Starting phenix.real_space_refine on Mon Aug 25 01:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_42941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_42941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_42941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_42941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v32_42941/08_2025/8v32_42941.map" } 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-2.0-5787/lib/python3.9/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: 5.75, per 1000 atoms: 0.23 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.85 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: 4.07 Time building geometry restraints manager: 2.59 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: 34350 2.75 - 5.51: 228 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: 3198 0.050 - 0.099: 568 0.099 - 0.149: 105 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: 3.670 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.970 Find NCS groups from input model: 0.500 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.003 0.099 25280 Z= 0.169 Angle : 0.604 13.771 34625 Z= 0.328 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00335 (25272) covalent geometry : angle 0.60234 (34616) hydrogen bonds : bond 0.17321 ( 1289) hydrogen bonds : angle 5.27161 ( 3530) metal coordination : bond 0.00421 ( 8) metal coordination : angle 3.17570 ( 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 : 0.980 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: 0.7076 (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: 0.7720 (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 368 GLU cc_start: 0.7051 (mp0) cc_final: 0.6820 (mp0) 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: 0.1835 time to fit residues: 165.8047 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 : 1.003 ------------------------------------------------------------------------------- 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: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 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 U 188 GLN V 186 GLN V 188 GLN J 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.145350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118574 restraints weight = 36596.883| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.01 r_work: 0.3364 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25280 Z= 0.201 Angle : 0.574 8.871 34625 Z= 0.305 Chirality : 0.042 0.161 3879 Planarity : 0.005 0.069 4117 Dihedral : 17.435 85.928 4320 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.29 % Allowed : 27.27 % Favored : 68.45 % 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 aren not related in a simple way. whole: 0.84 (0.17), residues: 2802 helix: 1.25 (0.13), residues: 1645 sheet: -1.00 (0.41), residues: 186 loop : -0.16 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 153 TYR 0.014 0.001 TYR R 183 PHE 0.019 0.002 PHE W 169 TRP 0.013 0.001 TRP J 284 HIS 0.007 0.001 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00466 (25272) covalent geometry : angle 0.57119 (34616) hydrogen bonds : bond 0.04938 ( 1289) hydrogen bonds : angle 4.26516 ( 3530) metal coordination : bond 0.00474 ( 8) metal coordination : angle 3.74329 ( 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 713 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 608 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 92 VAL cc_start: 0.8664 (p) cc_final: 0.8330 (t) REVERT: R 100 GLU cc_start: 0.7750 (pm20) cc_final: 0.7516 (pm20) REVERT: R 157 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7662 (mt-10) REVERT: R 307 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: R 333 GLU cc_start: 0.8026 (tp30) cc_final: 0.7822 (tp30) REVERT: S 135 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7441 (ttp-170) REVERT: S 148 VAL cc_start: 0.8265 (m) cc_final: 0.8055 (t) REVERT: S 172 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7622 (mm-30) REVERT: S 186 GLN cc_start: 0.7791 (tt0) cc_final: 0.7492 (tt0) REVERT: S 231 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7585 (ttp-110) REVERT: S 320 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8169 (ttmm) REVERT: S 345 LEU cc_start: 0.8747 (mt) cc_final: 0.8489 (mm) REVERT: T 54 PHE cc_start: 0.8187 (m-80) cc_final: 0.7849 (m-80) REVERT: T 63 LYS cc_start: 0.8374 (mtmm) cc_final: 0.7910 (mttm) REVERT: T 116 THR cc_start: 0.8411 (m) cc_final: 0.8196 (t) REVERT: T 186 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: T 268 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7738 (mt-10) REVERT: T 286 LYS cc_start: 0.8508 (tttp) cc_final: 0.8307 (tptp) REVERT: T 326 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7774 (mt-10) REVERT: T 338 ASN cc_start: 0.7296 (m-40) cc_final: 0.6950 (m-40) REVERT: T 340 ARG cc_start: 0.8267 (mtp85) cc_final: 0.8016 (mtt-85) REVERT: U 17 THR cc_start: 0.7916 (m) cc_final: 0.7675 (t) REVERT: U 54 PHE cc_start: 0.8231 (m-80) cc_final: 0.7727 (m-80) REVERT: U 69 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6950 (ttp-110) REVERT: U 95 GLU cc_start: 0.7734 (tt0) cc_final: 0.7473 (tt0) REVERT: U 178 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8552 (mttm) REVERT: U 242 GLN cc_start: 0.8296 (mm110) cc_final: 0.7949 (mm110) REVERT: U 253 GLN cc_start: 0.8321 (mt0) cc_final: 0.7864 (mp10) REVERT: U 273 ARG cc_start: 0.8255 (mmt90) cc_final: 0.7764 (mmt180) REVERT: U 286 LYS cc_start: 0.7435 (tmtm) cc_final: 0.7070 (tttm) REVERT: V 25 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.6681 (p0) REVERT: V 38 GLU cc_start: 0.7951 (tp30) cc_final: 0.7698 (tp30) REVERT: V 68 LEU cc_start: 0.8803 (mt) cc_final: 0.8566 (mp) REVERT: V 130 VAL cc_start: 0.8527 (t) cc_final: 0.8261 (p) REVERT: V 190 ASP cc_start: 0.8344 (m-30) cc_final: 0.7953 (m-30) REVERT: V 253 GLN cc_start: 0.7519 (mm110) cc_final: 0.7308 (mm110) REVERT: W 41 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7555 (mpp) REVERT: W 44 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7762 (mp) REVERT: W 52 PHE cc_start: 0.7715 (m-10) cc_final: 0.7327 (m-80) REVERT: W 112 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7067 (ttp80) REVERT: W 119 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6530 (pp20) REVERT: W 153 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7622 (mtp180) REVERT: W 154 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7256 (ttm110) REVERT: W 158 ASN cc_start: 0.8078 (m-40) cc_final: 0.7822 (m-40) REVERT: W 168 PHE cc_start: 0.8314 (t80) cc_final: 0.7799 (t80) REVERT: W 172 GLU cc_start: 0.7720 (tt0) cc_final: 0.7165 (tm-30) REVERT: W 227 ASP cc_start: 0.6377 (p0) cc_final: 0.6160 (p0) REVERT: W 327 ARG cc_start: 0.7376 (ptt-90) cc_final: 0.7104 (ptt-90) REVERT: W 336 VAL cc_start: 0.7548 (t) cc_final: 0.7285 (t) REVERT: J 69 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: J 86 ASN cc_start: 0.8027 (m-40) cc_final: 0.7602 (m110) REVERT: J 97 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7328 (mtp) REVERT: J 172 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7874 (mmmm) REVERT: J 310 VAL cc_start: 0.8423 (m) cc_final: 0.8153 (p) REVERT: J 366 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7264 (p) REVERT: J 367 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7355 (tpp) REVERT: J 368 GLU cc_start: 0.7102 (mp0) cc_final: 0.6696 (mp0) REVERT: J 395 LYS cc_start: 0.7209 (ttmm) cc_final: 0.6684 (ttmm) REVERT: J 414 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: J 431 GLU cc_start: 0.6929 (tt0) cc_final: 0.6656 (tp30) REVERT: J 446 TYR cc_start: 0.7369 (m-80) cc_final: 0.7009 (m-10) outliers start: 105 outliers final: 45 residues processed: 659 average time/residue: 0.1853 time to fit residues: 180.5883 Evaluate side-chains 648 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 589 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 123 ASP Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain Q residue 225 SER Chi-restraints excluded: chain R residue 24 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 135 ARG Chi-restraints excluded: chain S residue 171 ASP 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 186 GLN 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 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 25 ASN 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 112 ARG 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 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 69 ASN 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 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: 3.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 264 optimal weight: 1.9990 chunk 174 optimal weight: 0.0020 chunk 125 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 overall best weight: 0.3606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN S 188 GLN S 337 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 GLN U 105 ASN U 328 GLN V 142 ASN J 75 ASN J 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122133 restraints weight = 36433.543| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.99 r_work: 0.3400 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1235 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= 0.120 Angle : 0.511 8.116 34625 Z= 0.272 Chirality : 0.039 0.158 3879 Planarity : 0.004 0.054 4117 Dihedral : 17.097 88.138 4280 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.08 % Allowed : 26.94 % 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 aren not related in a simple way. whole: 1.00 (0.17), residues: 2802 helix: 1.44 (0.13), residues: 1644 sheet: -1.44 (0.44), residues: 144 loop : -0.21 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 153 TYR 0.023 0.001 TYR J 399 PHE 0.026 0.001 PHE J 323 TRP 0.013 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00261 (25272) covalent geometry : angle 0.50919 (34616) hydrogen bonds : bond 0.03956 ( 1289) hydrogen bonds : angle 3.97802 ( 3530) metal coordination : bond 0.00240 ( 8) metal coordination : angle 3.02345 ( 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 720 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 620 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7846 (tp30) cc_final: 0.7580 (mm-30) REVERT: Q 153 ARG cc_start: 0.8367 (ttt90) cc_final: 0.8145 (ttt90) REVERT: R 92 VAL cc_start: 0.8626 (p) cc_final: 0.8300 (t) REVERT: R 157 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7869 (tt0) REVERT: R 307 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: R 310 LEU cc_start: 0.8205 (mp) cc_final: 0.7994 (mt) REVERT: R 333 GLU cc_start: 0.8011 (tp30) cc_final: 0.7653 (tp30) REVERT: R 336 VAL cc_start: 0.7807 (t) cc_final: 0.7521 (m) REVERT: S 135 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7562 (ttp-170) REVERT: S 148 VAL cc_start: 0.8224 (m) cc_final: 0.8020 (t) REVERT: S 306 GLN cc_start: 0.8385 (mt0) cc_final: 0.8140 (mt0) REVERT: S 324 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7200 (mm-30) REVERT: S 327 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7784 (ttp-110) REVERT: S 345 LEU cc_start: 0.8775 (mt) cc_final: 0.8512 (mm) REVERT: T 63 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7689 (mttm) REVERT: T 73 LYS cc_start: 0.8335 (tptp) cc_final: 0.8039 (tptp) REVERT: T 116 THR cc_start: 0.8397 (m) cc_final: 0.8178 (t) REVERT: T 157 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8010 (tt0) REVERT: T 186 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: T 188 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7904 (mt0) REVERT: T 198 MET cc_start: 0.8304 (mtp) cc_final: 0.8104 (mtt) REVERT: T 268 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7732 (mt-10) REVERT: T 286 LYS cc_start: 0.8449 (tttp) cc_final: 0.8223 (tptp) REVERT: T 326 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7733 (mt-10) REVERT: T 338 ASN cc_start: 0.7254 (m-40) cc_final: 0.6885 (m-40) REVERT: T 340 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7891 (mtt180) REVERT: U 17 THR cc_start: 0.7883 (m) cc_final: 0.7646 (t) REVERT: U 52 PHE cc_start: 0.8134 (m-80) cc_final: 0.7933 (m-10) REVERT: U 69 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.6887 (ttp-110) REVERT: U 95 GLU cc_start: 0.7714 (tt0) cc_final: 0.7458 (tt0) REVERT: U 242 GLN cc_start: 0.8281 (mm110) cc_final: 0.7919 (mm110) REVERT: V 25 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6568 (p0) REVERT: V 39 ILE cc_start: 0.8142 (mt) cc_final: 0.7847 (mt) REVERT: V 68 LEU cc_start: 0.8775 (mt) cc_final: 0.8558 (mp) REVERT: V 130 VAL cc_start: 0.8462 (t) cc_final: 0.8196 (p) REVERT: V 190 ASP cc_start: 0.8328 (m-30) cc_final: 0.7901 (m-30) REVERT: V 327 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8084 (tmm160) REVERT: W 41 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7977 (mmp) REVERT: W 52 PHE cc_start: 0.7653 (m-10) cc_final: 0.7216 (m-80) REVERT: W 112 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7171 (ttp80) REVERT: W 118 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7278 (mm-30) REVERT: W 119 GLU cc_start: 0.6735 (pp20) cc_final: 0.6517 (pp20) REVERT: W 135 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7258 (mmm160) REVERT: W 153 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7657 (ttt-90) REVERT: W 154 ARG cc_start: 0.7465 (ttm110) cc_final: 0.7201 (ttm110) REVERT: W 158 ASN cc_start: 0.8065 (m-40) cc_final: 0.7793 (m-40) REVERT: W 168 PHE cc_start: 0.8182 (t80) cc_final: 0.7614 (t80) REVERT: W 172 GLU cc_start: 0.7743 (tt0) cc_final: 0.7136 (tm-30) REVERT: W 317 LYS cc_start: 0.8331 (ptpp) cc_final: 0.7926 (ptpp) REVERT: W 324 GLU cc_start: 0.8008 (tp30) cc_final: 0.7119 (tp30) REVERT: W 336 VAL cc_start: 0.7477 (t) cc_final: 0.7265 (t) REVERT: J 69 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: J 86 ASN cc_start: 0.8029 (m-40) cc_final: 0.7613 (m110) REVERT: J 87 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7138 (mtm-85) REVERT: J 97 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7145 (mtp) REVERT: J 135 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7548 (mtp85) REVERT: J 136 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7705 (ttpt) REVERT: J 155 GLU cc_start: 0.8014 (mp0) cc_final: 0.7744 (mt-10) REVERT: J 172 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7827 (mmmm) REVERT: J 310 VAL cc_start: 0.8447 (m) cc_final: 0.8153 (p) REVERT: J 366 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.6711 (p) REVERT: J 367 MET cc_start: 0.7770 (tpt) cc_final: 0.7364 (tpp) REVERT: J 368 GLU cc_start: 0.7134 (mp0) cc_final: 0.6092 (mp0) REVERT: J 395 LYS cc_start: 0.7009 (ttmm) cc_final: 0.6658 (ttmm) REVERT: J 398 ASN cc_start: 0.7326 (p0) cc_final: 0.7044 (p0) REVERT: J 414 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: J 431 GLU cc_start: 0.6810 (tt0) cc_final: 0.6560 (tp30) REVERT: J 446 TYR cc_start: 0.7278 (m-80) cc_final: 0.7017 (m-80) outliers start: 100 outliers final: 54 residues processed: 674 average time/residue: 0.1812 time to fit residues: 179.5861 Evaluate side-chains 652 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 585 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE 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 128 TYR Chi-restraints excluded: chain R residue 187 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 188 GLN Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 264 VAL 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 210 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 300 ILE 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 193 LYS 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 24 GLU Chi-restraints excluded: chain V residue 25 ASN Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 142 ASN 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 112 ARG 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 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 69 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 97 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS 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 366 THR 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: 3.9990 chunk 151 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 220 GLN R 316 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN S 337 GLN T 105 ASN T 323 GLN U 328 GLN J 75 ASN J 106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117499 restraints weight = 36315.327| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3355 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25280 Z= 0.235 Angle : 0.575 8.908 34625 Z= 0.303 Chirality : 0.043 0.165 3879 Planarity : 0.005 0.052 4117 Dihedral : 17.214 88.138 4274 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.24 % Allowed : 26.57 % Favored : 69.18 % 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 aren not related in a simple way. whole: 0.76 (0.16), residues: 2802 helix: 1.21 (0.13), residues: 1653 sheet: -1.13 (0.40), residues: 186 loop : -0.23 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 112 TYR 0.015 0.002 TYR J 72 PHE 0.023 0.002 PHE J 323 TRP 0.020 0.002 TRP J 284 HIS 0.008 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00550 (25272) covalent geometry : angle 0.57185 (34616) hydrogen bonds : bond 0.04578 ( 1289) hydrogen bonds : angle 4.05877 ( 3530) metal coordination : bond 0.00456 ( 8) metal coordination : angle 3.79763 ( 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 717 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 613 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 172 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7313 (mm-30) REVERT: Q 210 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6759 (tm-30) REVERT: R 92 VAL cc_start: 0.8522 (p) cc_final: 0.8283 (t) REVERT: R 153 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8033 (ttt90) REVERT: R 157 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7547 (mt-10) REVERT: S 135 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7591 (ttp-170) REVERT: S 171 ASP cc_start: 0.8243 (t0) cc_final: 0.7908 (t0) REVERT: S 186 GLN cc_start: 0.7719 (tt0) cc_final: 0.7338 (tt0) REVERT: S 246 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8168 (p) REVERT: S 324 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7124 (mm-30) REVERT: S 327 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.7710 (ttp-110) REVERT: S 332 THR cc_start: 0.8339 (p) cc_final: 0.8055 (t) REVERT: S 345 LEU cc_start: 0.8779 (mt) cc_final: 0.8492 (mm) REVERT: T 54 PHE cc_start: 0.8216 (m-80) cc_final: 0.7873 (m-80) REVERT: T 186 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: T 198 MET cc_start: 0.8336 (mtp) cc_final: 0.8133 (mtt) REVERT: T 286 LYS cc_start: 0.8387 (tttp) cc_final: 0.8109 (tptt) REVERT: T 338 ASN cc_start: 0.7266 (m-40) cc_final: 0.6906 (m-40) REVERT: T 340 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7949 (mtt180) REVERT: U 17 THR cc_start: 0.7992 (m) cc_final: 0.7751 (t) REVERT: U 69 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: U 95 GLU cc_start: 0.7703 (tt0) cc_final: 0.7440 (tt0) REVERT: U 142 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.7048 (t0) REVERT: U 144 GLU cc_start: 0.6789 (tp30) cc_final: 0.6477 (tp30) REVERT: U 242 GLN cc_start: 0.8280 (mm110) cc_final: 0.7917 (mm110) REVERT: U 273 ARG cc_start: 0.8270 (mmt90) cc_final: 0.8028 (mmt90) REVERT: U 282 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7346 (tttm) REVERT: V 25 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.6575 (p0) REVERT: V 38 GLU cc_start: 0.7930 (tp30) cc_final: 0.7593 (tp30) REVERT: V 39 ILE cc_start: 0.8160 (mt) cc_final: 0.7850 (mt) REVERT: V 76 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7700 (mt-10) REVERT: V 130 VAL cc_start: 0.8551 (t) cc_final: 0.8240 (p) REVERT: V 190 ASP cc_start: 0.8324 (m-30) cc_final: 0.8015 (m-30) REVERT: V 304 ASP cc_start: 0.6969 (m-30) cc_final: 0.6735 (m-30) REVERT: V 327 ARG cc_start: 0.8327 (ttp80) cc_final: 0.8100 (tmm160) REVERT: W 41 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: W 52 PHE cc_start: 0.7770 (m-10) cc_final: 0.7409 (m-80) REVERT: W 112 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7210 (ttp80) REVERT: W 116 THR cc_start: 0.8027 (t) cc_final: 0.7717 (m) REVERT: W 118 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7217 (mm-30) REVERT: W 119 GLU cc_start: 0.6765 (pp20) cc_final: 0.6558 (pp20) REVERT: W 158 ASN cc_start: 0.8039 (m-40) cc_final: 0.7775 (m-40) REVERT: W 168 PHE cc_start: 0.8299 (t80) cc_final: 0.7796 (t80) REVERT: W 172 GLU cc_start: 0.7765 (tt0) cc_final: 0.7075 (tm-30) REVERT: W 220 GLN cc_start: 0.7701 (tp40) cc_final: 0.6968 (tp40) REVERT: W 317 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7875 (ptpp) REVERT: J 86 ASN cc_start: 0.8055 (m-40) cc_final: 0.7663 (m110) REVERT: J 87 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6826 (mtm-85) REVERT: J 172 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7831 (mmmm) REVERT: J 236 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: J 263 LYS cc_start: 0.7019 (ttmt) cc_final: 0.6563 (ttpp) REVERT: J 288 SER cc_start: 0.8435 (m) cc_final: 0.8166 (p) REVERT: J 310 VAL cc_start: 0.8486 (m) cc_final: 0.8062 (p) REVERT: J 321 LYS cc_start: 0.8134 (tptt) cc_final: 0.7858 (tptt) REVERT: J 367 MET cc_start: 0.7767 (tpt) cc_final: 0.7455 (tpp) REVERT: J 395 LYS cc_start: 0.7014 (ttmm) cc_final: 0.6622 (ttmm) REVERT: J 398 ASN cc_start: 0.7338 (p0) cc_final: 0.7049 (p0) REVERT: J 431 GLU cc_start: 0.6885 (tt0) cc_final: 0.6628 (tp30) REVERT: J 446 TYR cc_start: 0.7600 (m-80) cc_final: 0.7174 (m-80) outliers start: 104 outliers final: 59 residues processed: 667 average time/residue: 0.1761 time to fit residues: 174.1387 Evaluate side-chains 666 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 595 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR 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 265 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 18 GLU 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 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 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 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 302 LEU Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 25 ASN Chi-restraints excluded: chain V residue 77 LEU 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 112 ARG 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 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 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 331 LEU Chi-restraints excluded: chain J residue 390 SER 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: 0.0170 chunk 25 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 264 optimal weight: 6.9990 chunk 168 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN T 197 ASN V 142 ASN V 197 ASN J 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119887 restraints weight = 36328.809| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.01 r_work: 0.3391 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1666 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= 0.121 Angle : 0.515 12.424 34625 Z= 0.272 Chirality : 0.039 0.154 3879 Planarity : 0.004 0.049 4117 Dihedral : 17.046 89.812 4270 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.08 % Allowed : 27.22 % Favored : 68.69 % 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 aren not related in a simple way. whole: 1.01 (0.17), residues: 2802 helix: 1.47 (0.13), residues: 1643 sheet: -1.65 (0.43), residues: 146 loop : -0.18 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 153 TYR 0.015 0.001 TYR J 399 PHE 0.021 0.001 PHE J 323 TRP 0.025 0.001 TRP J 284 HIS 0.005 0.001 HIS R 30 Details of bonding type rmsd covalent geometry : bond 0.00267 (25272) covalent geometry : angle 0.51236 (34616) hydrogen bonds : bond 0.03764 ( 1289) hydrogen bonds : angle 3.88534 ( 3530) metal coordination : bond 0.00290 ( 8) metal coordination : angle 3.33244 ( 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 714 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 614 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 153 ARG cc_start: 0.8360 (ttt90) cc_final: 0.8117 (ttt90) REVERT: Q 161 ILE cc_start: 0.8254 (mt) cc_final: 0.7974 (pt) REVERT: Q 172 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7319 (mm-30) REVERT: Q 210 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6735 (tm-30) REVERT: R 153 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8007 (ttt90) REVERT: R 157 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7665 (mt-10) REVERT: S 103 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: S 135 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: S 148 VAL cc_start: 0.8248 (m) cc_final: 0.8028 (t) REVERT: S 171 ASP cc_start: 0.8202 (t0) cc_final: 0.7881 (t0) REVERT: S 295 ARG cc_start: 0.7861 (ptp-110) cc_final: 0.7402 (ptm-80) REVERT: S 324 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7101 (mm-30) REVERT: S 327 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.7596 (ttp-110) REVERT: S 332 THR cc_start: 0.8347 (p) cc_final: 0.8063 (t) REVERT: S 345 LEU cc_start: 0.8802 (mt) cc_final: 0.8507 (mm) REVERT: T 17 THR cc_start: 0.8403 (m) cc_final: 0.8071 (p) REVERT: T 63 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7881 (mttp) REVERT: T 116 THR cc_start: 0.8460 (m) cc_final: 0.8229 (t) REVERT: T 186 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: T 188 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7913 (mt0) REVERT: T 338 ASN cc_start: 0.7296 (m-40) cc_final: 0.6967 (m-40) REVERT: T 340 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7961 (mtt180) REVERT: U 17 THR cc_start: 0.7965 (m) cc_final: 0.7723 (t) REVERT: U 95 GLU cc_start: 0.7701 (tt0) cc_final: 0.7437 (tt0) REVERT: U 242 GLN cc_start: 0.8262 (mm110) cc_final: 0.7903 (mm110) REVERT: U 282 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7348 (tttm) REVERT: U 331 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: V 12 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7182 (mt) REVERT: V 25 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6443 (p0) REVERT: V 38 GLU cc_start: 0.7881 (tp30) cc_final: 0.7571 (tp30) REVERT: V 39 ILE cc_start: 0.8165 (mt) cc_final: 0.7773 (mt) REVERT: V 68 LEU cc_start: 0.8781 (mt) cc_final: 0.8534 (mp) REVERT: V 130 VAL cc_start: 0.8506 (t) cc_final: 0.8194 (p) REVERT: V 190 ASP cc_start: 0.8311 (m-30) cc_final: 0.8016 (m-30) REVERT: V 253 GLN cc_start: 0.7620 (mm110) cc_final: 0.7395 (mm110) REVERT: V 304 ASP cc_start: 0.7009 (m-30) cc_final: 0.6800 (m-30) REVERT: V 327 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8107 (tmm160) REVERT: W 41 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: W 52 PHE cc_start: 0.7722 (m-10) cc_final: 0.7355 (m-80) REVERT: W 112 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7239 (ttp80) REVERT: W 116 THR cc_start: 0.7957 (t) cc_final: 0.7617 (m) REVERT: W 118 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7263 (mm-30) REVERT: W 158 ASN cc_start: 0.8034 (m-40) cc_final: 0.7768 (m-40) REVERT: W 168 PHE cc_start: 0.8144 (t80) cc_final: 0.7529 (t80) REVERT: W 172 GLU cc_start: 0.7767 (tt0) cc_final: 0.7057 (tm-30) REVERT: W 193 LYS cc_start: 0.7982 (ttpp) cc_final: 0.7758 (ttpp) REVERT: W 198 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: W 220 GLN cc_start: 0.7712 (tp40) cc_final: 0.6930 (tp40) REVERT: W 317 LYS cc_start: 0.8349 (ptpp) cc_final: 0.7927 (ptpp) REVERT: W 336 VAL cc_start: 0.7461 (t) cc_final: 0.7238 (t) REVERT: J 86 ASN cc_start: 0.8020 (m-40) cc_final: 0.7643 (m-40) REVERT: J 87 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6845 (mtm-85) REVERT: J 136 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8251 (mtpt) REVERT: J 172 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7865 (mmmm) REVERT: J 189 ASN cc_start: 0.8408 (t0) cc_final: 0.8009 (t0) REVERT: J 236 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: J 288 SER cc_start: 0.8433 (m) cc_final: 0.8197 (p) REVERT: J 310 VAL cc_start: 0.8468 (m) cc_final: 0.8022 (p) REVERT: J 367 MET cc_start: 0.7767 (tpt) cc_final: 0.7415 (tpp) REVERT: J 368 GLU cc_start: 0.7037 (mp0) cc_final: 0.6798 (mp0) REVERT: J 408 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6747 (tt) REVERT: J 414 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: J 431 GLU cc_start: 0.6799 (tt0) cc_final: 0.6548 (tp30) REVERT: J 446 TYR cc_start: 0.7516 (m-80) cc_final: 0.7076 (m-80) outliers start: 100 outliers final: 66 residues processed: 666 average time/residue: 0.1772 time to fit residues: 175.7346 Evaluate side-chains 687 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 605 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 Q residue 152 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR 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 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 249 LEU Chi-restraints excluded: chain S residue 264 VAL 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 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU 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 U residue 331 GLU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 25 ASN 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 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 112 ARG 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 78 ASN 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 136 LYS 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 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 4.9990 chunk 173 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 25 ASN R 158 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118650 restraints weight = 36183.241| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.05 r_work: 0.3364 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25280 Z= 0.168 Angle : 0.534 10.554 34625 Z= 0.282 Chirality : 0.040 0.157 3879 Planarity : 0.004 0.051 4117 Dihedral : 17.050 89.183 4270 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.61 % Allowed : 26.69 % Favored : 68.69 % 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 aren not related in a simple way. whole: 0.97 (0.17), residues: 2802 helix: 1.40 (0.13), residues: 1647 sheet: -1.16 (0.40), residues: 186 loop : -0.16 (0.22), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 112 TYR 0.013 0.001 TYR J 399 PHE 0.027 0.001 PHE J 323 TRP 0.026 0.001 TRP J 284 HIS 0.006 0.001 HIS J 147 Details of bonding type rmsd covalent geometry : bond 0.00391 (25272) covalent geometry : angle 0.53129 (34616) hydrogen bonds : bond 0.04031 ( 1289) hydrogen bonds : angle 3.88363 ( 3530) metal coordination : bond 0.00332 ( 8) metal coordination : angle 3.35112 ( 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 728 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 615 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8260 (mt) cc_final: 0.7986 (pt) REVERT: Q 172 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7362 (mm-30) REVERT: Q 210 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6761 (tm-30) REVERT: R 102 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7706 (ttm170) REVERT: R 153 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8034 (ttt90) REVERT: R 157 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7535 (mt-10) REVERT: S 41 MET cc_start: 0.8062 (mmt) cc_final: 0.7834 (mmm) REVERT: S 103 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: S 135 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7699 (ttp-170) REVERT: S 171 ASP cc_start: 0.8227 (t0) cc_final: 0.7890 (t0) REVERT: S 246 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8174 (p) REVERT: S 295 ARG cc_start: 0.7838 (ptp-110) cc_final: 0.7562 (ptm-80) REVERT: S 324 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7698 (mm-30) REVERT: S 327 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8130 (tmm160) REVERT: S 332 THR cc_start: 0.8351 (p) cc_final: 0.8063 (t) REVERT: S 345 LEU cc_start: 0.8802 (mt) cc_final: 0.8502 (mm) REVERT: T 17 THR cc_start: 0.8428 (m) cc_final: 0.8188 (p) REVERT: T 54 PHE cc_start: 0.8237 (m-80) cc_final: 0.7944 (m-80) REVERT: T 153 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.8294 (ttt-90) REVERT: T 186 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: T 188 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7937 (mt0) REVERT: T 338 ASN cc_start: 0.7284 (m-40) cc_final: 0.6956 (m-40) REVERT: T 340 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7971 (mtt180) REVERT: U 17 THR cc_start: 0.8000 (m) cc_final: 0.7757 (t) REVERT: U 69 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6864 (ttp-110) REVERT: U 127 ASP cc_start: 0.7832 (t0) cc_final: 0.7471 (t0) REVERT: U 142 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.7061 (t0) REVERT: U 242 GLN cc_start: 0.8262 (mm110) cc_final: 0.7887 (mm110) REVERT: U 273 ARG cc_start: 0.8267 (mmt90) cc_final: 0.7775 (mmt180) REVERT: U 282 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7351 (tttm) REVERT: V 12 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7203 (mt) REVERT: V 25 ASN cc_start: 0.6749 (OUTLIER) cc_final: 0.6487 (p0) REVERT: V 39 ILE cc_start: 0.8190 (mt) cc_final: 0.7822 (mt) REVERT: V 130 VAL cc_start: 0.8551 (t) cc_final: 0.8225 (p) REVERT: V 186 GLN cc_start: 0.8481 (tt0) cc_final: 0.8229 (tt0) REVERT: V 190 ASP cc_start: 0.8314 (m-30) cc_final: 0.8018 (m-30) REVERT: V 327 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8095 (tmm160) REVERT: W 32 ARG cc_start: 0.6951 (tpp-160) cc_final: 0.6563 (tpp80) REVERT: W 41 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7989 (mmp) REVERT: W 44 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7662 (mp) REVERT: W 52 PHE cc_start: 0.7778 (m-10) cc_final: 0.7421 (m-80) REVERT: W 112 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7225 (ttp80) REVERT: W 116 THR cc_start: 0.8051 (t) cc_final: 0.7745 (m) REVERT: W 118 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7286 (mm-30) REVERT: W 158 ASN cc_start: 0.8055 (m-40) cc_final: 0.7800 (m-40) REVERT: W 168 PHE cc_start: 0.8190 (t80) cc_final: 0.7607 (t80) REVERT: W 193 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7798 (ttpp) REVERT: W 198 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6945 (mtt) REVERT: W 220 GLN cc_start: 0.7694 (tp40) cc_final: 0.6985 (tp40) REVERT: J 86 ASN cc_start: 0.8018 (m-40) cc_final: 0.7639 (m-40) REVERT: J 87 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6847 (mtm-85) REVERT: J 115 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7904 (ptp90) REVERT: J 134 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7729 (m) REVERT: J 172 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7867 (mmmm) REVERT: J 236 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: J 288 SER cc_start: 0.8429 (m) cc_final: 0.8139 (p) REVERT: J 310 VAL cc_start: 0.8496 (m) cc_final: 0.8094 (p) REVERT: J 395 LYS cc_start: 0.7071 (ttmm) cc_final: 0.6799 (ttmm) REVERT: J 408 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6744 (tt) REVERT: J 414 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: J 431 GLU cc_start: 0.6838 (tt0) cc_final: 0.6586 (tp30) REVERT: J 446 TYR cc_start: 0.7655 (m-80) cc_final: 0.7203 (m-80) outliers start: 113 outliers final: 73 residues processed: 674 average time/residue: 0.1703 time to fit residues: 169.2289 Evaluate side-chains 694 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 601 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 286 LYS Chi-restraints excluded: chain R residue 304 ASP Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 24 GLU 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 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 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU 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 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 25 ASN 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 128 TYR Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 166 ASP 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 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 112 ARG 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 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 134 THR 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 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 0.9990 chunk 224 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 170 optimal weight: 0.0470 chunk 108 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN S 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119920 restraints weight = 36237.713| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.95 r_work: 0.3392 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1925 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= 0.138 Angle : 0.521 9.308 34625 Z= 0.276 Chirality : 0.039 0.162 3879 Planarity : 0.004 0.050 4117 Dihedral : 16.998 89.848 4270 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.24 % Allowed : 27.47 % Favored : 68.29 % 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 aren not related in a simple way. whole: 1.05 (0.17), residues: 2802 helix: 1.47 (0.13), residues: 1637 sheet: -1.13 (0.41), residues: 186 loop : -0.13 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 308 TYR 0.015 0.001 TYR J 399 PHE 0.025 0.001 PHE J 323 TRP 0.031 0.001 TRP J 284 HIS 0.005 0.001 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00314 (25272) covalent geometry : angle 0.51817 (34616) hydrogen bonds : bond 0.03764 ( 1289) hydrogen bonds : angle 3.82159 ( 3530) metal coordination : bond 0.00276 ( 8) metal coordination : angle 3.11609 ( 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 698 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 594 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8215 (mt) cc_final: 0.7917 (pt) REVERT: Q 172 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7277 (mm-30) REVERT: Q 210 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6668 (tm-30) REVERT: R 102 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7660 (ttm170) REVERT: R 153 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8007 (ttt90) REVERT: R 157 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7780 (tt0) REVERT: S 41 MET cc_start: 0.8052 (mmt) cc_final: 0.7794 (mmm) REVERT: S 103 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: S 135 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: S 148 VAL cc_start: 0.8242 (m) cc_final: 0.8020 (t) REVERT: S 201 ILE cc_start: 0.8771 (mm) cc_final: 0.8505 (mt) REVERT: S 246 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8180 (p) REVERT: S 295 ARG cc_start: 0.7828 (ptp-110) cc_final: 0.7589 (ptm-80) REVERT: S 324 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7657 (mm-30) REVERT: S 327 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.8101 (tmm160) REVERT: S 332 THR cc_start: 0.8351 (p) cc_final: 0.8062 (t) REVERT: S 345 LEU cc_start: 0.8798 (mt) cc_final: 0.8490 (mm) REVERT: T 17 THR cc_start: 0.8410 (m) cc_final: 0.8075 (p) REVERT: T 63 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7831 (mttp) REVERT: T 186 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: T 338 ASN cc_start: 0.7254 (m-40) cc_final: 0.6919 (m-40) REVERT: T 340 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7957 (mtt180) REVERT: U 17 THR cc_start: 0.7970 (m) cc_final: 0.7728 (t) REVERT: U 69 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6837 (ttp-110) REVERT: U 108 GLU cc_start: 0.8180 (tp30) cc_final: 0.7923 (tp30) REVERT: U 112 ARG cc_start: 0.8361 (mmt90) cc_final: 0.8137 (mmt180) REVERT: U 127 ASP cc_start: 0.7859 (t0) cc_final: 0.7605 (t0) REVERT: U 142 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7034 (t0) REVERT: U 242 GLN cc_start: 0.8241 (mm110) cc_final: 0.7863 (mm110) REVERT: U 282 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7337 (tttm) REVERT: U 286 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7362 (tttm) REVERT: V 25 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6461 (p0) REVERT: V 39 ILE cc_start: 0.8151 (mt) cc_final: 0.7860 (mt) REVERT: V 130 VAL cc_start: 0.8478 (t) cc_final: 0.8151 (p) REVERT: V 186 GLN cc_start: 0.8468 (tt0) cc_final: 0.8226 (tt0) REVERT: V 190 ASP cc_start: 0.8292 (m-30) cc_final: 0.7993 (m-30) REVERT: V 253 GLN cc_start: 0.7627 (mm110) cc_final: 0.7423 (mm110) REVERT: V 327 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8078 (tmm160) REVERT: W 41 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: W 52 PHE cc_start: 0.7750 (m-10) cc_final: 0.7391 (m-80) REVERT: W 116 THR cc_start: 0.7992 (t) cc_final: 0.7691 (m) REVERT: W 118 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7297 (mm-30) REVERT: W 158 ASN cc_start: 0.8024 (m-40) cc_final: 0.7752 (m-40) REVERT: W 168 PHE cc_start: 0.8091 (t80) cc_final: 0.7655 (t80) REVERT: W 198 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6759 (mtt) REVERT: W 220 GLN cc_start: 0.7659 (tp40) cc_final: 0.6842 (tp40) REVERT: W 336 VAL cc_start: 0.7463 (t) cc_final: 0.7235 (t) REVERT: J 86 ASN cc_start: 0.8004 (m-40) cc_final: 0.7608 (m-40) REVERT: J 87 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6849 (mtm-85) REVERT: J 115 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7829 (ptp90) REVERT: J 158 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (mt) REVERT: J 172 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7843 (mmmm) REVERT: J 189 ASN cc_start: 0.8413 (t0) cc_final: 0.7997 (t0) REVERT: J 236 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: J 310 VAL cc_start: 0.8490 (m) cc_final: 0.8046 (p) REVERT: J 408 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6771 (tt) REVERT: J 414 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: J 431 GLU cc_start: 0.6780 (tt0) cc_final: 0.6506 (tp30) REVERT: J 446 TYR cc_start: 0.7614 (m-80) cc_final: 0.7097 (m-80) outliers start: 104 outliers final: 72 residues processed: 646 average time/residue: 0.1760 time to fit residues: 168.4846 Evaluate side-chains 658 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 568 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 24 GLU 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 264 VAL 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 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU 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 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 286 LYS Chi-restraints excluded: chain U residue 302 LEU Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 25 ASN 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 128 TYR Chi-restraints excluded: chain V residue 166 ASP 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 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 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 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 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 0.8980 chunk 133 optimal weight: 0.3980 chunk 7 optimal weight: 0.0570 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 219 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 154 optimal weight: 0.0470 chunk 96 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 254 optimal weight: 0.0570 overall best weight: 0.0672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 188 GLN S 220 GLN J 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122712 restraints weight = 36259.331| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.04 r_work: 0.3431 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25280 Z= 0.106 Angle : 0.507 8.560 34625 Z= 0.269 Chirality : 0.038 0.160 3879 Planarity : 0.004 0.049 4117 Dihedral : 16.754 88.324 4270 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.39 % Allowed : 28.57 % Favored : 68.04 % 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 aren not related in a simple way. whole: 1.25 (0.17), residues: 2802 helix: 1.70 (0.13), residues: 1622 sheet: -1.55 (0.45), residues: 144 loop : -0.11 (0.21), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 231 TYR 0.018 0.001 TYR J 399 PHE 0.022 0.001 PHE J 323 TRP 0.044 0.002 TRP J 284 HIS 0.006 0.001 HIS V 30 Details of bonding type rmsd covalent geometry : bond 0.00224 (25272) covalent geometry : angle 0.50489 (34616) hydrogen bonds : bond 0.03333 ( 1289) hydrogen bonds : angle 3.70508 ( 3530) metal coordination : bond 0.00230 ( 8) metal coordination : angle 2.56286 ( 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 672 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 589 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 89 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7579 (p) REVERT: Q 161 ILE cc_start: 0.8159 (mt) cc_final: 0.7859 (pt) REVERT: Q 172 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7258 (mm-30) REVERT: Q 210 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6646 (tm-30) REVERT: R 10 GLU cc_start: 0.7896 (pm20) cc_final: 0.7568 (pm20) REVERT: R 102 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7760 (ttm170) REVERT: R 153 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7923 (ttt90) REVERT: R 157 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7788 (tt0) REVERT: R 174 GLN cc_start: 0.8140 (pm20) cc_final: 0.7771 (pt0) REVERT: S 76 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: S 103 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: S 135 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: S 201 ILE cc_start: 0.8787 (mm) cc_final: 0.8535 (mt) REVERT: S 231 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: S 295 ARG cc_start: 0.7811 (ptp-110) cc_final: 0.7596 (ptm-80) REVERT: S 324 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7692 (mm-30) REVERT: S 327 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8090 (tmm160) REVERT: S 332 THR cc_start: 0.8333 (p) cc_final: 0.8049 (t) REVERT: S 345 LEU cc_start: 0.8791 (mt) cc_final: 0.8516 (mm) REVERT: T 17 THR cc_start: 0.8462 (m) cc_final: 0.8123 (p) REVERT: T 54 PHE cc_start: 0.8230 (m-80) cc_final: 0.7821 (m-80) REVERT: T 116 THR cc_start: 0.8453 (m) cc_final: 0.8210 (t) REVERT: T 153 ARG cc_start: 0.8599 (tpt-90) cc_final: 0.8227 (ttt-90) REVERT: T 186 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: T 187 ASP cc_start: 0.7790 (m-30) cc_final: 0.7561 (m-30) REVERT: T 338 ASN cc_start: 0.7248 (m-40) cc_final: 0.6911 (m-40) REVERT: T 340 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7912 (mtt-85) REVERT: U 17 THR cc_start: 0.7935 (m) cc_final: 0.7712 (t) REVERT: U 69 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6828 (ttp-110) REVERT: U 127 ASP cc_start: 0.7901 (t0) cc_final: 0.7630 (t0) REVERT: U 242 GLN cc_start: 0.8262 (mm110) cc_final: 0.7904 (mm110) REVERT: U 282 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7314 (tttm) REVERT: U 286 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7358 (tttm) REVERT: U 331 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: V 38 GLU cc_start: 0.7849 (tp30) cc_final: 0.7514 (tp30) REVERT: V 61 VAL cc_start: 0.8372 (t) cc_final: 0.8125 (p) REVERT: V 130 VAL cc_start: 0.8471 (t) cc_final: 0.8189 (p) REVERT: V 186 GLN cc_start: 0.8481 (tt0) cc_final: 0.8189 (tt0) REVERT: V 190 ASP cc_start: 0.8320 (m-30) cc_final: 0.7930 (m-30) REVERT: V 253 GLN cc_start: 0.7646 (mm110) cc_final: 0.7427 (mm110) REVERT: W 41 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: W 52 PHE cc_start: 0.7670 (m-10) cc_final: 0.7143 (m-80) REVERT: W 116 THR cc_start: 0.7942 (t) cc_final: 0.7589 (m) REVERT: W 118 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7346 (mm-30) REVERT: W 158 ASN cc_start: 0.8032 (m-40) cc_final: 0.7786 (m-40) REVERT: W 168 PHE cc_start: 0.7743 (t80) cc_final: 0.7351 (t80) REVERT: W 188 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: W 193 LYS cc_start: 0.7958 (ttpp) cc_final: 0.7732 (ttpp) REVERT: W 220 GLN cc_start: 0.7680 (tp40) cc_final: 0.6727 (tp40) REVERT: W 224 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7081 (mtt90) REVERT: W 336 VAL cc_start: 0.7451 (t) cc_final: 0.7248 (t) REVERT: J 86 ASN cc_start: 0.8027 (m-40) cc_final: 0.7637 (m-40) REVERT: J 87 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7185 (mtm-85) REVERT: J 115 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7820 (ptp90) REVERT: J 135 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7591 (mtm180) REVERT: J 155 GLU cc_start: 0.8078 (mp0) cc_final: 0.7875 (mp0) REVERT: J 158 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8384 (mt) REVERT: J 172 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7856 (mmmm) REVERT: J 189 ASN cc_start: 0.8401 (t0) cc_final: 0.7942 (t0) REVERT: J 310 VAL cc_start: 0.8477 (m) cc_final: 0.8177 (p) REVERT: J 408 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6781 (tt) REVERT: J 431 GLU cc_start: 0.6714 (tt0) cc_final: 0.6494 (tp30) REVERT: J 446 TYR cc_start: 0.7454 (m-80) cc_final: 0.6964 (m-80) outliers start: 83 outliers final: 53 residues processed: 632 average time/residue: 0.1816 time to fit residues: 168.7461 Evaluate side-chains 651 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 582 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 123 ASP 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 345 LEU Chi-restraints excluded: chain S residue 24 GLU 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 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU 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 152 LEU 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 286 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain U residue 331 GLU 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 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 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 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 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 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 0.8980 chunk 32 optimal weight: 0.7980 chunk 262 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 157 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN S 220 GLN V 252 GLN J 106 GLN J 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120989 restraints weight = 36318.450| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.95 r_work: 0.3410 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25280 Z= 0.135 Angle : 0.523 8.002 34625 Z= 0.278 Chirality : 0.039 0.186 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.795 89.594 4270 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.02 % Allowed : 28.57 % Favored : 68.41 % 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 aren not related in a simple way. whole: 1.20 (0.17), residues: 2802 helix: 1.58 (0.13), residues: 1637 sheet: -1.01 (0.42), residues: 184 loop : -0.07 (0.22), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 153 TYR 0.016 0.001 TYR J 399 PHE 0.018 0.001 PHE J 323 TRP 0.040 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 Details of bonding type rmsd covalent geometry : bond 0.00310 (25272) covalent geometry : angle 0.52191 (34616) hydrogen bonds : bond 0.03603 ( 1289) hydrogen bonds : angle 3.72488 ( 3530) metal coordination : bond 0.00203 ( 8) metal coordination : angle 2.45190 ( 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 661 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 587 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 172 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7257 (mm-30) REVERT: Q 210 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6650 (tm-30) REVERT: R 10 GLU cc_start: 0.7913 (pm20) cc_final: 0.7596 (pm20) REVERT: R 102 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7688 (ttm170) REVERT: R 153 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7980 (ttt90) REVERT: R 157 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7535 (mt-10) REVERT: S 76 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: S 103 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: S 135 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7701 (ttp-170) REVERT: S 201 ILE cc_start: 0.8779 (mm) cc_final: 0.8522 (mt) REVERT: S 324 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7681 (mm-30) REVERT: S 327 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8073 (tmm160) REVERT: S 332 THR cc_start: 0.8362 (p) cc_final: 0.8084 (t) REVERT: S 345 LEU cc_start: 0.8758 (mt) cc_final: 0.8479 (mm) REVERT: T 17 THR cc_start: 0.8457 (m) cc_final: 0.8121 (p) REVERT: T 54 PHE cc_start: 0.8207 (m-80) cc_final: 0.7814 (m-80) REVERT: T 116 THR cc_start: 0.8451 (m) cc_final: 0.8214 (t) REVERT: T 153 ARG cc_start: 0.8624 (tpt-90) cc_final: 0.8195 (ttt-90) REVERT: T 157 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8028 (tt0) REVERT: T 186 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: T 268 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7723 (mt-10) REVERT: T 326 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7704 (mt-10) REVERT: T 338 ASN cc_start: 0.7268 (m-40) cc_final: 0.6936 (m-40) REVERT: T 340 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7944 (mtt-85) REVERT: U 17 THR cc_start: 0.7946 (m) cc_final: 0.7721 (t) REVERT: U 69 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6836 (ttp-110) REVERT: U 108 GLU cc_start: 0.8188 (tp30) cc_final: 0.7853 (tp30) REVERT: U 127 ASP cc_start: 0.7885 (t0) cc_final: 0.7605 (t0) REVERT: U 242 GLN cc_start: 0.8213 (mm110) cc_final: 0.7849 (mm110) REVERT: U 282 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7341 (tttm) REVERT: U 286 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7357 (tttm) REVERT: V 25 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6234 (p0) REVERT: V 130 VAL cc_start: 0.8493 (t) cc_final: 0.8179 (p) REVERT: V 186 GLN cc_start: 0.8477 (tt0) cc_final: 0.8151 (tt0) REVERT: V 190 ASP cc_start: 0.8308 (m-30) cc_final: 0.7880 (m-30) REVERT: V 253 GLN cc_start: 0.7665 (mm110) cc_final: 0.7453 (mm110) REVERT: W 41 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7885 (mmm) REVERT: W 52 PHE cc_start: 0.7731 (m-10) cc_final: 0.7223 (m-80) REVERT: W 116 THR cc_start: 0.7947 (t) cc_final: 0.7618 (m) REVERT: W 118 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7358 (mm-30) REVERT: W 158 ASN cc_start: 0.8030 (m-40) cc_final: 0.7758 (m-40) REVERT: W 168 PHE cc_start: 0.7881 (t80) cc_final: 0.7464 (t80) REVERT: W 193 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7718 (ttpp) REVERT: W 220 GLN cc_start: 0.7662 (tp40) cc_final: 0.7073 (tp40) REVERT: W 336 VAL cc_start: 0.7466 (t) cc_final: 0.7256 (t) REVERT: J 86 ASN cc_start: 0.8009 (m-40) cc_final: 0.7607 (m-40) REVERT: J 87 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: J 155 GLU cc_start: 0.8087 (mp0) cc_final: 0.7859 (mp0) REVERT: J 158 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8455 (mt) REVERT: J 172 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7875 (mmmm) REVERT: J 189 ASN cc_start: 0.8406 (t0) cc_final: 0.7967 (t0) REVERT: J 310 VAL cc_start: 0.8478 (m) cc_final: 0.8187 (p) REVERT: J 431 GLU cc_start: 0.6752 (tt0) cc_final: 0.6551 (tp30) REVERT: J 446 TYR cc_start: 0.7512 (m-80) cc_final: 0.6964 (m-80) outliers start: 74 outliers final: 49 residues processed: 622 average time/residue: 0.1776 time to fit residues: 163.7917 Evaluate side-chains 645 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 584 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 GLU 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 345 LEU Chi-restraints excluded: chain S residue 24 GLU 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 186 GLN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU 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 282 LYS Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 25 ASN 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 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 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 21 GLN 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 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 1.9990 chunk 51 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 199 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN S 220 GLN T 162 HIS U 197 ASN U 328 GLN V 175 HIS W 175 HIS J 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119991 restraints weight = 36171.063| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.94 r_work: 0.3393 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25280 Z= 0.162 Angle : 0.545 8.065 34625 Z= 0.290 Chirality : 0.041 0.184 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.887 87.853 4270 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.69 % Allowed : 29.02 % Favored : 68.29 % 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 aren not related in a simple way. whole: 1.07 (0.17), residues: 2802 helix: 1.47 (0.13), residues: 1636 sheet: -1.04 (0.41), residues: 184 loop : -0.11 (0.22), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 69 TYR 0.015 0.001 TYR J 399 PHE 0.020 0.001 PHE R 319 TRP 0.043 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00378 (25272) covalent geometry : angle 0.54346 (34616) hydrogen bonds : bond 0.03838 ( 1289) hydrogen bonds : angle 3.79783 ( 3530) metal coordination : bond 0.00343 ( 8) metal coordination : angle 2.75462 ( 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 654 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 588 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8327 (mt) cc_final: 0.8090 (pt) REVERT: Q 172 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7272 (mm-30) REVERT: Q 210 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6710 (tm-30) REVERT: R 153 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8044 (ttt90) REVERT: R 157 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7568 (mt-10) REVERT: S 76 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: S 103 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: S 135 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7793 (ttp-170) REVERT: S 201 ILE cc_start: 0.8768 (mm) cc_final: 0.8534 (mt) REVERT: S 324 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7681 (mm-30) REVERT: S 327 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.8086 (tmm160) REVERT: S 332 THR cc_start: 0.8365 (p) cc_final: 0.8081 (t) REVERT: S 345 LEU cc_start: 0.8785 (mt) cc_final: 0.8498 (mm) REVERT: T 17 THR cc_start: 0.8458 (m) cc_final: 0.8122 (p) REVERT: T 54 PHE cc_start: 0.8223 (m-80) cc_final: 0.7890 (m-80) REVERT: T 116 THR cc_start: 0.8428 (m) cc_final: 0.8202 (t) REVERT: T 153 ARG cc_start: 0.8618 (tpt-90) cc_final: 0.8217 (ttt-90) REVERT: T 157 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8043 (tt0) REVERT: T 186 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: T 326 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7702 (mt-10) REVERT: T 338 ASN cc_start: 0.7289 (m-40) cc_final: 0.6955 (m-40) REVERT: T 340 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7991 (mtt180) REVERT: U 17 THR cc_start: 0.7976 (m) cc_final: 0.7746 (t) REVERT: U 69 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6858 (ttp-110) REVERT: U 101 SER cc_start: 0.8537 (p) cc_final: 0.8172 (t) REVERT: U 108 GLU cc_start: 0.8201 (tp30) cc_final: 0.7855 (tp30) REVERT: U 127 ASP cc_start: 0.7888 (t0) cc_final: 0.7596 (t0) REVERT: U 142 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.7023 (t0) REVERT: U 242 GLN cc_start: 0.8199 (mm110) cc_final: 0.7836 (mm110) REVERT: U 282 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7365 (tttm) REVERT: U 286 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7378 (tttm) REVERT: V 25 ASN cc_start: 0.6516 (OUTLIER) cc_final: 0.6274 (p0) REVERT: V 130 VAL cc_start: 0.8491 (t) cc_final: 0.8154 (p) REVERT: V 186 GLN cc_start: 0.8473 (tt0) cc_final: 0.8132 (tt0) REVERT: V 190 ASP cc_start: 0.8325 (m-30) cc_final: 0.7911 (m-30) REVERT: V 253 GLN cc_start: 0.7663 (mm110) cc_final: 0.7424 (mm110) REVERT: V 293 LEU cc_start: 0.8706 (mt) cc_final: 0.8464 (mp) REVERT: W 41 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7886 (mmm) REVERT: W 52 PHE cc_start: 0.7767 (m-10) cc_final: 0.7292 (m-80) REVERT: W 63 LYS cc_start: 0.6890 (mtmm) cc_final: 0.6580 (mtmm) REVERT: W 116 THR cc_start: 0.8029 (t) cc_final: 0.7718 (m) REVERT: W 118 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7369 (mm-30) REVERT: W 154 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7152 (ttm110) REVERT: W 158 ASN cc_start: 0.8037 (m-40) cc_final: 0.7749 (m-40) REVERT: W 168 PHE cc_start: 0.7977 (t80) cc_final: 0.7643 (t80) REVERT: W 220 GLN cc_start: 0.7684 (tp40) cc_final: 0.7139 (tp40) REVERT: W 224 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7361 (mtt-85) REVERT: W 336 VAL cc_start: 0.7452 (t) cc_final: 0.7240 (t) REVERT: J 39 GLU cc_start: 0.7407 (tt0) cc_final: 0.7163 (tt0) REVERT: J 86 ASN cc_start: 0.7998 (m-40) cc_final: 0.7556 (m110) REVERT: J 87 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6846 (mtm-85) REVERT: J 115 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: J 158 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (mt) REVERT: J 172 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7885 (mmmm) REVERT: J 310 VAL cc_start: 0.8453 (m) cc_final: 0.8178 (p) REVERT: J 368 GLU cc_start: 0.7056 (mp0) cc_final: 0.6817 (mp0) REVERT: J 408 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6761 (tt) REVERT: J 431 GLU cc_start: 0.6754 (tt0) cc_final: 0.6507 (tp30) REVERT: J 446 TYR cc_start: 0.7596 (m-80) cc_final: 0.7155 (m-80) outliers start: 66 outliers final: 47 residues processed: 621 average time/residue: 0.1745 time to fit residues: 160.5088 Evaluate side-chains 644 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 582 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 GLU 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 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 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 69 ARG 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 282 LYS Chi-restraints excluded: chain U residue 286 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 25 ASN 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 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 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 21 GLN 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 131 LEU Chi-restraints excluded: chain J residue 158 LEU 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 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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: 2.9990 chunk 246 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 187 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN R 316 GLN S 186 GLN S 220 GLN U 197 ASN U 328 GLN V 252 GLN J 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119686 restraints weight = 36130.643| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.02 r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25280 Z= 0.160 Angle : 0.545 8.124 34625 Z= 0.291 Chirality : 0.040 0.189 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.915 87.306 4270 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 28.86 % Favored : 68.12 % 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 aren not related in a simple way. whole: 1.01 (0.17), residues: 2802 helix: 1.41 (0.13), residues: 1637 sheet: -1.00 (0.42), residues: 184 loop : -0.13 (0.22), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 69 TYR 0.015 0.001 TYR J 399 PHE 0.018 0.001 PHE R 319 TRP 0.043 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00372 (25272) covalent geometry : angle 0.54389 (34616) hydrogen bonds : bond 0.03862 ( 1289) hydrogen bonds : angle 3.80107 ( 3530) metal coordination : bond 0.00365 ( 8) metal coordination : angle 2.63873 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7298.17 seconds wall clock time: 125 minutes 8.73 seconds (7508.73 seconds total)