds : bond 0.03901 / 2.57 ( 1289) hydrogen bonds : angle 3.87663 / 2.77 ( 3530) metal coordination : bond 0.00305 / 0.21 ( 8) metal coordination : angle 3.27697 / 1.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 602 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8265 (mt) cc_final: 0.7994 (pt) REVERT: Q 172 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7279 (mm-30) REVERT: Q 210 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6706 (tm-30) REVERT: R 92 VAL cc_start: 0.8544 (p) cc_final: 0.8309 (t) REVERT: R 100 GLU cc_start: 0.7740 (pm20) cc_final: 0.7468 (pm20) REVERT: R 102 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7695 (ttm170) REVERT: R 153 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8000 (ttt90) REVERT: R 157 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7682 (mt-10) REVERT: R 307 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8025 (mtmt) REVERT: S 103 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: S 135 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7741 (ttp-170) REVERT: S 148 VAL cc_start: 0.8211 (m) cc_final: 0.7991 (t) REVERT: S 172 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7561 (mm-30) REVERT: S 201 ILE cc_start: 0.8748 (mm) cc_final: 0.8499 (mt) REVERT: S 295 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7429 (ptm-80) REVERT: S 324 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7674 (mm-30) REVERT: S 332 THR cc_start: 0.8323 (p) cc_final: 0.8050 (t) REVERT: S 345 LEU cc_start: 0.8755 (mt) cc_final: 0.8496 (mm) REVERT: T 17 THR cc_start: 0.8413 (m) cc_final: 0.8174 (p) REVERT: T 116 THR cc_start: 0.8451 (m) cc_final: 0.8221 (t) REVERT: T 186 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: T 188 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7878 (mt0) REVERT: T 268 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7728 (mt-10) REVERT: T 326 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7718 (mt-10) REVERT: T 338 ASN cc_start: 0.7282 (m-40) cc_final: 0.6941 (m-40) REVERT: T 340 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7938 (mtt180) REVERT: U 17 THR cc_start: 0.7979 (m) cc_final: 0.7753 (t) REVERT: U 69 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7671 (ttt180) REVERT: U 95 GLU cc_start: 0.7679 (tt0) cc_final: 0.7426 (tt0) REVERT: U 127 ASP cc_start: 0.7845 (t0) cc_final: 0.7445 (t0) REVERT: U 242 GLN cc_start: 0.8265 (mm110) cc_final: 0.7901 (mm110) REVERT: U 282 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7373 (tttm) REVERT: U 323 GLN cc_start: 0.7901 (mt0) cc_final: 0.7686 (mt0) REVERT: V 12 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7179 (mt) REVERT: V 39 ILE cc_start: 0.8158 (mt) cc_final: 0.7878 (mt) REVERT: V 130 VAL cc_start: 0.8504 (t) cc_final: 0.8187 (p) REVERT: V 144 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: V 190 ASP cc_start: 0.8317 (m-30) cc_final: 0.8023 (m-30) REVERT: V 304 ASP cc_start: 0.6976 (m-30) cc_final: 0.6733 (m-30) REVERT: W 41 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: W 44 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7721 (mp) REVERT: W 52 PHE cc_start: 0.7748 (m-10) cc_final: 0.7379 (m-80) REVERT: W 116 THR cc_start: 0.8101 (t) cc_final: 0.7713 (m) REVERT: W 118 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7317 (mm-30) REVERT: W 135 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7152 (mmm160) REVERT: W 153 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7832 (ttt-90) REVERT: W 158 ASN cc_start: 0.8055 (m-40) cc_final: 0.7786 (m-40) REVERT: W 168 PHE cc_start: 0.8132 (t80) cc_final: 0.7535 (t80) REVERT: W 198 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6951 (mtt) REVERT: W 220 GLN cc_start: 0.7554 (tp40) cc_final: 0.6937 (tp40) REVERT: W 224 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7372 (mtt90) REVERT: W 324 GLU cc_start: 0.7909 (tp30) cc_final: 0.7003 (tp30) REVERT: W 327 ARG cc_start: 0.7341 (ptt-90) cc_final: 0.7074 (ptt-90) REVERT: W 336 VAL cc_start: 0.7467 (t) cc_final: 0.7246 (t) REVERT: J 86 ASN cc_start: 0.8029 (m-40) cc_final: 0.7601 (m110) REVERT: J 87 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7188 (mtm-85) REVERT: J 115 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7882 (ptp90) REVERT: J 158 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8464 (mt) REVERT: J 172 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7844 (mmmm) REVERT: J 236 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: J 263 LYS cc_start: 0.6959 (ttmt) cc_final: 0.6692 (ttpt) REVERT: J 310 VAL cc_start: 0.8470 (m) cc_final: 0.8034 (p) REVERT: J 398 ASN cc_start: 0.7381 (p0) cc_final: 0.7138 (p0) REVERT: J 405 LEU cc_start: 0.6813 (tt) cc_final: 0.6471 (tt) REVERT: J 408 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6837 (tt) REVERT: J 411 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7110 (tp) REVERT: J 414 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: J 431 GLU cc_start: 0.6787 (tt0) cc_final: 0.6503 (tp30) REVERT: J 446 TYR cc_start: 0.7595 (m-80) cc_final: 0.7142 (m-80) outliers start: 101 outliers final: 68 residues processed: 656 average time/residue: 0.1776 time to fit residues: 173.7033 Evaluate side-chains 665 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 578 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain V residue 343 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 44 ILE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 152 optimal weight: 2.9990 chunk 133 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 254 optimal weight: 0.0370 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN J 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119680 restraints weight = 36207.460| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.02 r_work: 0.3387 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25280 Z= 0.126 Angle : 0.525 8.397 34625 Z= 0.281 Chirality : 0.040 0.244 3879 Planarity : 0.004 0.051 4117 Dihedral : 17.236 87.003 4270 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.88 % Allowed : 27.55 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2802 helix: 1.45 (0.13), residues: 1642 sheet: -1.65 (0.44), residues: 146 loop : -0.13 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 231 TYR 0.014 0.001 TYR J 399 PHE 0.024 0.001 PHE J 323 TRP 0.037 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (25272) covalent geometry : angle 0.52299 / 0.28 (34616) hydrogen bonds : bond 0.03843 / 2.54 ( 1289) hydrogen bonds : angle 3.84034 / 2.74 ( 3530) metal coordination : bond 0.00283 / 0.20 ( 8) metal coordination : angle 3.03421 / 1.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 601 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7872 (tp30) cc_final: 0.7630 (mm-30) REVERT: Q 161 ILE cc_start: 0.8247 (mt) cc_final: 0.7976 (pt) REVERT: Q 172 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7307 (mm-30) REVERT: Q 210 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6716 (tm-30) REVERT: R 92 VAL cc_start: 0.8542 (p) cc_final: 0.8321 (t) REVERT: R 102 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7686 (ttm170) REVERT: R 153 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8009 (ttt90) REVERT: R 157 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7690 (mt-10) REVERT: R 307 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8034 (mtmt) REVERT: R 336 VAL cc_start: 0.7752 (t) cc_final: 0.7523 (m) REVERT: S 103 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: S 135 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7729 (ttp-170) REVERT: S 148 VAL cc_start: 0.8228 (m) cc_final: 0.8006 (t) REVERT: S 171 ASP cc_start: 0.8208 (t0) cc_final: 0.7854 (t0) REVERT: S 201 ILE cc_start: 0.8762 (mm) cc_final: 0.8523 (mt) REVERT: S 295 ARG cc_start: 0.7831 (ptp-110) cc_final: 0.7451 (ptm-80) REVERT: S 324 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7667 (mm-30) REVERT: S 332 THR cc_start: 0.8335 (p) cc_final: 0.8067 (t) REVERT: S 345 LEU cc_start: 0.8740 (mt) cc_final: 0.8491 (mm) REVERT: T 17 THR cc_start: 0.8426 (m) cc_final: 0.8091 (p) REVERT: T 54 PHE cc_start: 0.8188 (m-80) cc_final: 0.7906 (m-80) REVERT: T 116 THR cc_start: 0.8449 (m) cc_final: 0.8216 (t) REVERT: T 186 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: T 188 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7866 (mt0) REVERT: T 338 ASN cc_start: 0.7300 (m-40) cc_final: 0.6961 (m-40) REVERT: T 340 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7938 (mtt-85) REVERT: U 17 THR cc_start: 0.7976 (m) cc_final: 0.7743 (t) REVERT: U 69 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7662 (ttt180) REVERT: U 95 GLU cc_start: 0.7665 (tt0) cc_final: 0.7415 (tt0) REVERT: U 127 ASP cc_start: 0.7862 (t0) cc_final: 0.7501 (t0) REVERT: U 242 GLN cc_start: 0.8273 (mm110) cc_final: 0.7910 (mm110) REVERT: U 282 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7348 (tttm) REVERT: V 12 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7170 (mt) REVERT: V 39 ILE cc_start: 0.8164 (mt) cc_final: 0.7878 (mt) REVERT: V 130 VAL cc_start: 0.8491 (t) cc_final: 0.8163 (p) REVERT: V 186 GLN cc_start: 0.8492 (tt0) cc_final: 0.8154 (tt0) REVERT: V 190 ASP cc_start: 0.8307 (m-30) cc_final: 0.7892 (m-30) REVERT: V 253 GLN cc_start: 0.7588 (mm110) cc_final: 0.7386 (mm110) REVERT: V 304 ASP cc_start: 0.7002 (m-30) cc_final: 0.6785 (m-30) REVERT: W 41 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7852 (mmm) REVERT: W 52 PHE cc_start: 0.7745 (m-10) cc_final: 0.7369 (m-80) REVERT: W 116 THR cc_start: 0.8077 (t) cc_final: 0.7686 (m) REVERT: W 118 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7324 (mm-30) REVERT: W 135 ARG cc_start: 0.7370 (mtp180) cc_final: 0.7133 (mmm160) REVERT: W 158 ASN cc_start: 0.8054 (m-40) cc_final: 0.7780 (m-40) REVERT: W 168 PHE cc_start: 0.8089 (t80) cc_final: 0.7664 (t80) REVERT: W 198 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: W 220 GLN cc_start: 0.7555 (tp40) cc_final: 0.6938 (tp40) REVERT: W 224 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7256 (mtt90) REVERT: W 317 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8087 (ptpp) REVERT: W 324 GLU cc_start: 0.7883 (tp30) cc_final: 0.6974 (tp30) REVERT: W 327 ARG cc_start: 0.7323 (ptt-90) cc_final: 0.7027 (ptt-90) REVERT: W 336 VAL cc_start: 0.7465 (t) cc_final: 0.7243 (t) REVERT: J 86 ASN cc_start: 0.8009 (m-40) cc_final: 0.7625 (m-40) REVERT: J 87 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7221 (mtm-85) REVERT: J 115 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7855 (ptp90) REVERT: J 155 GLU cc_start: 0.8119 (mp0) cc_final: 0.7819 (mp0) REVERT: J 158 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8459 (mt) REVERT: J 172 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7866 (mmmm) REVERT: J 189 ASN cc_start: 0.8410 (t0) cc_final: 0.7984 (t0) REVERT: J 236 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: J 263 LYS cc_start: 0.6977 (ttmt) cc_final: 0.6706 (ttpt) REVERT: J 310 VAL cc_start: 0.8506 (m) cc_final: 0.8081 (p) REVERT: J 405 LEU cc_start: 0.6806 (tt) cc_final: 0.6463 (tt) REVERT: J 408 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6844 (tt) REVERT: J 411 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7113 (tp) REVERT: J 414 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: J 431 GLU cc_start: 0.6782 (tt0) cc_final: 0.6510 (tp30) REVERT: J 446 TYR cc_start: 0.7579 (m-80) cc_final: 0.7139 (m-80) outliers start: 95 outliers final: 69 residues processed: 651 average time/residue: 0.1975 time to fit residues: 190.7590 Evaluate side-chains 684 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 598 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 128 TYR Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 196 optimal weight: 4.9990 chunk 276 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 262 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 248 optimal weight: 0.0570 chunk 185 optimal weight: 0.1980 chunk 139 optimal weight: 2.9990 chunk 157 optimal weight: 0.0470 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN S 220 GLN S 337 GLN V 197 ASN J 106 GLN J 162 ASN J 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120900 restraints weight = 36480.104| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.04 r_work: 0.3409 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.002 0.061 25280 Z= 0.111 Angle : 0.518 8.558 34625 Z= 0.278 Chirality : 0.039 0.237 3879 Planarity : 0.004 0.051 4117 Dihedral : 17.155 87.872 4270 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.51 % Allowed : 27.51 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2802 helix: 1.52 (0.13), residues: 1643 sheet: -1.63 (0.45), residues: 144 loop : -0.09 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 231 TYR 0.015 0.001 TYR J 399 PHE 0.023 0.001 PHE J 323 TRP 0.040 0.001 TRP J 284 HIS 0.006 0.001 HIS V 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (25272) covalent geometry : angle 0.51654 / 0.28 (34616) hydrogen bonds : bond 0.03609 / 2.37 ( 1289) hydrogen bonds : angle 3.77247 / 2.69 ( 3530) metal coordination : bond 0.00247 / 0.16 ( 8) metal coordination : angle 2.59526 / 1.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 596 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7866 (tp30) cc_final: 0.7603 (mm-30) REVERT: Q 153 ARG cc_start: 0.8364 (ttt90) cc_final: 0.8132 (ttt90) REVERT: Q 161 ILE cc_start: 0.8216 (mt) cc_final: 0.7949 (pt) REVERT: Q 172 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7287 (mm-30) REVERT: Q 210 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6671 (tm-30) REVERT: R 100 GLU cc_start: 0.7753 (pm20) cc_final: 0.7442 (pm20) REVERT: R 102 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7659 (ttm170) REVERT: R 153 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7951 (ttt90) REVERT: R 157 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7799 (tt0) REVERT: R 307 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8033 (mtmt) REVERT: R 316 GLN cc_start: 0.8058 (mt0) cc_final: 0.7827 (mt0) REVERT: S 41 MET cc_start: 0.8045 (mmt) cc_final: 0.7798 (mmm) REVERT: S 103 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: S 135 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: S 201 ILE cc_start: 0.8769 (mm) cc_final: 0.8540 (mt) REVERT: S 295 ARG cc_start: 0.7842 (ptp-110) cc_final: 0.7596 (ptm-80) REVERT: S 324 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7141 (mm-30) REVERT: S 327 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.7577 (ttp-110) REVERT: S 345 LEU cc_start: 0.8727 (mt) cc_final: 0.8480 (mm) REVERT: T 17 THR cc_start: 0.8440 (m) cc_final: 0.8109 (p) REVERT: T 54 PHE cc_start: 0.8218 (m-80) cc_final: 0.7871 (m-80) REVERT: T 63 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7878 (mttp) REVERT: T 116 THR cc_start: 0.8443 (m) cc_final: 0.8208 (t) REVERT: T 186 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: T 338 ASN cc_start: 0.7280 (m-40) cc_final: 0.6937 (m-40) REVERT: T 340 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7905 (mtt-85) REVERT: U 17 THR cc_start: 0.7946 (m) cc_final: 0.7710 (t) REVERT: U 69 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.6868 (ttp-110) REVERT: U 95 GLU cc_start: 0.7679 (tt0) cc_final: 0.7438 (tt0) REVERT: U 108 GLU cc_start: 0.8239 (tp30) cc_final: 0.7778 (tp30) REVERT: U 127 ASP cc_start: 0.7872 (t0) cc_final: 0.7599 (t0) REVERT: U 242 GLN cc_start: 0.8259 (mm110) cc_final: 0.7899 (mm110) REVERT: U 282 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7334 (tttm) REVERT: V 39 ILE cc_start: 0.8144 (mt) cc_final: 0.7770 (mt) REVERT: V 46 GLU cc_start: 0.7154 (tp30) cc_final: 0.6867 (tp30) REVERT: V 61 VAL cc_start: 0.8423 (t) cc_final: 0.8182 (p) REVERT: V 130 VAL cc_start: 0.8473 (t) cc_final: 0.8187 (p) REVERT: V 186 GLN cc_start: 0.8483 (tt0) cc_final: 0.8156 (tt0) REVERT: V 190 ASP cc_start: 0.8308 (m-30) cc_final: 0.7896 (m-30) REVERT: V 253 GLN cc_start: 0.7630 (mm110) cc_final: 0.7411 (mm110) REVERT: V 304 ASP cc_start: 0.7006 (m-30) cc_final: 0.6806 (m-30) REVERT: W 41 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: W 52 PHE cc_start: 0.7722 (m-10) cc_final: 0.7268 (m-80) REVERT: W 118 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7331 (mm-30) REVERT: W 153 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7832 (ttt-90) REVERT: W 158 ASN cc_start: 0.8045 (m-40) cc_final: 0.7784 (m-40) REVERT: W 168 PHE cc_start: 0.7930 (t80) cc_final: 0.7488 (t80) REVERT: W 220 GLN cc_start: 0.7554 (tp40) cc_final: 0.6748 (tp40) REVERT: W 224 ARG cc_start: 0.7729 (mtt-85) cc_final: 0.7134 (mtt90) REVERT: W 324 GLU cc_start: 0.7888 (tp30) cc_final: 0.6981 (tp30) REVERT: W 327 ARG cc_start: 0.7283 (ptt-90) cc_final: 0.6972 (ptt-90) REVERT: W 336 VAL cc_start: 0.7445 (t) cc_final: 0.7243 (t) REVERT: J 86 ASN cc_start: 0.8019 (m-40) cc_final: 0.7614 (m-40) REVERT: J 87 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7209 (mtm-85) REVERT: J 97 MET cc_start: 0.7554 (mtm) cc_final: 0.7274 (mtp) REVERT: J 115 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7843 (ptp90) REVERT: J 155 GLU cc_start: 0.8112 (mp0) cc_final: 0.7831 (mp0) REVERT: J 158 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (mt) REVERT: J 172 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7845 (mmmm) REVERT: J 189 ASN cc_start: 0.8400 (t0) cc_final: 0.7959 (t0) REVERT: J 236 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: J 283 LEU cc_start: 0.8011 (mm) cc_final: 0.7722 (mm) REVERT: J 310 VAL cc_start: 0.8498 (m) cc_final: 0.8077 (p) REVERT: J 366 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6900 (p) REVERT: J 405 LEU cc_start: 0.6795 (tt) cc_final: 0.6447 (tt) REVERT: J 408 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6846 (tt) REVERT: J 411 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7105 (tp) REVERT: J 414 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: J 431 GLU cc_start: 0.6771 (tt0) cc_final: 0.6515 (tp30) REVERT: J 446 TYR cc_start: 0.7480 (m-80) cc_final: 0.7076 (m-80) outliers start: 86 outliers final: 56 residues processed: 641 average time/residue: 0.1700 time to fit residues: 161.0357 Evaluate side-chains 659 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 587 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain V residue 343 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 366 THR Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 211 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN T 323 GLN V 252 GLN J 106 GLN J 144 GLN J 148 GLN J 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120110 restraints weight = 36197.871| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.95 r_work: 0.3399 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25280 Z= 0.141 Angle : 0.539 8.199 34625 Z= 0.287 Chirality : 0.041 0.245 3879 Planarity : 0.004 0.052 4117 Dihedral : 17.173 89.999 4270 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.35 % Allowed : 28.00 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2802 helix: 1.48 (0.13), residues: 1642 sheet: -1.06 (0.42), residues: 184 loop : -0.07 (0.22), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 231 TYR 0.013 0.001 TYR J 399 PHE 0.023 0.001 PHE T 126 TRP 0.041 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (25272) covalent geometry : angle 0.53680 / 0.29 (34616) hydrogen bonds : bond 0.03845 / 2.53 ( 1289) hydrogen bonds : angle 3.80020 / 2.72 ( 3530) metal coordination : bond 0.00294 / 0.21 ( 8) metal coordination : angle 2.76291 / 1.40 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 595 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7844 (tp30) cc_final: 0.7597 (mm-30) REVERT: Q 153 ARG cc_start: 0.8347 (ttt90) cc_final: 0.8112 (ttt90) REVERT: Q 161 ILE cc_start: 0.8226 (mt) cc_final: 0.7946 (pt) REVERT: Q 172 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7283 (mm-30) REVERT: Q 210 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6664 (tm-30) REVERT: R 102 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7649 (ttm170) REVERT: R 153 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8002 (ttt90) REVERT: R 157 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7805 (tt0) REVERT: R 307 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: S 41 MET cc_start: 0.8040 (mmt) cc_final: 0.7826 (mmm) REVERT: S 103 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: S 135 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7711 (ttp-170) REVERT: S 201 ILE cc_start: 0.8749 (mm) cc_final: 0.8544 (mt) REVERT: S 295 ARG cc_start: 0.7819 (ptp-110) cc_final: 0.7593 (ptm-80) REVERT: S 324 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7663 (mm-30) REVERT: S 332 THR cc_start: 0.8338 (p) cc_final: 0.8062 (t) REVERT: S 345 LEU cc_start: 0.8738 (mt) cc_final: 0.8484 (mm) REVERT: T 17 THR cc_start: 0.8441 (m) cc_final: 0.8095 (p) REVERT: T 54 PHE cc_start: 0.8218 (m-80) cc_final: 0.7884 (m-80) REVERT: T 116 THR cc_start: 0.8426 (m) cc_final: 0.8182 (t) REVERT: T 186 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: T 338 ASN cc_start: 0.7299 (m-40) cc_final: 0.6950 (m-40) REVERT: T 340 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7931 (mtt-85) REVERT: U 17 THR cc_start: 0.7941 (m) cc_final: 0.7703 (t) REVERT: U 69 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.6847 (ttp-110) REVERT: U 101 SER cc_start: 0.8527 (p) cc_final: 0.8153 (t) REVERT: U 108 GLU cc_start: 0.8237 (tp30) cc_final: 0.7746 (tp30) REVERT: U 127 ASP cc_start: 0.7860 (t0) cc_final: 0.7564 (t0) REVERT: U 242 GLN cc_start: 0.8207 (mm110) cc_final: 0.7841 (mm110) REVERT: U 282 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7352 (tttm) REVERT: V 39 ILE cc_start: 0.8137 (mt) cc_final: 0.7774 (mt) REVERT: V 46 GLU cc_start: 0.7263 (tp30) cc_final: 0.6981 (tp30) REVERT: V 130 VAL cc_start: 0.8482 (t) cc_final: 0.8186 (p) REVERT: V 186 GLN cc_start: 0.8466 (tt0) cc_final: 0.8121 (tt0) REVERT: V 190 ASP cc_start: 0.8296 (m-30) cc_final: 0.7862 (m-30) REVERT: V 253 GLN cc_start: 0.7647 (mm110) cc_final: 0.7398 (mm110) REVERT: V 304 ASP cc_start: 0.7024 (m-30) cc_final: 0.6822 (m-30) REVERT: W 41 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: W 52 PHE cc_start: 0.7743 (m-10) cc_final: 0.7269 (m-80) REVERT: W 116 THR cc_start: 0.7872 (t) cc_final: 0.7482 (m) REVERT: W 118 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7312 (mm-30) REVERT: W 158 ASN cc_start: 0.8034 (m-40) cc_final: 0.7765 (m-40) REVERT: W 168 PHE cc_start: 0.7957 (t80) cc_final: 0.7594 (t80) REVERT: W 198 MET cc_start: 0.7160 (mtt) cc_final: 0.6913 (mtt) REVERT: W 220 GLN cc_start: 0.7561 (tp40) cc_final: 0.6903 (tp40) REVERT: W 224 ARG cc_start: 0.7723 (mtt-85) cc_final: 0.7036 (mtm-85) REVERT: W 324 GLU cc_start: 0.7862 (tp30) cc_final: 0.6961 (tp30) REVERT: W 327 ARG cc_start: 0.7309 (ptt-90) cc_final: 0.6984 (ptt-90) REVERT: W 336 VAL cc_start: 0.7494 (t) cc_final: 0.7279 (t) REVERT: J 86 ASN cc_start: 0.8002 (m-40) cc_final: 0.7603 (m-40) REVERT: J 87 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: J 115 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7866 (ptp90) REVERT: J 155 GLU cc_start: 0.8109 (mp0) cc_final: 0.7812 (mp0) REVERT: J 158 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8466 (mt) REVERT: J 172 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7851 (mmmm) REVERT: J 189 ASN cc_start: 0.8415 (t0) cc_final: 0.7971 (t0) REVERT: J 236 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: J 283 LEU cc_start: 0.8000 (mm) cc_final: 0.7709 (mm) REVERT: J 310 VAL cc_start: 0.8459 (m) cc_final: 0.8040 (p) REVERT: J 408 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6856 (tt) REVERT: J 411 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7065 (tp) REVERT: J 414 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: J 431 GLU cc_start: 0.6767 (tt0) cc_final: 0.6531 (tp30) REVERT: J 446 TYR cc_start: 0.7513 (m-80) cc_final: 0.7088 (m-80) outliers start: 82 outliers final: 63 residues processed: 637 average time/residue: 0.1926 time to fit residues: 182.3958 Evaluate side-chains 663 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 585 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 320 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 185 SER Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 287 GLN Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 36 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 252 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 158 ASN S 220 GLN S 337 GLN T 162 HIS U 328 GLN J 106 GLN J 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.145610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118685 restraints weight = 36252.731| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.03 r_work: 0.3374 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25280 Z= 0.170 Angle : 0.558 8.250 34625 Z= 0.298 Chirality : 0.042 0.252 3879 Planarity : 0.004 0.053 4117 Dihedral : 17.264 88.376 4270 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.47 % Allowed : 27.96 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2802 helix: 1.34 (0.13), residues: 1647 sheet: -1.07 (0.41), residues: 184 loop : -0.10 (0.22), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 295 TYR 0.024 0.001 TYR J 399 PHE 0.023 0.002 PHE T 126 TRP 0.039 0.002 TRP J 284 HIS 0.006 0.001 HIS U 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (25272) covalent geometry : angle 0.55599 / 0.30 (34616) hydrogen bonds : bond 0.04108 / 2.69 ( 1289) hydrogen bonds : angle 3.86360 / 2.76 ( 3530) metal coordination : bond 0.00369 / 0.26 ( 8) metal coordination : angle 3.12219 / 1.59 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7670.05 seconds wall clock time: 131 minutes 32.71 seconds (7892.71 seconds total)