Starting phenix.real_space_refine on Sat Jun 21 02:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v32_42941/06_2025/8v32_42941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v32_42941/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v32_42941/06_2025/8v32_42941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v32_42941/06_2025/8v32_42941.map" model { file = "/net/cci-nas-00/data/ceres_data/8v32_42941/06_2025/8v32_42941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v32_42941/06_2025/8v32_42941.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.32, per 1000 atoms: 0.62 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: 6.20 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS J 170 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 142 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 167 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 139 " pdb=" ZN J 502 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 200 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 178 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 197 " pdb="ZN ZN J 502 " - pdb=" SG CYS J 181 " Number of angles added : 9 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 11 sheets defined 62.4% alpha, 5.2% beta 38 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 8.34 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: 8.21 Time building geometry restraints manager: 7.23 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: 2.750 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: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 65.620 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.310 ------------------------------------------------------------------------------- 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 : 9.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.022 0.001 TRP J 284 HIS 0.005 0.001 HIS T 164 PHE 0.037 0.001 PHE W 169 TYR 0.027 0.001 TYR W 37 ARG 0.016 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.17321 ( 1289) hydrogen bonds : angle 5.27161 ( 3530) metal coordination : bond 0.00421 ( 8) metal coordination : angle 3.17570 ( 9) covalent geometry : bond 0.00335 (25272) covalent geometry : angle 0.60234 (34616) *********************** 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 : 2.535 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: 0.4175 time to fit residues: 374.6033 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 : 2.657 ------------------------------------------------------------------------------- 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 243 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 225 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 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 = 0.3871 r_free = 0.3871 target = 0.146081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119307 restraints weight = 36447.423| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.01 r_work: 0.3375 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25280 Z= 0.178 Angle : 0.562 8.845 34625 Z= 0.298 Chirality : 0.041 0.158 3879 Planarity : 0.005 0.070 4117 Dihedral : 17.395 86.920 4320 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.29 % Allowed : 27.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2802 helix: 1.30 (0.13), residues: 1645 sheet: -0.99 (0.41), residues: 186 loop : -0.15 (0.22), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 284 HIS 0.007 0.001 HIS Q 30 PHE 0.020 0.001 PHE W 169 TYR 0.013 0.001 TYR R 183 ARG 0.006 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1289) hydrogen bonds : angle 4.23826 ( 3530) metal coordination : bond 0.00402 ( 8) metal coordination : angle 3.57107 ( 9) covalent geometry : bond 0.00404 (25272) covalent geometry : angle 0.55862 (34616) *********************** 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 709 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 604 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 100 GLU cc_start: 0.7739 (pm20) cc_final: 0.7509 (pm20) REVERT: R 157 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7650 (mt-10) REVERT: R 307 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: R 333 GLU cc_start: 0.8020 (tp30) cc_final: 0.7808 (tp30) REVERT: S 135 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7441 (ttp-170) REVERT: S 148 VAL cc_start: 0.8252 (m) cc_final: 0.8052 (t) REVERT: S 172 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7622 (mm-30) REVERT: S 186 GLN cc_start: 0.7790 (tt0) cc_final: 0.7500 (tt0) REVERT: S 268 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8132 (mt-10) REVERT: S 320 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8135 (ttmm) REVERT: S 345 LEU cc_start: 0.8748 (mt) cc_final: 0.8495 (mm) REVERT: T 54 PHE cc_start: 0.8187 (m-80) cc_final: 0.7856 (m-80) REVERT: T 63 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7889 (mttm) REVERT: T 116 THR cc_start: 0.8404 (m) cc_final: 0.8184 (t) REVERT: T 131 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8366 (mtt-85) REVERT: T 186 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: T 268 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7716 (mt-10) REVERT: T 326 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7765 (mt-10) REVERT: T 338 ASN cc_start: 0.7289 (m-40) cc_final: 0.6942 (m-40) REVERT: T 340 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7934 (mtt-85) REVERT: U 17 THR cc_start: 0.7899 (m) cc_final: 0.7652 (t) REVERT: U 54 PHE cc_start: 0.8219 (m-80) cc_final: 0.7725 (m-80) REVERT: U 69 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6913 (ttp-110) REVERT: U 95 GLU cc_start: 0.7731 (tt0) cc_final: 0.7470 (tt0) REVERT: U 178 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8542 (mttm) REVERT: U 242 GLN cc_start: 0.8301 (mm110) cc_final: 0.7956 (mm110) REVERT: U 253 GLN cc_start: 0.8301 (mt0) cc_final: 0.7864 (mp10) REVERT: U 273 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7762 (mmt180) REVERT: U 286 LYS cc_start: 0.7414 (tmtm) cc_final: 0.7048 (tttm) REVERT: U 324 GLU cc_start: 0.8024 (tp30) cc_final: 0.7716 (tp30) REVERT: V 38 GLU cc_start: 0.7936 (tp30) cc_final: 0.7686 (tp30) REVERT: V 68 LEU cc_start: 0.8804 (mt) cc_final: 0.8569 (mp) REVERT: V 130 VAL cc_start: 0.8486 (t) cc_final: 0.8227 (p) REVERT: V 190 ASP cc_start: 0.8333 (m-30) cc_final: 0.7916 (m-30) REVERT: V 253 GLN cc_start: 0.7518 (mm110) cc_final: 0.7308 (mm110) REVERT: W 41 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7502 (mpp) REVERT: W 44 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7710 (mp) REVERT: W 52 PHE cc_start: 0.7701 (m-10) cc_final: 0.7284 (m-80) REVERT: W 112 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: W 117 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (tt) REVERT: W 119 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6479 (pp20) REVERT: W 153 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7605 (mtp180) REVERT: W 154 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7267 (ttm110) REVERT: W 158 ASN cc_start: 0.8077 (m-40) cc_final: 0.7834 (m-40) REVERT: W 168 PHE cc_start: 0.8275 (t80) cc_final: 0.7728 (t80) REVERT: W 172 GLU cc_start: 0.7723 (tt0) cc_final: 0.7168 (tm-30) REVERT: W 327 ARG cc_start: 0.7370 (ptt-90) cc_final: 0.7101 (ptt-90) REVERT: W 336 VAL cc_start: 0.7552 (t) cc_final: 0.7298 (t) REVERT: J 69 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: J 86 ASN cc_start: 0.8027 (m-40) cc_final: 0.7595 (m110) REVERT: J 97 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7201 (mtp) REVERT: J 135 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7593 (mtp85) REVERT: J 172 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7865 (mmmm) REVERT: J 310 VAL cc_start: 0.8413 (m) cc_final: 0.8137 (p) REVERT: J 366 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7111 (p) REVERT: J 367 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7407 (tpp) REVERT: J 368 GLU cc_start: 0.7061 (mp0) cc_final: 0.6522 (mp0) REVERT: J 414 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: J 431 GLU cc_start: 0.6910 (tt0) cc_final: 0.6644 (tp30) REVERT: J 446 TYR cc_start: 0.7308 (m-80) cc_final: 0.7021 (m-10) outliers start: 105 outliers final: 45 residues processed: 655 average time/residue: 0.4254 time to fit residues: 409.0200 Evaluate side-chains 649 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 590 time to evaluate : 2.874 ------------------------------------------------------------------------------- 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 T residue 166 ASP 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 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 117 LEU 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 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 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 111 optimal weight: 0.0030 chunk 66 optimal weight: 0.0770 chunk 207 optimal weight: 0.3980 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 337 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 GLN U 328 GLN V 142 ASN J 75 ASN J 106 GLN J 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121809 restraints weight = 36092.856| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.97 r_work: 0.3399 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25280 Z= 0.126 Angle : 0.511 8.179 34625 Z= 0.272 Chirality : 0.039 0.173 3879 Planarity : 0.004 0.055 4117 Dihedral : 17.094 88.612 4280 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.92 % Allowed : 27.22 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2802 helix: 1.44 (0.13), residues: 1644 sheet: -1.42 (0.44), residues: 144 loop : -0.20 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 PHE 0.023 0.001 PHE J 323 TYR 0.021 0.001 TYR J 399 ARG 0.007 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1289) hydrogen bonds : angle 3.99038 ( 3530) metal coordination : bond 0.00231 ( 8) metal coordination : angle 3.04585 ( 9) covalent geometry : bond 0.00276 (25272) covalent geometry : angle 0.50882 (34616) *********************** 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 708 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 612 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7850 (tp30) cc_final: 0.7585 (mm-30) REVERT: Q 153 ARG cc_start: 0.8366 (ttt90) cc_final: 0.8139 (ttt90) REVERT: R 92 VAL cc_start: 0.8628 (p) cc_final: 0.8298 (t) REVERT: R 157 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7859 (tt0) REVERT: R 307 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8071 (mtmt) REVERT: R 310 LEU cc_start: 0.8202 (mp) cc_final: 0.7981 (mt) REVERT: R 333 GLU cc_start: 0.8013 (tp30) cc_final: 0.7646 (tp30) REVERT: R 336 VAL cc_start: 0.7791 (t) cc_final: 0.7505 (m) REVERT: S 135 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: S 148 VAL cc_start: 0.8224 (m) cc_final: 0.8023 (t) REVERT: S 306 GLN cc_start: 0.8390 (mt0) cc_final: 0.8147 (mt0) REVERT: S 324 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7226 (mm-30) REVERT: S 327 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7803 (ttp-110) REVERT: S 345 LEU cc_start: 0.8767 (mt) cc_final: 0.8507 (mm) REVERT: T 63 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7680 (mttm) REVERT: T 73 LYS cc_start: 0.8316 (tptp) cc_final: 0.8043 (tptp) REVERT: T 116 THR cc_start: 0.8396 (m) cc_final: 0.8176 (t) REVERT: T 157 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8021 (tt0) REVERT: T 186 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: T 268 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7733 (mt-10) REVERT: T 326 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7727 (mt-10) REVERT: T 338 ASN cc_start: 0.7261 (m-40) cc_final: 0.6881 (m-40) REVERT: T 340 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7891 (mtt180) REVERT: U 17 THR cc_start: 0.7867 (m) cc_final: 0.7629 (t) REVERT: U 69 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6874 (ttp-110) REVERT: U 95 GLU cc_start: 0.7701 (tt0) cc_final: 0.7454 (tt0) REVERT: U 178 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8513 (mttm) REVERT: U 242 GLN cc_start: 0.8277 (mm110) cc_final: 0.7917 (mm110) REVERT: U 253 GLN cc_start: 0.8262 (mt0) cc_final: 0.7755 (mt0) REVERT: U 327 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7939 (ttp80) REVERT: V 38 GLU cc_start: 0.7868 (tp30) cc_final: 0.7645 (tp30) REVERT: V 39 ILE cc_start: 0.8137 (mt) cc_final: 0.7851 (mt) REVERT: V 68 LEU cc_start: 0.8776 (mt) cc_final: 0.8555 (mp) REVERT: V 130 VAL cc_start: 0.8462 (t) cc_final: 0.8199 (p) REVERT: V 190 ASP cc_start: 0.8325 (m-30) cc_final: 0.7877 (m-30) REVERT: V 327 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8074 (tmm160) REVERT: W 41 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7944 (mmm) REVERT: W 52 PHE cc_start: 0.7656 (m-10) cc_final: 0.7219 (m-80) REVERT: W 112 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7162 (ttp80) REVERT: W 118 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7227 (mm-30) REVERT: W 119 GLU cc_start: 0.6739 (pp20) cc_final: 0.6526 (pp20) REVERT: W 158 ASN cc_start: 0.8085 (m-40) cc_final: 0.7830 (m-40) REVERT: W 168 PHE cc_start: 0.8195 (t80) cc_final: 0.7741 (t80) REVERT: W 172 GLU cc_start: 0.7739 (tt0) cc_final: 0.7140 (tm-30) REVERT: W 198 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6910 (mtt) REVERT: W 227 ASP cc_start: 0.6279 (p0) cc_final: 0.6060 (p0) REVERT: W 244 PHE cc_start: 0.5505 (t80) cc_final: 0.5294 (t80) REVERT: W 317 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7923 (ptpp) REVERT: W 324 GLU cc_start: 0.8007 (tp30) cc_final: 0.7120 (tp30) REVERT: W 336 VAL cc_start: 0.7492 (t) cc_final: 0.7258 (t) REVERT: J 69 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: J 86 ASN cc_start: 0.8015 (m-40) cc_final: 0.7603 (m110) REVERT: J 87 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7146 (mtm-85) REVERT: J 97 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7099 (mtp) REVERT: J 135 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7542 (mtp85) REVERT: J 136 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7933 (ttpt) REVERT: J 172 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7824 (mmmm) REVERT: J 310 VAL cc_start: 0.8446 (m) cc_final: 0.8152 (p) REVERT: J 366 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.6686 (p) REVERT: J 367 MET cc_start: 0.7759 (tpt) cc_final: 0.7371 (tpp) REVERT: J 368 GLU cc_start: 0.7094 (mp0) cc_final: 0.6005 (mp0) REVERT: J 395 LYS cc_start: 0.7000 (ttmm) cc_final: 0.6654 (ttmm) REVERT: J 398 ASN cc_start: 0.7317 (p0) cc_final: 0.7047 (p0) REVERT: J 414 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: J 431 GLU cc_start: 0.6816 (tt0) cc_final: 0.6566 (tp30) REVERT: J 446 TYR cc_start: 0.7261 (m-80) cc_final: 0.6861 (m-10) outliers start: 96 outliers final: 53 residues processed: 665 average time/residue: 0.4399 time to fit residues: 429.4449 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 : 2.557 ------------------------------------------------------------------------------- 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 249 LEU 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 239 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 300 ILE 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 24 GLU 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 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 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 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 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 177 LEU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 326 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 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 184 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 286 optimal weight: 0.2980 chunk 222 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 220 GLN S 337 GLN T 105 ASN T 323 GLN U 328 GLN W 220 GLN J 75 ASN J 106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118420 restraints weight = 36593.109| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.99 r_work: 0.3367 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25280 Z= 0.189 Angle : 0.545 8.545 34625 Z= 0.288 Chirality : 0.041 0.191 3879 Planarity : 0.005 0.052 4117 Dihedral : 17.130 89.313 4274 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.08 % Allowed : 26.82 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2802 helix: 1.35 (0.13), residues: 1643 sheet: -1.08 (0.40), residues: 186 loop : -0.19 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 284 HIS 0.007 0.001 HIS J 147 PHE 0.025 0.002 PHE J 323 TYR 0.014 0.001 TYR R 183 ARG 0.008 0.000 ARG S 112 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 1289) hydrogen bonds : angle 3.98020 ( 3530) metal coordination : bond 0.00357 ( 8) metal coordination : angle 3.39719 ( 9) covalent geometry : bond 0.00439 (25272) covalent geometry : angle 0.54195 (34616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5604 Ramachandran restraints generated. 2802 Oldfield, 0 Emsley, 2802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 622 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7857 (tp30) cc_final: 0.7648 (mm-30) REVERT: Q 172 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7320 (mm-30) REVERT: Q 210 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6763 (tm-30) REVERT: R 92 VAL cc_start: 0.8580 (p) cc_final: 0.8313 (t) REVERT: R 157 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7567 (mt-10) REVERT: R 249 LEU cc_start: 0.8500 (tp) cc_final: 0.8294 (tp) REVERT: S 88 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7494 (tpt-90) REVERT: S 135 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: S 148 VAL cc_start: 0.8295 (m) cc_final: 0.8051 (t) REVERT: S 171 ASP cc_start: 0.8226 (t0) cc_final: 0.7893 (t0) REVERT: S 246 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (p) REVERT: S 295 ARG cc_start: 0.7869 (ptp-110) cc_final: 0.7416 (ptm-80) REVERT: S 324 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7137 (mm-30) REVERT: S 327 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.7722 (ttp-110) REVERT: S 332 THR cc_start: 0.8337 (p) cc_final: 0.7990 (t) REVERT: S 345 LEU cc_start: 0.8789 (mt) cc_final: 0.8506 (mm) REVERT: T 54 PHE cc_start: 0.8225 (m-80) cc_final: 0.7883 (m-80) REVERT: T 186 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: T 198 MET cc_start: 0.8345 (mtp) cc_final: 0.8128 (mtt) REVERT: T 268 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7736 (mt-10) REVERT: T 326 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7720 (mt-10) REVERT: T 338 ASN cc_start: 0.7275 (m-40) cc_final: 0.6917 (m-40) REVERT: T 340 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7941 (mtt180) REVERT: U 17 THR cc_start: 0.7952 (m) cc_final: 0.7709 (t) REVERT: U 69 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7646 (ttt180) REVERT: U 95 GLU cc_start: 0.7712 (tt0) cc_final: 0.7448 (tt0) REVERT: U 142 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.7040 (t0) REVERT: U 144 GLU cc_start: 0.6769 (tp30) cc_final: 0.6465 (tp30) REVERT: U 242 GLN cc_start: 0.8292 (mm110) cc_final: 0.7936 (mm110) REVERT: U 273 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7986 (mmt90) REVERT: U 282 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7335 (tttm) REVERT: U 323 GLN cc_start: 0.7907 (mt0) cc_final: 0.7645 (mt0) REVERT: V 38 GLU cc_start: 0.7912 (tp30) cc_final: 0.7577 (tp30) REVERT: V 39 ILE cc_start: 0.8151 (mt) cc_final: 0.7848 (mt) REVERT: V 71 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8039 (mt-10) REVERT: V 130 VAL cc_start: 0.8536 (t) cc_final: 0.8245 (p) REVERT: V 190 ASP cc_start: 0.8325 (m-30) cc_final: 0.8020 (m-30) REVERT: V 304 ASP cc_start: 0.6944 (m-30) cc_final: 0.6708 (m-30) REVERT: V 327 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8113 (tmm160) REVERT: W 32 ARG cc_start: 0.7033 (tpp-160) cc_final: 0.6555 (tpt-90) REVERT: W 41 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7988 (mmm) REVERT: W 52 PHE cc_start: 0.7740 (m-10) cc_final: 0.7363 (m-80) REVERT: W 112 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7097 (ttp80) REVERT: W 118 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7173 (mm-30) REVERT: W 158 ASN cc_start: 0.8051 (m-40) cc_final: 0.7788 (m-40) REVERT: W 168 PHE cc_start: 0.8246 (t80) cc_final: 0.7713 (t80) REVERT: W 172 GLU cc_start: 0.7742 (tt0) cc_final: 0.7047 (tm-30) REVERT: W 198 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6864 (mtt) REVERT: W 317 LYS cc_start: 0.8320 (ptpp) cc_final: 0.7880 (ptpp) REVERT: W 336 VAL cc_start: 0.7530 (t) cc_final: 0.7291 (t) REVERT: J 39 GLU cc_start: 0.7346 (tt0) cc_final: 0.7118 (tt0) REVERT: J 69 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8124 (m-40) REVERT: J 86 ASN cc_start: 0.8025 (m-40) cc_final: 0.7616 (m110) REVERT: J 87 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6838 (mtm-85) REVERT: J 172 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7820 (mmmm) REVERT: J 236 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: J 263 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6629 (tttt) REVERT: J 288 SER cc_start: 0.8426 (m) cc_final: 0.8144 (p) REVERT: J 310 VAL cc_start: 0.8475 (m) cc_final: 0.8026 (p) REVERT: J 367 MET cc_start: 0.7744 (tpt) cc_final: 0.7421 (tpp) REVERT: J 395 LYS cc_start: 0.7006 (ttmm) cc_final: 0.6615 (ttmm) REVERT: J 398 ASN cc_start: 0.7349 (p0) cc_final: 0.7060 (p0) REVERT: J 411 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7167 (tp) REVERT: J 414 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: J 431 GLU cc_start: 0.6860 (tt0) cc_final: 0.6613 (tp30) REVERT: J 446 TYR cc_start: 0.7509 (m-80) cc_final: 0.7130 (m-80) outliers start: 100 outliers final: 62 residues processed: 674 average time/residue: 0.4178 time to fit residues: 415.6494 Evaluate side-chains 672 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 596 time to evaluate : 2.817 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain Q residue 225 SER 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 187 ASP Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 296 GLU Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain 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 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 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU 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 294 ASP Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain V residue 343 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 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 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 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 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 71 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 145 optimal weight: 0.0670 chunk 260 optimal weight: 0.0070 chunk 100 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 164 HIS S 220 GLN T 197 ASN V 142 ASN V 197 ASN J 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.146552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119919 restraints weight = 36431.793| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3394 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1635 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= 0.124 Angle : 0.508 12.615 34625 Z= 0.269 Chirality : 0.039 0.151 3879 Planarity : 0.004 0.049 4117 Dihedral : 16.989 89.207 4270 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.96 % Allowed : 27.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2802 helix: 1.52 (0.13), residues: 1638 sheet: -1.59 (0.44), residues: 146 loop : -0.16 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 284 HIS 0.005 0.001 HIS U 30 PHE 0.020 0.001 PHE J 323 TYR 0.012 0.001 TYR W 37 ARG 0.007 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1289) hydrogen bonds : angle 3.84339 ( 3530) metal coordination : bond 0.00223 ( 8) metal coordination : angle 2.93811 ( 9) covalent geometry : bond 0.00275 (25272) covalent geometry : angle 0.50592 (34616) *********************** 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 708 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 611 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 153 ARG cc_start: 0.8357 (ttt90) cc_final: 0.8116 (ttt90) REVERT: Q 161 ILE cc_start: 0.8245 (mt) cc_final: 0.7969 (pt) REVERT: Q 172 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7318 (mm-30) REVERT: Q 210 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6738 (tm-30) REVERT: R 88 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5757 (tpt170) REVERT: R 92 VAL cc_start: 0.8550 (p) cc_final: 0.8321 (t) REVERT: R 153 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8003 (ttt180) REVERT: R 157 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7680 (mt-10) REVERT: R 307 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (mtmt) REVERT: S 135 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: S 148 VAL cc_start: 0.8279 (m) cc_final: 0.8041 (t) REVERT: S 201 ILE cc_start: 0.8764 (mm) cc_final: 0.8494 (mt) REVERT: S 295 ARG cc_start: 0.7838 (ptp-110) cc_final: 0.7564 (ptm-80) REVERT: S 324 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7087 (mm-30) REVERT: S 327 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.7624 (ttp-110) REVERT: S 332 THR cc_start: 0.8340 (p) cc_final: 0.8058 (t) REVERT: S 345 LEU cc_start: 0.8796 (mt) cc_final: 0.8507 (mm) REVERT: T 17 THR cc_start: 0.8429 (m) cc_final: 0.8072 (p) REVERT: T 63 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7887 (mttp) REVERT: T 116 THR cc_start: 0.8459 (m) cc_final: 0.8211 (t) REVERT: T 186 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: T 338 ASN cc_start: 0.7289 (m-40) cc_final: 0.6957 (m-40) REVERT: T 340 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7965 (mtt180) REVERT: U 17 THR cc_start: 0.7939 (m) cc_final: 0.7694 (t) REVERT: U 69 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6857 (ttp-110) REVERT: U 95 GLU cc_start: 0.7706 (tt0) cc_final: 0.7451 (tt0) REVERT: U 108 GLU cc_start: 0.8275 (tp30) cc_final: 0.7933 (tp30) REVERT: U 242 GLN cc_start: 0.8285 (mm110) cc_final: 0.7922 (mm110) REVERT: U 282 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7324 (tttm) REVERT: U 327 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7979 (ttp80) REVERT: V 12 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7189 (mt) REVERT: V 38 GLU cc_start: 0.7886 (tp30) cc_final: 0.7568 (tp30) REVERT: V 39 ILE cc_start: 0.8162 (mt) cc_final: 0.7883 (mt) REVERT: V 71 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8093 (mt-10) REVERT: V 130 VAL cc_start: 0.8499 (t) cc_final: 0.8207 (p) REVERT: V 186 GLN cc_start: 0.8490 (tt0) cc_final: 0.8234 (tt0) REVERT: V 190 ASP cc_start: 0.8316 (m-30) cc_final: 0.8013 (m-30) REVERT: V 253 GLN cc_start: 0.7619 (mm110) cc_final: 0.7389 (mm110) REVERT: V 304 ASP cc_start: 0.6997 (m-30) cc_final: 0.6791 (m-30) REVERT: V 327 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8114 (tmm160) REVERT: W 41 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: W 52 PHE cc_start: 0.7709 (m-10) cc_final: 0.7311 (m-80) REVERT: W 112 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7230 (ttp80) REVERT: W 116 THR cc_start: 0.7903 (t) cc_final: 0.7580 (m) REVERT: W 118 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7315 (mm-30) REVERT: W 135 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7174 (mmm160) REVERT: W 153 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7848 (ttt-90) REVERT: W 154 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7278 (ttm110) REVERT: W 158 ASN cc_start: 0.8057 (m-40) cc_final: 0.7805 (m-40) REVERT: W 168 PHE cc_start: 0.8119 (t80) cc_final: 0.7670 (t80) REVERT: W 172 GLU cc_start: 0.7767 (tt0) cc_final: 0.7058 (tm-30) REVERT: W 193 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7759 (ttpp) REVERT: W 198 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6921 (mtt) REVERT: W 317 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7958 (ptpp) REVERT: W 327 ARG cc_start: 0.7642 (ptt-90) cc_final: 0.7227 (ppt-90) REVERT: W 336 VAL cc_start: 0.7462 (t) cc_final: 0.7244 (t) REVERT: J 39 GLU cc_start: 0.7314 (tt0) cc_final: 0.7090 (tt0) REVERT: J 86 ASN cc_start: 0.8028 (m-40) cc_final: 0.7651 (m-40) REVERT: J 87 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7188 (mtm-85) REVERT: J 135 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7419 (mtp85) REVERT: J 136 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8238 (mtpt) REVERT: J 158 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8441 (mt) REVERT: J 172 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7861 (mmmm) REVERT: J 189 ASN cc_start: 0.8427 (t0) cc_final: 0.8028 (t0) REVERT: J 310 VAL cc_start: 0.8462 (m) cc_final: 0.8154 (p) REVERT: J 367 MET cc_start: 0.7749 (tpt) cc_final: 0.7416 (tpp) REVERT: J 395 LYS cc_start: 0.6977 (ttmm) cc_final: 0.6648 (ttmm) REVERT: J 408 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6805 (tt) REVERT: J 411 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7123 (tp) REVERT: J 414 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: J 431 GLU cc_start: 0.6802 (tt0) cc_final: 0.6562 (tp30) REVERT: J 446 TYR cc_start: 0.7457 (m-80) cc_final: 0.7099 (m-80) outliers start: 97 outliers final: 64 residues processed: 659 average time/residue: 0.4204 time to fit residues: 407.3833 Evaluate side-chains 662 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 581 time to evaluate : 2.841 ------------------------------------------------------------------------------- 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 27 THR Chi-restraints excluded: chain R residue 88 ARG 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 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 249 LEU Chi-restraints excluded: chain S residue 264 VAL Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 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 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 166 ASP 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 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 199 LYS 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 411 LEU Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 175 optimal weight: 0.0030 chunk 267 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 220 GLN J 106 GLN J 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119882 restraints weight = 36257.065| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.98 r_work: 0.3389 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1747 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= 0.141 Angle : 0.515 10.509 34625 Z= 0.274 Chirality : 0.039 0.147 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.957 88.377 4270 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.73 % Allowed : 26.33 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2802 helix: 1.52 (0.13), residues: 1637 sheet: -1.07 (0.41), residues: 186 loop : -0.10 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 PHE 0.031 0.001 PHE J 323 TYR 0.013 0.001 TYR R 22 ARG 0.008 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 1289) hydrogen bonds : angle 3.81795 ( 3530) metal coordination : bond 0.00254 ( 8) metal coordination : angle 3.01750 ( 9) covalent geometry : bond 0.00323 (25272) covalent geometry : angle 0.51317 (34616) *********************** 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 716 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 600 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8241 (mt) cc_final: 0.7952 (pt) REVERT: Q 172 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7297 (mm-30) REVERT: Q 210 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6713 (tm-30) REVERT: R 88 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.5836 (tpt170) REVERT: R 92 VAL cc_start: 0.8547 (p) cc_final: 0.8335 (t) REVERT: R 153 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8020 (ttt90) REVERT: R 157 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7690 (mt-10) REVERT: R 307 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7981 (mtmt) REVERT: S 100 GLU cc_start: 0.7938 (pm20) cc_final: 0.7714 (pm20) REVERT: S 103 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: S 135 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7714 (ttp-170) REVERT: S 148 VAL cc_start: 0.8284 (m) cc_final: 0.8046 (t) REVERT: S 171 ASP cc_start: 0.8200 (t0) cc_final: 0.7862 (t0) REVERT: S 201 ILE cc_start: 0.8772 (mm) cc_final: 0.8499 (mt) REVERT: S 295 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7556 (ptm-80) REVERT: S 324 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7103 (mm-30) REVERT: S 327 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7580 (ttp-110) REVERT: S 332 THR cc_start: 0.8353 (p) cc_final: 0.8069 (t) REVERT: S 345 LEU cc_start: 0.8782 (mt) cc_final: 0.8492 (mm) REVERT: T 17 THR cc_start: 0.8456 (m) cc_final: 0.8096 (p) REVERT: T 54 PHE cc_start: 0.8221 (m-80) cc_final: 0.7928 (m-80) REVERT: T 153 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8363 (tpt-90) REVERT: T 186 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: T 338 ASN cc_start: 0.7272 (m-40) cc_final: 0.6946 (m-40) REVERT: T 340 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7957 (mtt180) REVERT: U 17 THR cc_start: 0.7951 (m) cc_final: 0.7706 (t) REVERT: U 69 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6846 (ttp-110) REVERT: U 127 ASP cc_start: 0.7810 (t0) cc_final: 0.7464 (t0) REVERT: U 142 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.7054 (t0) REVERT: U 242 GLN cc_start: 0.8268 (mm110) cc_final: 0.7898 (mm110) REVERT: U 273 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7770 (mmt180) REVERT: U 282 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7307 (tttm) REVERT: U 327 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7967 (ttp80) REVERT: U 331 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: V 12 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7193 (mt) REVERT: V 38 GLU cc_start: 0.7897 (tp30) cc_final: 0.7578 (tp30) REVERT: V 39 ILE cc_start: 0.8150 (mt) cc_final: 0.7775 (mt) REVERT: V 71 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8081 (mt-10) REVERT: V 130 VAL cc_start: 0.8513 (t) cc_final: 0.8206 (p) REVERT: V 186 GLN cc_start: 0.8472 (tt0) cc_final: 0.8222 (tt0) REVERT: V 190 ASP cc_start: 0.8306 (m-30) cc_final: 0.8006 (m-30) REVERT: V 327 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8099 (tmm160) REVERT: W 41 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (mmm) REVERT: W 52 PHE cc_start: 0.7741 (m-10) cc_final: 0.7363 (m-80) REVERT: W 116 THR cc_start: 0.7974 (t) cc_final: 0.7646 (m) REVERT: W 118 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7398 (mm-30) REVERT: W 154 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7246 (ttm110) REVERT: W 158 ASN cc_start: 0.8039 (m-40) cc_final: 0.7777 (m-40) REVERT: W 168 PHE cc_start: 0.8096 (t80) cc_final: 0.7642 (t80) REVERT: W 198 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6900 (mtt) REVERT: W 317 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7973 (ptpp) REVERT: W 336 VAL cc_start: 0.7478 (t) cc_final: 0.7259 (t) REVERT: J 69 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (m-40) REVERT: J 86 ASN cc_start: 0.8038 (m-40) cc_final: 0.7607 (m110) REVERT: J 87 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7184 (mtm-85) REVERT: J 158 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8439 (mt) REVERT: J 172 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7851 (mmmm) REVERT: J 236 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: J 310 VAL cc_start: 0.8478 (m) cc_final: 0.8041 (p) REVERT: J 367 MET cc_start: 0.7751 (tpt) cc_final: 0.7406 (tpp) REVERT: J 395 LYS cc_start: 0.7030 (ttmm) cc_final: 0.6826 (ttmm) REVERT: J 408 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6796 (tt) REVERT: J 411 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7071 (tp) REVERT: J 431 GLU cc_start: 0.6805 (tt0) cc_final: 0.6561 (tp30) REVERT: J 446 TYR cc_start: 0.7520 (m-80) cc_final: 0.7141 (m-80) outliers start: 116 outliers final: 71 residues processed: 657 average time/residue: 0.4678 time to fit residues: 452.4984 Evaluate side-chains 675 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 585 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 ARG 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 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 239 GLU 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 265 ASP Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain U residue 331 GLU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 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 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 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 69 ASN 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 101 LEU 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 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 287 GLN 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 411 LEU 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 48 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 168 optimal weight: 0.0050 chunk 285 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 220 GLN U 328 GLN J 106 GLN J 144 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119825 restraints weight = 36276.609| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.95 r_work: 0.3393 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1858 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= 0.144 Angle : 0.522 9.348 34625 Z= 0.277 Chirality : 0.039 0.174 3879 Planarity : 0.004 0.052 4117 Dihedral : 16.941 88.365 4270 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.00 % Allowed : 27.06 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2802 helix: 1.49 (0.13), residues: 1637 sheet: -1.06 (0.41), residues: 184 loop : -0.12 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 PHE 0.029 0.001 PHE J 323 TYR 0.014 0.001 TYR J 399 ARG 0.009 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1289) hydrogen bonds : angle 3.79516 ( 3530) metal coordination : bond 0.00267 ( 8) metal coordination : angle 2.95409 ( 9) covalent geometry : bond 0.00331 (25272) covalent geometry : angle 0.51977 (34616) *********************** 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 702 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 604 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8227 (mt) cc_final: 0.7925 (pt) REVERT: Q 172 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7275 (mm-30) REVERT: Q 210 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6709 (tm-30) REVERT: R 88 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5861 (tpt170) REVERT: R 102 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7697 (ttm170) REVERT: R 153 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7979 (ttt90) REVERT: R 157 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7690 (mt-10) REVERT: R 307 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7999 (mtmt) REVERT: S 10 GLU cc_start: 0.7070 (pp20) cc_final: 0.6869 (pp20) REVERT: S 103 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: S 135 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7702 (ttp-170) REVERT: S 148 VAL cc_start: 0.8279 (m) cc_final: 0.8035 (t) REVERT: S 171 ASP cc_start: 0.8187 (t0) cc_final: 0.7847 (t0) REVERT: S 295 ARG cc_start: 0.7794 (ptp-110) cc_final: 0.7580 (ptm-80) REVERT: S 324 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7293 (mm-30) REVERT: S 327 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7701 (ttp-110) REVERT: S 332 THR cc_start: 0.8351 (p) cc_final: 0.8069 (t) REVERT: S 345 LEU cc_start: 0.8779 (mt) cc_final: 0.8484 (mm) REVERT: T 17 THR cc_start: 0.8459 (m) cc_final: 0.8100 (p) REVERT: T 54 PHE cc_start: 0.8229 (m-80) cc_final: 0.7894 (m-80) REVERT: T 63 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7826 (mttp) REVERT: T 186 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: T 338 ASN cc_start: 0.7287 (m-40) cc_final: 0.6964 (m-40) REVERT: T 340 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7972 (mtt180) REVERT: U 17 THR cc_start: 0.7959 (m) cc_final: 0.7713 (t) REVERT: U 69 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.6834 (ttp-110) REVERT: U 101 SER cc_start: 0.8541 (p) cc_final: 0.8163 (t) REVERT: U 127 ASP cc_start: 0.7856 (t0) cc_final: 0.7603 (t0) REVERT: U 142 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7032 (t0) REVERT: U 242 GLN cc_start: 0.8263 (mm110) cc_final: 0.7897 (mm110) REVERT: U 282 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7313 (tttm) REVERT: U 286 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7258 (tttm) REVERT: U 327 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7902 (ttp80) REVERT: V 38 GLU cc_start: 0.7891 (tp30) cc_final: 0.7580 (tp30) REVERT: V 39 ILE cc_start: 0.8164 (mt) cc_final: 0.7799 (mt) REVERT: V 71 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8085 (mt-10) REVERT: V 130 VAL cc_start: 0.8508 (t) cc_final: 0.8195 (p) REVERT: V 186 GLN cc_start: 0.8466 (tt0) cc_final: 0.8224 (tt0) REVERT: V 190 ASP cc_start: 0.8292 (m-30) cc_final: 0.7994 (m-30) REVERT: V 253 GLN cc_start: 0.7606 (mm110) cc_final: 0.7382 (mm110) REVERT: V 327 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8083 (tmm160) REVERT: W 41 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: W 52 PHE cc_start: 0.7745 (m-10) cc_final: 0.7327 (m-80) REVERT: W 116 THR cc_start: 0.7984 (t) cc_final: 0.7657 (m) REVERT: W 153 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7837 (mtp180) REVERT: W 154 ARG cc_start: 0.7448 (ttm110) cc_final: 0.7217 (ttm110) REVERT: W 158 ASN cc_start: 0.8031 (m-40) cc_final: 0.7766 (m-40) REVERT: W 168 PHE cc_start: 0.8039 (t80) cc_final: 0.7657 (t80) REVERT: W 198 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6938 (mtt) REVERT: W 336 VAL cc_start: 0.7495 (t) cc_final: 0.7283 (t) REVERT: J 39 GLU cc_start: 0.7330 (tt0) cc_final: 0.7058 (tt0) REVERT: J 69 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.8100 (m-40) REVERT: J 86 ASN cc_start: 0.8034 (m-40) cc_final: 0.7600 (m110) REVERT: J 87 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7205 (mtm-85) REVERT: J 115 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7859 (ptp90) REVERT: J 158 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8443 (mt) REVERT: J 172 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7837 (mmmm) REVERT: J 236 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: J 310 VAL cc_start: 0.8478 (m) cc_final: 0.8026 (p) REVERT: J 367 MET cc_start: 0.7745 (tpt) cc_final: 0.7397 (tpp) REVERT: J 408 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6789 (tt) REVERT: J 431 GLU cc_start: 0.6778 (tt0) cc_final: 0.6523 (tp30) REVERT: J 446 TYR cc_start: 0.7560 (m-80) cc_final: 0.7125 (m-80) outliers start: 98 outliers final: 72 residues processed: 654 average time/residue: 0.4841 time to fit residues: 467.5924 Evaluate side-chains 681 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 591 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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 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 88 ARG 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 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 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 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 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 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 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 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 287 GLN Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 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 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 111 optimal weight: 0.2980 chunk 159 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN T 323 GLN J 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120429 restraints weight = 36078.226| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.95 r_work: 0.3399 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1951 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= 0.136 Angle : 0.520 8.550 34625 Z= 0.277 Chirality : 0.039 0.166 3879 Planarity : 0.004 0.052 4117 Dihedral : 16.904 86.244 4270 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.00 % Allowed : 27.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2802 helix: 1.54 (0.13), residues: 1632 sheet: -1.06 (0.41), residues: 184 loop : -0.11 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 284 HIS 0.007 0.001 HIS V 162 PHE 0.027 0.001 PHE J 323 TYR 0.015 0.001 TYR J 399 ARG 0.010 0.000 ARG T 153 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1289) hydrogen bonds : angle 3.77911 ( 3530) metal coordination : bond 0.00257 ( 8) metal coordination : angle 2.85655 ( 9) covalent geometry : bond 0.00311 (25272) covalent geometry : angle 0.51815 (34616) *********************** 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 682 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 584 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 153 ARG cc_start: 0.8319 (ttt90) cc_final: 0.8098 (ttt90) REVERT: Q 161 ILE cc_start: 0.8201 (mt) cc_final: 0.7908 (pt) REVERT: Q 172 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7273 (mm-30) REVERT: Q 210 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6695 (tm-30) REVERT: R 88 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.5827 (tpt170) REVERT: R 102 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7700 (ttm170) REVERT: R 153 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7972 (ttt90) REVERT: R 157 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7675 (mt-10) REVERT: R 307 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7978 (mtmt) REVERT: S 103 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: S 135 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7738 (ttp-170) REVERT: S 148 VAL cc_start: 0.8228 (m) cc_final: 0.8005 (t) REVERT: S 324 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7285 (mm-30) REVERT: S 327 ARG cc_start: 0.8321 (ttp-110) cc_final: 0.7667 (ttp-110) REVERT: S 332 THR cc_start: 0.8335 (p) cc_final: 0.8052 (t) REVERT: S 345 LEU cc_start: 0.8778 (mt) cc_final: 0.8489 (mm) REVERT: T 17 THR cc_start: 0.8450 (m) cc_final: 0.8102 (p) REVERT: T 186 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: T 338 ASN cc_start: 0.7277 (m-40) cc_final: 0.6943 (m-40) REVERT: T 340 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7966 (mtt180) REVERT: U 17 THR cc_start: 0.7942 (m) cc_final: 0.7697 (t) REVERT: U 69 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.6822 (ttp-110) REVERT: U 101 SER cc_start: 0.8515 (p) cc_final: 0.8147 (t) REVERT: U 108 GLU cc_start: 0.8168 (tp30) cc_final: 0.7755 (tp30) REVERT: U 127 ASP cc_start: 0.7862 (t0) cc_final: 0.7587 (t0) REVERT: U 142 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.7031 (t0) REVERT: U 242 GLN cc_start: 0.8243 (mm110) cc_final: 0.7881 (mm110) REVERT: U 282 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7308 (tttm) REVERT: U 286 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7352 (tttm) REVERT: U 327 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7969 (ttp80) REVERT: V 39 ILE cc_start: 0.8128 (mt) cc_final: 0.7851 (mt) REVERT: V 71 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8061 (mt-10) REVERT: V 95 GLU cc_start: 0.7732 (tt0) cc_final: 0.7526 (tt0) REVERT: V 130 VAL cc_start: 0.8482 (t) cc_final: 0.8182 (p) REVERT: V 186 GLN cc_start: 0.8457 (tt0) cc_final: 0.8220 (tt0) REVERT: V 190 ASP cc_start: 0.8297 (m-30) cc_final: 0.8002 (m-30) REVERT: V 253 GLN cc_start: 0.7646 (mm110) cc_final: 0.7432 (mm110) REVERT: V 327 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8082 (tmm160) REVERT: W 52 PHE cc_start: 0.7749 (m-10) cc_final: 0.7291 (m-80) REVERT: W 116 THR cc_start: 0.7948 (t) cc_final: 0.7544 (m) REVERT: W 119 GLU cc_start: 0.6572 (pp20) cc_final: 0.6282 (pp20) REVERT: W 153 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7796 (mtp180) REVERT: W 158 ASN cc_start: 0.8064 (m-40) cc_final: 0.7813 (m-40) REVERT: W 168 PHE cc_start: 0.8017 (t80) cc_final: 0.7646 (t80) REVERT: W 198 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6911 (mtt) REVERT: W 224 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7062 (mtt90) REVERT: W 336 VAL cc_start: 0.7484 (t) cc_final: 0.7276 (t) REVERT: J 86 ASN cc_start: 0.8027 (m-40) cc_final: 0.7576 (m110) REVERT: J 87 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7203 (mtm-85) REVERT: J 115 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7857 (ptp90) REVERT: J 158 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8454 (mt) REVERT: J 172 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7850 (mmmm) REVERT: J 236 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: J 310 VAL cc_start: 0.8479 (m) cc_final: 0.8048 (p) REVERT: J 408 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6784 (tt) REVERT: J 431 GLU cc_start: 0.6766 (tt0) cc_final: 0.6503 (tp30) REVERT: J 446 TYR cc_start: 0.7533 (m-80) cc_final: 0.7108 (m-80) outliers start: 98 outliers final: 72 residues processed: 630 average time/residue: 0.4299 time to fit residues: 396.7846 Evaluate side-chains 670 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 582 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 ARG 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 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 239 GLU 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 265 ASP Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain U residue 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 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 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 33 LEU Chi-restraints excluded: chain V residue 89 VAL Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 166 ASP 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 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 78 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 287 GLN Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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 234 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN T 162 HIS T 323 GLN V 203 HIS 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 = 0.3843 r_free = 0.3843 target = 0.143646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116906 restraints weight = 36241.687| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 25280 Z= 0.280 Angle : 0.620 8.118 34625 Z= 0.327 Chirality : 0.045 0.207 3879 Planarity : 0.005 0.054 4117 Dihedral : 17.234 86.542 4270 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.84 % Allowed : 27.51 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2802 helix: 1.13 (0.13), residues: 1637 sheet: -1.17 (0.40), residues: 186 loop : -0.25 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP J 284 HIS 0.010 0.001 HIS J 147 PHE 0.022 0.002 PHE T 270 TYR 0.017 0.002 TYR V 56 ARG 0.008 0.001 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 1289) hydrogen bonds : angle 4.04439 ( 3530) metal coordination : bond 0.00523 ( 8) metal coordination : angle 4.04811 ( 9) covalent geometry : bond 0.00663 (25272) covalent geometry : angle 0.61622 (34616) *********************** 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 696 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 602 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8300 (mt) cc_final: 0.8015 (pt) REVERT: Q 172 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7367 (mm-30) REVERT: Q 210 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6746 (tm-30) REVERT: R 102 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7706 (ttm170) REVERT: R 153 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8118 (ttt90) REVERT: R 157 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7527 (mt-10) REVERT: R 307 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: S 103 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: S 135 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7818 (ttp-170) REVERT: S 171 ASP cc_start: 0.8240 (t0) cc_final: 0.7895 (t0) REVERT: S 246 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8155 (p) REVERT: S 295 ARG cc_start: 0.7668 (ptm-80) cc_final: 0.7236 (ptm-80) REVERT: S 324 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7295 (mm-30) REVERT: S 327 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7725 (ttp-110) REVERT: S 332 THR cc_start: 0.8409 (p) cc_final: 0.8104 (t) REVERT: T 17 THR cc_start: 0.8497 (m) cc_final: 0.8209 (p) REVERT: T 54 PHE cc_start: 0.8188 (m-80) cc_final: 0.7845 (m-80) REVERT: T 186 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: T 338 ASN cc_start: 0.7303 (m-40) cc_final: 0.6988 (m-40) REVERT: T 340 ARG cc_start: 0.8276 (mtp85) cc_final: 0.8072 (mtt180) REVERT: U 17 THR cc_start: 0.8053 (m) cc_final: 0.7808 (t) REVERT: U 127 ASP cc_start: 0.7892 (t0) cc_final: 0.7598 (t0) REVERT: U 142 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.7037 (t0) REVERT: U 242 GLN cc_start: 0.8248 (mm110) cc_final: 0.7880 (mm110) REVERT: U 253 GLN cc_start: 0.8305 (mt0) cc_final: 0.8070 (mt0) REVERT: U 282 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7370 (tttm) REVERT: V 71 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8048 (mt-10) REVERT: V 76 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7633 (mt-10) REVERT: V 95 GLU cc_start: 0.7716 (tt0) cc_final: 0.7514 (tt0) REVERT: V 144 GLU cc_start: 0.7536 (pm20) cc_final: 0.7227 (mp0) REVERT: V 186 GLN cc_start: 0.8487 (tt0) cc_final: 0.8088 (tt0) REVERT: V 190 ASP cc_start: 0.8331 (m-30) cc_final: 0.7856 (m-30) REVERT: W 52 PHE cc_start: 0.7797 (m-10) cc_final: 0.7493 (m-80) REVERT: W 116 THR cc_start: 0.8089 (t) cc_final: 0.7822 (m) REVERT: W 168 PHE cc_start: 0.8277 (t80) cc_final: 0.7773 (t80) REVERT: W 198 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6770 (mtt) REVERT: J 39 GLU cc_start: 0.7362 (tt0) cc_final: 0.7037 (tt0) REVERT: J 86 ASN cc_start: 0.8076 (m-40) cc_final: 0.7646 (m110) REVERT: J 87 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6874 (mtm-85) REVERT: J 115 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: J 172 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7894 (mmmm) REVERT: J 236 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: J 310 VAL cc_start: 0.8499 (m) cc_final: 0.8058 (p) REVERT: J 431 GLU cc_start: 0.6800 (tt0) cc_final: 0.6518 (tp30) outliers start: 94 outliers final: 64 residues processed: 644 average time/residue: 0.4430 time to fit residues: 428.8499 Evaluate side-chains 672 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 596 time to evaluate : 3.356 ------------------------------------------------------------------------------- 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 264 VAL 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 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 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 U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 100 GLU 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 W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 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 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 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 287 GLN Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE 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 259 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 262 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN S 186 GLN S 220 GLN T 323 GLN U 328 GLN W 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119942 restraints weight = 35956.730| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.94 r_work: 0.3395 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25280 Z= 0.134 Angle : 0.541 8.658 34625 Z= 0.288 Chirality : 0.039 0.186 3879 Planarity : 0.004 0.081 4117 Dihedral : 17.079 85.959 4270 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.02 % Allowed : 28.33 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2802 helix: 1.31 (0.13), residues: 1646 sheet: -1.09 (0.41), residues: 184 loop : -0.11 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP J 284 HIS 0.006 0.001 HIS U 30 PHE 0.017 0.001 PHE J 323 TYR 0.015 0.001 TYR J 399 ARG 0.006 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 1289) hydrogen bonds : angle 3.85875 ( 3530) metal coordination : bond 0.00270 ( 8) metal coordination : angle 3.00639 ( 9) covalent geometry : bond 0.00303 (25272) covalent geometry : angle 0.53938 (34616) ********************** 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 665 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 591 time to evaluate : 3.296 Fit side-chains revert: symmetry clash REVERT: Q 153 ARG cc_start: 0.8315 (ttt90) cc_final: 0.8073 (ttt90) REVERT: Q 161 ILE cc_start: 0.8216 (mt) cc_final: 0.7928 (pt) REVERT: Q 172 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7267 (mm-30) REVERT: Q 210 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6703 (tm-30) REVERT: R 153 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7985 (ttt90) REVERT: R 157 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7524 (mt-10) REVERT: R 307 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7985 (mtmt) REVERT: S 103 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: S 135 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7806 (ttp-170) REVERT: S 201 ILE cc_start: 0.8744 (mm) cc_final: 0.8478 (mt) REVERT: S 246 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8170 (p) REVERT: S 295 ARG cc_start: 0.7647 (ptm-80) cc_final: 0.7213 (ptm-80) REVERT: S 324 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7622 (mm-30) REVERT: S 327 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8105 (tmm160) REVERT: T 17 THR cc_start: 0.8499 (m) cc_final: 0.8155 (p) REVERT: T 54 PHE cc_start: 0.8176 (m-80) cc_final: 0.7788 (m-80) REVERT: T 63 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7831 (mttp) REVERT: T 116 THR cc_start: 0.8442 (m) cc_final: 0.8209 (t) REVERT: T 186 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: T 338 ASN cc_start: 0.7284 (m-40) cc_final: 0.6959 (m-40) REVERT: T 340 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8034 (mtt180) REVERT: U 17 THR cc_start: 0.7994 (m) cc_final: 0.7758 (t) REVERT: U 127 ASP cc_start: 0.7876 (t0) cc_final: 0.7612 (t0) REVERT: U 142 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7049 (t0) REVERT: U 242 GLN cc_start: 0.8248 (mm110) cc_final: 0.7888 (mm110) REVERT: U 282 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7360 (tttm) REVERT: U 327 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7993 (ttp80) REVERT: V 39 ILE cc_start: 0.8167 (mt) cc_final: 0.7838 (mt) REVERT: V 71 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8066 (mt-10) REVERT: V 76 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7597 (mt-10) REVERT: V 95 GLU cc_start: 0.7720 (tt0) cc_final: 0.7487 (tt0) REVERT: V 190 ASP cc_start: 0.8331 (m-30) cc_final: 0.7859 (m-30) REVERT: W 52 PHE cc_start: 0.7728 (m-10) cc_final: 0.7336 (m-80) REVERT: W 116 THR cc_start: 0.8033 (t) cc_final: 0.7719 (m) REVERT: W 153 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7819 (ttt-90) REVERT: W 158 ASN cc_start: 0.7972 (m-40) cc_final: 0.7723 (m-40) REVERT: W 168 PHE cc_start: 0.8013 (t80) cc_final: 0.7652 (t80) REVERT: W 198 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: W 224 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: W 336 VAL cc_start: 0.7466 (t) cc_final: 0.7244 (t) REVERT: J 86 ASN cc_start: 0.8009 (m-40) cc_final: 0.7571 (m110) REVERT: J 87 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.6869 (mtm-85) REVERT: J 115 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7797 (ptp90) REVERT: J 158 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8445 (mt) REVERT: J 172 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7854 (mmmm) REVERT: J 236 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: J 263 LYS cc_start: 0.6862 (ttmt) cc_final: 0.6632 (tttt) REVERT: J 310 VAL cc_start: 0.8451 (m) cc_final: 0.8060 (p) REVERT: J 321 LYS cc_start: 0.8123 (tptp) cc_final: 0.7883 (tptt) REVERT: J 408 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6677 (tt) REVERT: J 431 GLU cc_start: 0.6729 (tt0) cc_final: 0.6449 (tp30) REVERT: J 446 TYR cc_start: 0.7708 (m-80) cc_final: 0.7157 (m-80) outliers start: 74 outliers final: 56 residues processed: 622 average time/residue: 0.6251 time to fit residues: 582.6889 Evaluate side-chains 643 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 573 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 116 THR 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 307 LYS Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 76 GLU Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 320 LYS Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 265 ASP Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 24 GLU Chi-restraints excluded: chain V residue 100 GLU Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 63 LYS Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 78 ASN 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 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 287 GLN Chi-restraints excluded: chain J residue 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 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 106 optimal weight: 4.9990 chunk 155 optimal weight: 0.0030 chunk 13 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 overall best weight: 0.3306 ------------------------------------------------------------------------------- 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 U 328 GLN W 175 HIS J 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120746 restraints weight = 36061.092| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.97 r_work: 0.3407 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25280 Z= 0.123 Angle : 0.530 8.123 34625 Z= 0.282 Chirality : 0.039 0.167 3879 Planarity : 0.004 0.075 4117 Dihedral : 16.890 84.688 4270 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.14 % Allowed : 28.12 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2802 helix: 1.42 (0.13), residues: 1645 sheet: -1.59 (0.45), residues: 144 loop : -0.08 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP J 284 HIS 0.005 0.001 HIS U 30 PHE 0.015 0.001 PHE W 169 TYR 0.013 0.001 TYR J 399 ARG 0.006 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1289) hydrogen bonds : angle 3.77852 ( 3530) metal coordination : bond 0.00210 ( 8) metal coordination : angle 2.44348 ( 9) covalent geometry : bond 0.00275 (25272) covalent geometry : angle 0.52906 (34616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18124.11 seconds wall clock time: 318 minutes 55.77 seconds (19135.77 seconds total)