Starting phenix.real_space_refine on Fri May 23 15:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v32_42941/05_2025/8v32_42941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v32_42941/05_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_42941/05_2025/8v32_42941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v32_42941/05_2025/8v32_42941.map" model { file = "/net/cci-nas-00/data/ceres_data/8v32_42941/05_2025/8v32_42941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v32_42941/05_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-5687/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: 15.21, 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: 6.12 Conformation dependent library (CDL) restraints added in 2.7 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: 8.08 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: 7.62 Time building geometry restraints manager: 7.09 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: 2.190 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: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 62.310 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.950 ------------------------------------------------------------------------------- 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 : 2.501 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: 0.4060 time to fit residues: 361.8055 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 : 2.493 ------------------------------------------------------------------------------- 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 = 0.119324 restraints weight = 36447.420| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.01 r_work: 0.3375 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 4.23825 ( 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 : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 100 GLU cc_start: 0.7744 (pm20) cc_final: 0.7514 (pm20) REVERT: R 157 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7649 (mt-10) REVERT: R 307 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: R 333 GLU cc_start: 0.8014 (tp30) cc_final: 0.7803 (tp30) REVERT: S 135 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7440 (ttp-170) REVERT: S 172 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7623 (mm-30) REVERT: S 186 GLN cc_start: 0.7789 (tt0) cc_final: 0.7501 (tt0) REVERT: S 268 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8129 (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: 0.8494 (mm) REVERT: T 54 PHE cc_start: 0.8195 (m-80) cc_final: 0.7861 (m-80) REVERT: T 63 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7898 (mttm) REVERT: T 116 THR cc_start: 0.8405 (m) cc_final: 0.8182 (t) REVERT: T 131 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.8364 (mtt-85) REVERT: T 186 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7671 (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: 0.7293 (m-40) cc_final: 0.6947 (m-40) REVERT: T 340 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7932 (mtt-85) REVERT: U 17 THR cc_start: 0.7900 (m) cc_final: 0.7654 (t) REVERT: U 54 PHE cc_start: 0.8217 (m-80) cc_final: 0.7724 (m-80) REVERT: U 69 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6913 (ttp-110) REVERT: U 95 GLU cc_start: 0.7731 (tt0) cc_final: 0.7469 (tt0) REVERT: U 178 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8539 (mttm) REVERT: U 242 GLN cc_start: 0.8309 (mm110) cc_final: 0.7964 (mm110) REVERT: U 253 GLN cc_start: 0.8302 (mt0) cc_final: 0.7865 (mp10) REVERT: U 273 ARG cc_start: 0.8247 (mmt90) cc_final: 0.7764 (mmt180) REVERT: U 286 LYS cc_start: 0.7419 (tmtm) cc_final: 0.7052 (tttm) REVERT: U 324 GLU cc_start: 0.8024 (tp30) cc_final: 0.7716 (tp30) REVERT: V 38 GLU cc_start: 0.7938 (tp30) cc_final: 0.7690 (tp30) REVERT: V 68 LEU cc_start: 0.8803 (mt) cc_final: 0.8569 (mp) REVERT: V 130 VAL cc_start: 0.8485 (t) cc_final: 0.8226 (p) REVERT: V 190 ASP cc_start: 0.8331 (m-30) cc_final: 0.7914 (m-30) REVERT: V 253 GLN cc_start: 0.7517 (mm110) cc_final: 0.7305 (mm110) REVERT: W 41 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7504 (mpp) REVERT: W 44 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7708 (mp) REVERT: W 52 PHE cc_start: 0.7706 (m-10) cc_final: 0.7285 (m-80) REVERT: W 112 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: W 117 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (tt) REVERT: W 119 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: W 153 ARG cc_start: 0.8000 (mtp180) cc_final: 0.7602 (mtp180) REVERT: W 154 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7266 (ttm110) REVERT: W 158 ASN cc_start: 0.8074 (m-40) cc_final: 0.7832 (m-40) REVERT: W 168 PHE cc_start: 0.8271 (t80) cc_final: 0.7726 (t80) REVERT: W 172 GLU cc_start: 0.7722 (tt0) cc_final: 0.7168 (tm-30) REVERT: W 327 ARG cc_start: 0.7366 (ptt-90) cc_final: 0.7098 (ptt-90) REVERT: W 336 VAL cc_start: 0.7550 (t) cc_final: 0.7297 (t) REVERT: J 69 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8113 (m-40) REVERT: J 86 ASN cc_start: 0.8023 (m-40) cc_final: 0.7593 (m110) REVERT: J 97 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7202 (mtp) REVERT: J 135 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7592 (mtp85) REVERT: J 172 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7869 (mmmm) REVERT: J 310 VAL cc_start: 0.8415 (m) cc_final: 0.8140 (p) REVERT: J 366 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7112 (p) REVERT: J 367 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: J 368 GLU cc_start: 0.7054 (mp0) cc_final: 0.6522 (mp0) REVERT: J 414 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: J 431 GLU cc_start: 0.6918 (tt0) cc_final: 0.6648 (tp30) REVERT: J 446 TYR cc_start: 0.7306 (m-80) cc_final: 0.7018 (m-10) outliers start: 105 outliers final: 45 residues processed: 655 average time/residue: 0.4229 time to fit residues: 404.1333 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 : 2.568 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 111 optimal weight: 0.0000 chunk 66 optimal weight: 0.0670 chunk 207 optimal weight: 4.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.147034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120500 restraints weight = 36142.965| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.97 r_work: 0.3395 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25280 Z= 0.131 Angle : 0.514 8.097 34625 Z= 0.273 Chirality : 0.039 0.184 3879 Planarity : 0.004 0.054 4117 Dihedral : 17.102 89.154 4280 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.12 % Allowed : 26.90 % 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: 0.97 (0.17), residues: 2802 helix: 1.42 (0.13), residues: 1644 sheet: -1.45 (0.44), residues: 144 loop : -0.21 (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 0.024 0.001 PHE J 323 TYR 0.021 0.001 TYR J 399 ARG 0.005 0.000 ARG W 224 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1289) hydrogen bonds : angle 3.98148 ( 3530) metal coordination : bond 0.00235 ( 8) metal coordination : angle 3.10507 ( 9) covalent geometry : bond 0.00293 (25272) covalent geometry : angle 0.51126 (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 716 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 615 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7842 (tp30) cc_final: 0.7583 (mm-30) REVERT: Q 153 ARG cc_start: 0.8365 (ttt90) cc_final: 0.8122 (ttt90) REVERT: R 92 VAL cc_start: 0.8619 (p) cc_final: 0.8300 (t) REVERT: R 157 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7827 (tt0) REVERT: R 295 ARG cc_start: 0.7956 (ptp90) cc_final: 0.7730 (ptp-170) REVERT: R 307 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8058 (mtmt) REVERT: R 310 LEU cc_start: 0.8209 (mp) cc_final: 0.7987 (mt) REVERT: R 333 GLU cc_start: 0.8008 (tp30) cc_final: 0.7641 (tp30) REVERT: R 336 VAL cc_start: 0.7791 (t) cc_final: 0.7507 (m) REVERT: S 135 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7565 (ttp-170) REVERT: S 306 GLN cc_start: 0.8385 (mt0) cc_final: 0.8138 (mt0) REVERT: S 324 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7197 (mm-30) REVERT: S 327 ARG cc_start: 0.8378 (ttp-110) cc_final: 0.7794 (ttp-110) REVERT: S 345 LEU cc_start: 0.8770 (mt) cc_final: 0.8502 (mm) REVERT: T 63 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7665 (mttm) REVERT: T 73 LYS cc_start: 0.8314 (tptp) cc_final: 0.8024 (tptp) REVERT: T 116 THR cc_start: 0.8394 (m) cc_final: 0.8172 (t) REVERT: T 157 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8021 (tt0) REVERT: T 186 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: T 188 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7897 (mt0) REVERT: T 268 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7736 (mt-10) REVERT: T 326 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7727 (mt-10) REVERT: T 338 ASN cc_start: 0.7249 (m-40) cc_final: 0.6877 (m-40) REVERT: T 340 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7891 (mtt180) REVERT: U 17 THR cc_start: 0.7881 (m) cc_final: 0.7642 (t) REVERT: U 69 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6874 (ttp-110) REVERT: U 95 GLU cc_start: 0.7719 (tt0) cc_final: 0.7467 (tt0) REVERT: U 242 GLN cc_start: 0.8279 (mm110) cc_final: 0.7913 (mm110) REVERT: U 324 GLU cc_start: 0.8075 (tp30) cc_final: 0.7837 (tp30) REVERT: U 327 ARG cc_start: 0.8220 (ttp-110) cc_final: 0.8016 (ttp80) REVERT: V 38 GLU cc_start: 0.7867 (tp30) cc_final: 0.7641 (tp30) REVERT: V 39 ILE cc_start: 0.8124 (mt) cc_final: 0.7834 (mt) REVERT: V 68 LEU cc_start: 0.8765 (mt) cc_final: 0.8542 (mp) REVERT: V 130 VAL cc_start: 0.8473 (t) cc_final: 0.8194 (p) REVERT: V 144 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: V 190 ASP cc_start: 0.8322 (m-30) cc_final: 0.7891 (m-30) REVERT: V 327 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8076 (tmm160) REVERT: W 41 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: W 52 PHE cc_start: 0.7670 (m-10) cc_final: 0.7235 (m-80) REVERT: W 112 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7179 (ttp80) REVERT: W 118 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7228 (mm-30) REVERT: W 119 GLU cc_start: 0.6744 (pp20) cc_final: 0.6523 (pp20) REVERT: W 158 ASN cc_start: 0.8065 (m-40) cc_final: 0.7807 (m-40) REVERT: W 168 PHE cc_start: 0.8201 (t80) cc_final: 0.7610 (t80) REVERT: W 172 GLU cc_start: 0.7764 (tt0) cc_final: 0.7150 (tm-30) REVERT: W 198 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6937 (mtt) REVERT: W 317 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7934 (ptpp) REVERT: W 324 GLU cc_start: 0.8006 (tp30) cc_final: 0.7119 (tp30) REVERT: W 336 VAL cc_start: 0.7490 (t) cc_final: 0.7263 (t) REVERT: J 69 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8113 (m-40) REVERT: J 86 ASN cc_start: 0.8026 (m-40) cc_final: 0.7609 (m110) REVERT: J 87 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7149 (mtm-85) REVERT: J 97 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: J 135 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7545 (mtp85) REVERT: J 136 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7917 (ttpt) REVERT: J 172 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7824 (mmmm) REVERT: J 288 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8069 (p) REVERT: J 310 VAL cc_start: 0.8450 (m) cc_final: 0.8158 (p) REVERT: J 366 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7011 (p) REVERT: J 367 MET cc_start: 0.7765 (tpt) cc_final: 0.7385 (tpp) REVERT: J 398 ASN cc_start: 0.7315 (p0) cc_final: 0.7036 (p0) REVERT: J 431 GLU cc_start: 0.6822 (tt0) cc_final: 0.6593 (tp30) REVERT: J 446 TYR cc_start: 0.7298 (m-80) cc_final: 0.7029 (m-80) outliers start: 101 outliers final: 54 residues processed: 669 average time/residue: 0.4605 time to fit residues: 453.7266 Evaluate side-chains 648 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 580 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 264 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 144 GLU Chi-restraints excluded: chain V residue 305 LEU Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 112 ARG Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain 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 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: 0.6980 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 220 GLN R 316 GLN S 220 GLN S 337 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 GLN U 328 GLN W 220 GLN J 75 ASN J 106 GLN J 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119540 restraints weight = 36669.256| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.05 r_work: 0.3372 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25280 Z= 0.154 Angle : 0.522 8.636 34625 Z= 0.276 Chirality : 0.040 0.173 3879 Planarity : 0.004 0.051 4117 Dihedral : 17.063 89.019 4274 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.16 % Allowed : 27.02 % Favored : 68.82 % 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: 1.03 (0.17), residues: 2802 helix: 1.46 (0.13), residues: 1636 sheet: -1.09 (0.40), residues: 186 loop : -0.15 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 PHE 0.024 0.001 PHE J 323 TYR 0.013 0.001 TYR J 399 ARG 0.008 0.000 ARG S 112 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1289) hydrogen bonds : angle 3.92500 ( 3530) metal coordination : bond 0.00278 ( 8) metal coordination : angle 3.13376 ( 9) covalent geometry : bond 0.00356 (25272) covalent geometry : angle 0.51954 (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 713 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 611 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 38 GLU cc_start: 0.7882 (tp30) cc_final: 0.7657 (mm-30) REVERT: Q 172 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7308 (mm-30) REVERT: Q 210 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6753 (tm-30) REVERT: R 92 VAL cc_start: 0.8589 (p) cc_final: 0.8322 (t) REVERT: R 153 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8010 (ttt90) REVERT: R 157 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7551 (mt-10) REVERT: R 307 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8063 (mtmt) REVERT: R 310 LEU cc_start: 0.8206 (mp) cc_final: 0.7996 (mt) REVERT: R 333 GLU cc_start: 0.8022 (tp30) cc_final: 0.7660 (tp30) REVERT: R 336 VAL cc_start: 0.7787 (t) cc_final: 0.7499 (m) REVERT: S 135 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7603 (ttp-170) REVERT: S 171 ASP cc_start: 0.8223 (t0) cc_final: 0.7888 (t0) REVERT: S 295 ARG cc_start: 0.7875 (ptp-110) cc_final: 0.7391 (ptm-80) REVERT: S 324 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7744 (mm-30) REVERT: S 332 THR cc_start: 0.8313 (p) cc_final: 0.7976 (t) REVERT: S 345 LEU cc_start: 0.8797 (mt) cc_final: 0.8512 (mm) REVERT: T 54 PHE cc_start: 0.8229 (m-80) cc_final: 0.7923 (m-80) REVERT: T 63 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7689 (mttm) REVERT: T 186 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: T 188 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7924 (mt0) REVERT: T 198 MET cc_start: 0.8352 (mtp) cc_final: 0.8137 (mtt) REVERT: T 338 ASN cc_start: 0.7284 (m-40) cc_final: 0.6920 (m-40) REVERT: T 340 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7930 (mtt180) REVERT: U 17 THR cc_start: 0.7940 (m) cc_final: 0.7701 (t) REVERT: U 69 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.6930 (ttp-110) REVERT: U 95 GLU cc_start: 0.7739 (tt0) cc_final: 0.7474 (tt0) REVERT: U 144 GLU cc_start: 0.6743 (tp30) cc_final: 0.6487 (tp30) REVERT: U 242 GLN cc_start: 0.8296 (mm110) cc_final: 0.7943 (mm110) REVERT: U 273 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7779 (mmt180) REVERT: U 282 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: U 323 GLN cc_start: 0.7914 (mt0) cc_final: 0.7661 (mt0) REVERT: V 39 ILE cc_start: 0.8152 (mt) cc_final: 0.7870 (mt) REVERT: V 71 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8070 (mt-10) REVERT: V 130 VAL cc_start: 0.8522 (t) cc_final: 0.8226 (p) REVERT: V 190 ASP cc_start: 0.8337 (m-30) cc_final: 0.8030 (m-30) REVERT: V 304 ASP cc_start: 0.6937 (m-30) cc_final: 0.6704 (m-30) REVERT: V 327 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8131 (tmm160) REVERT: W 32 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6485 (tpt-90) REVERT: W 41 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7989 (mmm) REVERT: W 52 PHE cc_start: 0.7725 (m-10) cc_final: 0.7328 (m-80) REVERT: W 118 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7175 (mm-30) REVERT: W 158 ASN cc_start: 0.8071 (m-40) cc_final: 0.7803 (m-40) REVERT: W 168 PHE cc_start: 0.8201 (t80) cc_final: 0.7641 (t80) REVERT: W 172 GLU cc_start: 0.7763 (tt0) cc_final: 0.7068 (tm-30) REVERT: W 198 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6890 (mtt) REVERT: W 220 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7015 (tp40) REVERT: W 317 LYS cc_start: 0.8343 (ptpp) cc_final: 0.7901 (ptpp) REVERT: W 336 VAL cc_start: 0.7503 (t) cc_final: 0.7262 (t) REVERT: J 69 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: J 86 ASN cc_start: 0.8038 (m-40) cc_final: 0.7629 (m110) REVERT: J 87 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6844 (mtm-85) REVERT: J 97 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7265 (mtp) REVERT: J 172 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7863 (mmmm) REVERT: J 236 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: J 263 LYS cc_start: 0.6987 (ttmt) cc_final: 0.6710 (ttpt) REVERT: J 288 SER cc_start: 0.8441 (m) cc_final: 0.8171 (p) REVERT: J 310 VAL cc_start: 0.8469 (m) cc_final: 0.8024 (p) REVERT: J 367 MET cc_start: 0.7772 (tpt) cc_final: 0.7392 (tpp) REVERT: J 368 GLU cc_start: 0.7070 (mp0) cc_final: 0.6755 (mp0) REVERT: J 398 ASN cc_start: 0.7363 (p0) cc_final: 0.7078 (p0) REVERT: J 414 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: J 431 GLU cc_start: 0.6845 (tt0) cc_final: 0.6596 (tp30) REVERT: J 446 TYR cc_start: 0.7438 (m-80) cc_final: 0.7090 (m-80) outliers start: 102 outliers final: 63 residues processed: 663 average time/residue: 0.4316 time to fit residues: 418.9235 Evaluate side-chains 677 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 600 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 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 122 ILE 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 128 TYR Chi-restraints excluded: chain S residue 135 ARG 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 30 HIS Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 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 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 220 GLN 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 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 97 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 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: 0.4980 chunk 217 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 0.0980 chunk 126 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 145 optimal weight: 0.0000 chunk 260 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 316 GLN S 220 GLN S 337 GLN ** T 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 197 ASN V 142 ASN V 197 ASN J 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120540 restraints weight = 36473.284| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.05 r_work: 0.3394 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25280 Z= 0.120 Angle : 0.505 12.321 34625 Z= 0.267 Chirality : 0.038 0.145 3879 Planarity : 0.004 0.048 4117 Dihedral : 16.954 86.203 4270 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.16 % Allowed : 27.35 % Favored : 68.49 % 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: 1.56 (0.13), residues: 1638 sheet: -1.52 (0.44), residues: 144 loop : -0.15 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 284 HIS 0.005 0.001 HIS Q 30 PHE 0.022 0.001 PHE J 323 TYR 0.013 0.001 TYR J 399 ARG 0.006 0.000 ARG S 153 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1289) hydrogen bonds : angle 3.83807 ( 3530) metal coordination : bond 0.00212 ( 8) metal coordination : angle 2.83741 ( 9) covalent geometry : bond 0.00264 (25272) covalent geometry : angle 0.50288 (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 710 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 608 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: Q 153 ARG cc_start: 0.8358 (ttt90) cc_final: 0.8110 (ttt90) REVERT: Q 161 ILE cc_start: 0.8243 (mt) cc_final: 0.7934 (pt) REVERT: Q 172 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7297 (mm-30) REVERT: Q 210 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6741 (tm-30) REVERT: R 88 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5688 (tpt170) REVERT: R 92 VAL cc_start: 0.8565 (p) cc_final: 0.8318 (t) REVERT: R 157 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7664 (mt-10) REVERT: R 307 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8046 (mtmt) REVERT: R 333 GLU cc_start: 0.8022 (tp30) cc_final: 0.7679 (tp30) REVERT: R 336 VAL cc_start: 0.7794 (t) cc_final: 0.7535 (m) REVERT: S 135 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7678 (ttp-170) REVERT: S 171 ASP cc_start: 0.8209 (t0) cc_final: 0.7872 (t0) REVERT: S 246 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8203 (p) REVERT: S 295 ARG cc_start: 0.7839 (ptp-110) cc_final: 0.7386 (ptm-80) REVERT: S 324 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7067 (mm-30) REVERT: S 327 ARG cc_start: 0.8302 (tmm160) cc_final: 0.7681 (ttp-110) REVERT: S 332 THR cc_start: 0.8314 (p) cc_final: 0.7971 (t) REVERT: S 345 LEU cc_start: 0.8793 (mt) cc_final: 0.8517 (mm) REVERT: T 17 THR cc_start: 0.8402 (m) cc_final: 0.8051 (p) REVERT: T 63 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7685 (mttm) REVERT: T 116 THR cc_start: 0.8459 (m) cc_final: 0.8205 (t) REVERT: T 186 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: T 338 ASN cc_start: 0.7287 (m-40) cc_final: 0.6960 (m-40) REVERT: T 340 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7913 (mtt-85) REVERT: U 17 THR cc_start: 0.7930 (m) cc_final: 0.7690 (t) REVERT: U 69 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6870 (ttp-110) REVERT: U 95 GLU cc_start: 0.7718 (tt0) cc_final: 0.7472 (tt0) REVERT: U 108 GLU cc_start: 0.8274 (tp30) cc_final: 0.7969 (tp30) REVERT: U 142 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.7020 (t0) REVERT: U 242 GLN cc_start: 0.8275 (mm110) cc_final: 0.7918 (mm110) REVERT: U 282 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7309 (tttm) REVERT: V 12 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7191 (mt) REVERT: V 38 GLU cc_start: 0.7896 (tp30) cc_final: 0.7682 (tp30) REVERT: V 39 ILE cc_start: 0.8150 (mt) cc_final: 0.7864 (mt) REVERT: V 130 VAL cc_start: 0.8496 (t) cc_final: 0.8200 (p) REVERT: V 144 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: V 186 GLN cc_start: 0.8487 (tt0) cc_final: 0.8254 (tt0) REVERT: V 190 ASP cc_start: 0.8321 (m-30) cc_final: 0.8035 (m-30) REVERT: V 327 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8132 (tmm160) REVERT: W 41 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: W 52 PHE cc_start: 0.7699 (m-10) cc_final: 0.7280 (m-80) REVERT: W 116 THR cc_start: 0.7911 (t) cc_final: 0.7554 (m) REVERT: W 118 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7306 (mm-30) REVERT: W 153 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7770 (ttt-90) REVERT: W 154 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7277 (ttm110) REVERT: W 158 ASN cc_start: 0.8046 (m-40) cc_final: 0.7784 (m-40) REVERT: W 168 PHE cc_start: 0.8102 (t80) cc_final: 0.7664 (t80) REVERT: W 172 GLU cc_start: 0.7774 (tt0) cc_final: 0.7071 (tm-30) REVERT: W 198 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: W 317 LYS cc_start: 0.8363 (ptpp) cc_final: 0.7961 (ptpp) REVERT: W 327 ARG cc_start: 0.7612 (ptt-90) cc_final: 0.7215 (ppt-90) REVERT: W 336 VAL cc_start: 0.7461 (t) cc_final: 0.7239 (t) REVERT: J 86 ASN cc_start: 0.8041 (m-40) cc_final: 0.7669 (m-40) REVERT: J 87 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: J 97 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7198 (mtp) REVERT: J 135 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7441 (mtp85) REVERT: J 136 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: J 158 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (mt) REVERT: J 172 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7853 (mmmm) REVERT: J 189 ASN cc_start: 0.8428 (t0) cc_final: 0.8023 (t0) REVERT: J 236 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: J 288 SER cc_start: 0.8417 (m) cc_final: 0.8160 (p) REVERT: J 310 VAL cc_start: 0.8464 (m) cc_final: 0.8012 (p) REVERT: J 368 GLU cc_start: 0.7078 (mp0) cc_final: 0.6765 (mp0) REVERT: J 408 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6726 (tt) REVERT: J 414 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: J 431 GLU cc_start: 0.6814 (tt0) cc_final: 0.6577 (tp30) REVERT: J 446 TYR cc_start: 0.7402 (m-80) cc_final: 0.7060 (m-80) outliers start: 102 outliers final: 63 residues processed: 658 average time/residue: 0.4266 time to fit residues: 410.0511 Evaluate side-chains 674 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 592 time to evaluate : 2.681 ------------------------------------------------------------------------------- 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 123 ASP Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 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 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 128 TYR Chi-restraints excluded: chain S residue 135 ARG Chi-restraints excluded: chain S residue 246 SER Chi-restraints excluded: chain S residue 249 LEU Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain 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 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 144 GLU 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 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 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 97 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 136 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 177 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 175 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN S 220 GLN S 337 GLN T 105 ASN T 323 GLN U 328 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 ASN J 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119101 restraints weight = 36249.265| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.98 r_work: 0.3377 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25280 Z= 0.168 Angle : 0.531 10.353 34625 Z= 0.281 Chirality : 0.040 0.175 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.998 89.572 4270 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.49 % Allowed : 26.57 % 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: 1.03 (0.17), residues: 2802 helix: 1.44 (0.13), residues: 1642 sheet: -1.11 (0.41), residues: 186 loop : -0.12 (0.22), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 284 HIS 0.006 0.001 HIS Q 30 PHE 0.032 0.001 PHE J 323 TYR 0.013 0.001 TYR R 22 ARG 0.007 0.000 ARG S 112 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1289) hydrogen bonds : angle 3.87210 ( 3530) metal coordination : bond 0.00310 ( 8) metal coordination : angle 3.08552 ( 9) covalent geometry : bond 0.00390 (25272) covalent geometry : angle 0.52849 (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 715 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 605 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8248 (mt) cc_final: 0.7963 (pt) REVERT: Q 172 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7335 (mm-30) REVERT: Q 210 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6725 (tm-30) REVERT: R 88 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5849 (tpt170) REVERT: R 100 GLU cc_start: 0.7832 (pm20) cc_final: 0.7585 (pm20) REVERT: R 102 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7705 (ttm170) REVERT: R 153 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8017 (ttt90) REVERT: R 157 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7534 (mt-10) REVERT: S 100 GLU cc_start: 0.7929 (pm20) cc_final: 0.7667 (pm20) REVERT: S 103 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: S 135 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7697 (ttp-170) REVERT: S 171 ASP cc_start: 0.8208 (t0) cc_final: 0.7884 (t0) REVERT: S 201 ILE cc_start: 0.8763 (mm) cc_final: 0.8504 (mt) REVERT: S 246 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8199 (p) REVERT: S 295 ARG cc_start: 0.7831 (ptp-110) cc_final: 0.7566 (ptm-80) REVERT: S 324 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7047 (mm-30) REVERT: S 327 ARG cc_start: 0.8304 (tmm160) cc_final: 0.7666 (ttp-110) REVERT: S 332 THR cc_start: 0.8336 (p) cc_final: 0.8058 (t) REVERT: S 345 LEU cc_start: 0.8788 (mt) cc_final: 0.8497 (mm) REVERT: T 17 THR cc_start: 0.8428 (m) cc_final: 0.8086 (p) REVERT: T 54 PHE cc_start: 0.8213 (m-80) cc_final: 0.7917 (m-80) REVERT: T 186 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: T 338 ASN cc_start: 0.7286 (m-40) cc_final: 0.6959 (m-40) REVERT: T 340 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7952 (mtt180) REVERT: U 17 THR cc_start: 0.7988 (m) cc_final: 0.7742 (t) REVERT: U 69 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6865 (ttp-110) REVERT: U 127 ASP cc_start: 0.7813 (t0) cc_final: 0.7578 (t0) REVERT: U 142 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7036 (t0) REVERT: U 242 GLN cc_start: 0.8258 (mm110) cc_final: 0.7889 (mm110) REVERT: U 273 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7767 (mmt180) REVERT: U 282 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7307 (tttm) REVERT: U 331 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: V 12 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7180 (mt) REVERT: V 38 GLU cc_start: 0.7913 (tp30) cc_final: 0.7696 (tp30) REVERT: V 39 ILE cc_start: 0.8163 (mt) cc_final: 0.7876 (mt) REVERT: V 71 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7976 (mt-10) REVERT: V 130 VAL cc_start: 0.8549 (t) cc_final: 0.8227 (p) REVERT: V 144 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: V 186 GLN cc_start: 0.8473 (tt0) cc_final: 0.8223 (tt0) REVERT: V 190 ASP cc_start: 0.8310 (m-30) cc_final: 0.8015 (m-30) REVERT: V 327 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8099 (tmm160) REVERT: W 41 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7844 (mmm) REVERT: W 44 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7694 (mp) REVERT: W 52 PHE cc_start: 0.7749 (m-10) cc_final: 0.7371 (m-80) REVERT: W 116 THR cc_start: 0.8018 (t) cc_final: 0.7673 (m) REVERT: W 118 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7411 (mm-30) REVERT: W 154 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7206 (ttm110) REVERT: W 158 ASN cc_start: 0.8039 (m-40) cc_final: 0.7772 (m-40) REVERT: W 168 PHE cc_start: 0.8164 (t80) cc_final: 0.7594 (t80) REVERT: W 172 GLU cc_start: 0.7727 (tt0) cc_final: 0.6996 (tm-30) REVERT: W 198 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (mtt) REVERT: W 317 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7908 (ptpp) REVERT: W 336 VAL cc_start: 0.7511 (t) cc_final: 0.7289 (t) REVERT: J 69 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: J 86 ASN cc_start: 0.8021 (m-40) cc_final: 0.7596 (m110) REVERT: J 87 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6847 (mtm-85) REVERT: J 158 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8460 (mt) REVERT: J 172 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7857 (mmmm) REVERT: J 236 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: J 288 SER cc_start: 0.8404 (m) cc_final: 0.8197 (p) REVERT: J 310 VAL cc_start: 0.8485 (m) cc_final: 0.8076 (p) REVERT: J 368 GLU cc_start: 0.6999 (mp0) cc_final: 0.6197 (mp0) REVERT: J 408 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6748 (tt) REVERT: J 414 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: J 431 GLU cc_start: 0.6793 (tt0) cc_final: 0.6544 (tp30) REVERT: J 446 TYR cc_start: 0.7559 (m-80) cc_final: 0.7162 (m-80) outliers start: 110 outliers final: 72 residues processed: 657 average time/residue: 0.4299 time to fit residues: 415.2063 Evaluate side-chains 690 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 597 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain Q residue 225 SER Chi-restraints excluded: chain R residue 24 GLU 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 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 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 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain U residue 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 144 GLU 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 44 ILE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 198 MET Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 12 TRP Chi-restraints excluded: chain J residue 21 GLN Chi-restraints excluded: chain J residue 69 ASN Chi-restraints excluded: chain J residue 81 PHE Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 48 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 285 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 211 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 25 ASN R 158 ASN ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 GLN S 220 GLN S 337 GLN U 328 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN J 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119369 restraints weight = 36219.137| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.94 r_work: 0.3383 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25280 Z= 0.161 Angle : 0.529 9.170 34625 Z= 0.281 Chirality : 0.040 0.159 3879 Planarity : 0.004 0.051 4117 Dihedral : 16.997 87.951 4270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.16 % Allowed : 27.14 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.13), residues: 1637 sheet: -1.12 (0.41), residues: 186 loop : -0.14 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 284 HIS 0.006 0.001 HIS J 147 PHE 0.030 0.001 PHE J 323 TYR 0.011 0.001 TYR J 72 ARG 0.012 0.000 ARG T 153 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1289) hydrogen bonds : angle 3.85185 ( 3530) metal coordination : bond 0.00322 ( 8) metal coordination : angle 3.15084 ( 9) covalent geometry : bond 0.00373 (25272) covalent geometry : angle 0.52621 (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 715 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 613 time to evaluate : 2.831 Fit side-chains revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8235 (mt) cc_final: 0.7940 (pt) REVERT: Q 172 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7302 (mm-30) REVERT: Q 210 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6710 (tm-30) REVERT: R 88 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5891 (tpt170) REVERT: R 102 ARG cc_start: 0.7896 (ttm170) cc_final: 0.7695 (ttm170) REVERT: R 153 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8018 (ttt90) REVERT: R 157 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7520 (mt-10) REVERT: S 103 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: S 135 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7740 (ttp-170) REVERT: S 171 ASP cc_start: 0.8193 (t0) cc_final: 0.7857 (t0) REVERT: S 201 ILE cc_start: 0.8764 (mm) cc_final: 0.8527 (mt) REVERT: S 246 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8199 (p) REVERT: S 295 ARG cc_start: 0.7817 (ptp-110) cc_final: 0.7587 (ptm-80) REVERT: S 324 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7670 (mm-30) REVERT: S 332 THR cc_start: 0.8335 (p) cc_final: 0.8058 (t) REVERT: S 345 LEU cc_start: 0.8787 (mt) cc_final: 0.8491 (mm) REVERT: T 17 THR cc_start: 0.8404 (m) cc_final: 0.8063 (p) REVERT: T 54 PHE cc_start: 0.8219 (m-80) cc_final: 0.7867 (m-80) REVERT: T 186 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: T 338 ASN cc_start: 0.7270 (m-40) cc_final: 0.6944 (m-40) REVERT: T 340 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7976 (mtt180) REVERT: U 17 THR cc_start: 0.7987 (m) cc_final: 0.7739 (t) REVERT: U 69 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6873 (ttp-110) REVERT: U 127 ASP cc_start: 0.7848 (t0) cc_final: 0.7521 (t0) REVERT: U 142 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7043 (t0) REVERT: U 242 GLN cc_start: 0.8253 (mm110) cc_final: 0.7891 (mm110) REVERT: U 282 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7343 (tttm) REVERT: U 286 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (tttm) REVERT: V 39 ILE cc_start: 0.8178 (mt) cc_final: 0.7811 (mt) REVERT: V 71 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8027 (mt-10) REVERT: V 130 VAL cc_start: 0.8550 (t) cc_final: 0.8217 (p) REVERT: V 186 GLN cc_start: 0.8468 (tt0) cc_final: 0.8081 (tt0) REVERT: V 190 ASP cc_start: 0.8310 (m-30) cc_final: 0.7856 (m-30) REVERT: V 327 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8073 (tmm160) REVERT: W 41 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7955 (mmp) REVERT: W 44 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7656 (mp) REVERT: W 52 PHE cc_start: 0.7757 (m-10) cc_final: 0.7371 (m-80) REVERT: W 116 THR cc_start: 0.8046 (t) cc_final: 0.7722 (m) REVERT: W 153 ARG cc_start: 0.8048 (mtp180) cc_final: 0.7573 (mtp180) REVERT: W 154 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7213 (ttm110) REVERT: W 158 ASN cc_start: 0.8043 (m-40) cc_final: 0.7769 (m-40) REVERT: W 168 PHE cc_start: 0.8128 (t80) cc_final: 0.7555 (t80) REVERT: W 224 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7370 (mtt90) REVERT: W 317 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7951 (ptpp) REVERT: W 336 VAL cc_start: 0.7503 (t) cc_final: 0.7288 (t) REVERT: J 39 GLU cc_start: 0.7339 (tt0) cc_final: 0.7072 (tt0) REVERT: J 69 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8089 (m-40) REVERT: J 86 ASN cc_start: 0.8013 (m-40) cc_final: 0.7582 (m110) REVERT: J 87 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6868 (mtm-85) REVERT: J 158 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8475 (mt) REVERT: J 172 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7844 (mmmm) REVERT: J 236 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: J 288 SER cc_start: 0.8442 (m) cc_final: 0.8230 (p) REVERT: J 310 VAL cc_start: 0.8480 (m) cc_final: 0.8066 (p) REVERT: J 367 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7241 (tpp) REVERT: J 408 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6766 (tt) REVERT: J 414 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6022 (mp0) REVERT: J 431 GLU cc_start: 0.6756 (tt0) cc_final: 0.6503 (tp30) REVERT: J 446 TYR cc_start: 0.7614 (m-80) cc_final: 0.7159 (m-80) outliers start: 102 outliers final: 68 residues processed: 663 average time/residue: 0.4328 time to fit residues: 422.6335 Evaluate side-chains 686 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 599 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain Q residue 198 MET 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 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 246 SER Chi-restraints excluded: chain S residue 264 VAL 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 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 44 ILE Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 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 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 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 158 ASN S 220 GLN S 337 GLN U 328 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.146085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119579 restraints weight = 36043.015| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.94 r_work: 0.3386 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25280 Z= 0.160 Angle : 0.535 8.332 34625 Z= 0.284 Chirality : 0.040 0.186 3879 Planarity : 0.004 0.052 4117 Dihedral : 16.997 89.854 4270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.24 % Allowed : 27.59 % Favored : 68.16 % 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: 0.99 (0.17), residues: 2802 helix: 1.42 (0.13), residues: 1637 sheet: -1.16 (0.40), residues: 186 loop : -0.14 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 284 HIS 0.008 0.001 HIS V 162 PHE 0.027 0.001 PHE J 323 TYR 0.010 0.001 TYR W 37 ARG 0.007 0.000 ARG T 153 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 1289) hydrogen bonds : angle 3.85226 ( 3530) metal coordination : bond 0.00325 ( 8) metal coordination : angle 3.21928 ( 9) covalent geometry : bond 0.00370 (25272) covalent geometry : angle 0.53251 (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 713 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 609 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8212 (mt) cc_final: 0.7914 (pt) REVERT: Q 172 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7260 (mm-30) REVERT: Q 210 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6690 (tm-30) REVERT: R 88 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6019 (tpt170) REVERT: R 102 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7684 (ttm170) REVERT: R 153 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8022 (ttt90) REVERT: R 157 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7522 (mt-10) REVERT: R 201 ILE cc_start: 0.8593 (mm) cc_final: 0.8349 (mt) REVERT: S 103 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: S 135 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7740 (ttp-170) REVERT: S 171 ASP cc_start: 0.8195 (t0) cc_final: 0.7857 (t0) REVERT: S 201 ILE cc_start: 0.8750 (mm) cc_final: 0.8537 (mt) REVERT: S 246 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8184 (p) REVERT: S 295 ARG cc_start: 0.7804 (ptp-110) cc_final: 0.7600 (ptm-80) REVERT: S 324 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7641 (mm-30) REVERT: S 332 THR cc_start: 0.8331 (p) cc_final: 0.8056 (t) REVERT: S 345 LEU cc_start: 0.8786 (mt) cc_final: 0.8479 (mm) REVERT: T 17 THR cc_start: 0.8418 (m) cc_final: 0.8081 (p) REVERT: T 54 PHE cc_start: 0.8237 (m-80) cc_final: 0.7922 (m-80) REVERT: T 186 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: T 338 ASN cc_start: 0.7263 (m-40) cc_final: 0.6930 (m-40) REVERT: T 340 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7964 (mtt180) REVERT: U 17 THR cc_start: 0.7982 (m) cc_final: 0.7739 (t) REVERT: U 69 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.6839 (ttp-110) REVERT: U 127 ASP cc_start: 0.7869 (t0) cc_final: 0.7589 (t0) REVERT: U 142 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.7033 (t0) REVERT: U 242 GLN cc_start: 0.8259 (mm110) cc_final: 0.7888 (mm110) REVERT: U 282 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7328 (tttm) REVERT: U 286 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7343 (tttm) REVERT: V 38 GLU cc_start: 0.7936 (tp30) cc_final: 0.7722 (tp30) REVERT: V 39 ILE cc_start: 0.8161 (mt) cc_final: 0.7831 (mt) REVERT: V 71 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7929 (mt-10) REVERT: V 130 VAL cc_start: 0.8495 (t) cc_final: 0.8203 (p) REVERT: V 144 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: V 190 ASP cc_start: 0.8299 (m-30) cc_final: 0.7850 (m-30) REVERT: V 327 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8068 (tmm160) REVERT: W 41 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mmm) REVERT: W 52 PHE cc_start: 0.7769 (m-10) cc_final: 0.7375 (m-80) REVERT: W 116 THR cc_start: 0.8010 (t) cc_final: 0.7719 (m) REVERT: W 153 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7544 (mtp180) REVERT: W 154 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7162 (ttm110) REVERT: W 158 ASN cc_start: 0.8056 (m-40) cc_final: 0.7775 (m-40) REVERT: W 168 PHE cc_start: 0.8096 (t80) cc_final: 0.7498 (t80) REVERT: W 198 MET cc_start: 0.7174 (mtt) cc_final: 0.6852 (mpp) REVERT: W 224 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7285 (mtt90) REVERT: W 336 VAL cc_start: 0.7480 (t) cc_final: 0.7279 (t) REVERT: J 39 GLU cc_start: 0.7341 (tt0) cc_final: 0.7079 (tt0) REVERT: J 86 ASN cc_start: 0.8025 (m-40) cc_final: 0.7619 (m-40) REVERT: J 87 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7198 (mtm-85) REVERT: J 115 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7818 (ptp90) REVERT: J 158 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8455 (mt) REVERT: J 172 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7840 (mmmm) REVERT: J 236 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: J 288 SER cc_start: 0.8451 (m) cc_final: 0.8245 (p) REVERT: J 310 VAL cc_start: 0.8486 (m) cc_final: 0.8079 (p) REVERT: J 367 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7244 (tpp) REVERT: J 408 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6826 (tt) REVERT: J 414 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: J 431 GLU cc_start: 0.6742 (tt0) cc_final: 0.6464 (tp30) REVERT: J 446 TYR cc_start: 0.7651 (m-80) cc_final: 0.7136 (m-80) outliers start: 104 outliers final: 70 residues processed: 664 average time/residue: 0.4287 time to fit residues: 416.3661 Evaluate side-chains 678 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 589 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 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 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 246 SER Chi-restraints excluded: chain S residue 264 VAL Chi-restraints excluded: chain S residue 274 THR Chi-restraints excluded: chain S residue 303 LYS Chi-restraints excluded: chain S residue 320 LYS Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain T residue 186 GLN Chi-restraints excluded: chain T residue 210 GLU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 293 LEU Chi-restraints excluded: chain U residue 69 ARG Chi-restraints excluded: chain U residue 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 100 GLU Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 144 GLU Chi-restraints excluded: chain V residue 166 ASP Chi-restraints excluded: chain V residue 294 ASP Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 329 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain W residue 121 LEU Chi-restraints excluded: chain W residue 133 ILE Chi-restraints excluded: chain W residue 176 PHE Chi-restraints excluded: chain W residue 188 GLN Chi-restraints excluded: chain W residue 210 GLU Chi-restraints excluded: chain W residue 274 THR Chi-restraints excluded: chain W residue 329 LEU Chi-restraints excluded: chain J residue 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 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 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 234 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 275 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 S 337 GLN T 162 HIS U 328 GLN V 252 GLN 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 = 0.3854 r_free = 0.3854 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117605 restraints weight = 36251.003| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.03 r_work: 0.3351 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25280 Z= 0.225 Angle : 0.579 8.060 34625 Z= 0.307 Chirality : 0.043 0.192 3879 Planarity : 0.005 0.053 4117 Dihedral : 17.160 88.895 4270 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.00 % Allowed : 27.71 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.16), residues: 2802 helix: 1.23 (0.13), residues: 1637 sheet: -1.16 (0.40), residues: 186 loop : -0.24 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J 284 HIS 0.008 0.001 HIS J 147 PHE 0.021 0.002 PHE J 323 TYR 0.013 0.002 TYR J 72 ARG 0.006 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 1289) hydrogen bonds : angle 3.98792 ( 3530) metal coordination : bond 0.00422 ( 8) metal coordination : angle 3.65958 ( 9) covalent geometry : bond 0.00530 (25272) covalent geometry : angle 0.57612 (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 686 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 588 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8258 (mt) cc_final: 0.7956 (pt) REVERT: Q 172 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7357 (mm-30) REVERT: Q 210 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6747 (tm-30) REVERT: R 88 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6252 (tpt170) REVERT: R 102 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7703 (ttm170) REVERT: R 118 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7570 (mm-30) REVERT: R 153 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8113 (ttt90) REVERT: R 157 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7563 (mt-10) REVERT: R 201 ILE cc_start: 0.8642 (mm) cc_final: 0.8438 (mt) REVERT: S 103 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: S 135 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7868 (ttp-170) REVERT: S 171 ASP cc_start: 0.8222 (t0) cc_final: 0.7902 (t0) REVERT: S 172 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7561 (mm-30) REVERT: S 246 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8178 (p) REVERT: S 324 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7647 (mm-30) REVERT: S 332 THR cc_start: 0.8400 (p) cc_final: 0.8095 (t) REVERT: S 345 LEU cc_start: 0.8769 (mt) cc_final: 0.8451 (mm) REVERT: T 17 THR cc_start: 0.8464 (m) cc_final: 0.8215 (p) REVERT: T 186 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: T 338 ASN cc_start: 0.7313 (m-40) cc_final: 0.6993 (m-40) REVERT: T 340 ARG cc_start: 0.8244 (mtp85) cc_final: 0.8034 (mtt180) REVERT: U 17 THR cc_start: 0.8047 (m) cc_final: 0.7804 (t) REVERT: U 69 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7717 (ttt180) REVERT: U 108 GLU cc_start: 0.8165 (tp30) cc_final: 0.7752 (tp30) REVERT: U 127 ASP cc_start: 0.7900 (t0) cc_final: 0.7594 (t0) REVERT: U 142 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7081 (t0) REVERT: U 242 GLN cc_start: 0.8273 (mm110) cc_final: 0.7907 (mm110) REVERT: U 282 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7358 (tttm) REVERT: V 38 GLU cc_start: 0.7972 (tp30) cc_final: 0.7753 (tp30) REVERT: V 71 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7988 (mt-10) REVERT: V 76 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7661 (mt-10) REVERT: V 130 VAL cc_start: 0.8507 (t) cc_final: 0.8197 (p) REVERT: V 190 ASP cc_start: 0.8337 (m-30) cc_final: 0.7863 (m-30) REVERT: V 321 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: W 116 THR cc_start: 0.8123 (t) cc_final: 0.7784 (m) REVERT: W 158 ASN cc_start: 0.8124 (m-40) cc_final: 0.7922 (m110) REVERT: W 168 PHE cc_start: 0.8152 (t80) cc_final: 0.7681 (t80) REVERT: W 193 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7807 (ttpp) REVERT: J 39 GLU cc_start: 0.7345 (tt0) cc_final: 0.7093 (tt0) REVERT: J 86 ASN cc_start: 0.8082 (m-40) cc_final: 0.7649 (m110) REVERT: J 87 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6882 (mtm-85) REVERT: J 115 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7911 (ptp90) REVERT: J 172 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7896 (mmmm) REVERT: J 236 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7099 (tm-30) REVERT: J 310 VAL cc_start: 0.8464 (m) cc_final: 0.8050 (p) REVERT: J 367 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7281 (tpp) REVERT: J 414 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: J 431 GLU cc_start: 0.6793 (tt0) cc_final: 0.6509 (tp30) outliers start: 98 outliers final: 68 residues processed: 638 average time/residue: 0.4239 time to fit residues: 399.4943 Evaluate side-chains 651 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 568 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 198 MET 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 265 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 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 246 SER Chi-restraints excluded: chain S residue 264 VAL 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 U residue 69 ARG Chi-restraints excluded: chain U residue 72 GLN Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 100 GLU Chi-restraints excluded: chain U residue 142 ASN Chi-restraints excluded: chain U residue 148 VAL Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 247 VAL Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain U residue 282 LYS Chi-restraints excluded: chain U residue 310 LEU Chi-restraints excluded: chain V residue 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 294 ASP Chi-restraints excluded: chain V residue 310 LEU Chi-restraints excluded: chain V residue 321 GLU 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 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 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 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 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 259 optimal weight: 0.0050 chunk 12 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 279 optimal weight: 0.1980 chunk 91 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN T 323 GLN U 328 GLN V 252 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN J 148 GLN J 207 ASN J 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.146884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120474 restraints weight = 35980.484| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.94 r_work: 0.3401 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25280 Z= 0.132 Angle : 0.536 8.446 34625 Z= 0.286 Chirality : 0.039 0.165 3879 Planarity : 0.004 0.051 4117 Dihedral : 17.008 86.106 4270 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.18 % Allowed : 28.69 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.17), residues: 2802 helix: 1.40 (0.13), residues: 1637 sheet: -1.11 (0.41), residues: 186 loop : -0.13 (0.22), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 284 HIS 0.005 0.001 HIS U 30 PHE 0.034 0.001 PHE J 323 TYR 0.011 0.001 TYR W 37 ARG 0.006 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1289) hydrogen bonds : angle 3.84263 ( 3530) metal coordination : bond 0.00280 ( 8) metal coordination : angle 2.90783 ( 9) covalent geometry : bond 0.00297 (25272) covalent geometry : angle 0.53376 (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 682 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 604 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: Q 161 ILE cc_start: 0.8187 (mt) cc_final: 0.7891 (pt) REVERT: Q 172 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7257 (mm-30) REVERT: Q 210 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6682 (tm-30) REVERT: R 88 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6109 (tpt170) REVERT: R 102 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7620 (ttm170) REVERT: R 153 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7985 (ttt90) REVERT: R 157 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7677 (mt-10) REVERT: R 201 ILE cc_start: 0.8600 (mm) cc_final: 0.8364 (mt) REVERT: S 103 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: S 135 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7819 (ttp-170) REVERT: S 171 ASP cc_start: 0.8177 (t0) cc_final: 0.7850 (t0) REVERT: S 246 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8184 (p) REVERT: S 324 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7631 (mm-30) REVERT: S 332 THR cc_start: 0.8367 (p) cc_final: 0.8066 (t) REVERT: S 345 LEU cc_start: 0.8768 (mt) cc_final: 0.8479 (mm) REVERT: T 17 THR cc_start: 0.8459 (m) cc_final: 0.8128 (p) REVERT: T 54 PHE cc_start: 0.8248 (m-80) cc_final: 0.7865 (m-80) REVERT: T 116 THR cc_start: 0.8438 (m) cc_final: 0.8204 (t) REVERT: T 186 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: T 338 ASN cc_start: 0.7279 (m-40) cc_final: 0.6944 (m-40) REVERT: T 340 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8023 (mtt180) REVERT: U 17 THR cc_start: 0.7986 (m) cc_final: 0.7755 (t) REVERT: U 69 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: U 108 GLU cc_start: 0.8123 (tp30) cc_final: 0.7686 (tp30) REVERT: U 127 ASP cc_start: 0.7886 (t0) cc_final: 0.7597 (t0) REVERT: U 142 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.7033 (t0) REVERT: U 242 GLN cc_start: 0.8243 (mm110) cc_final: 0.7868 (mm110) REVERT: U 282 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7350 (tttm) REVERT: V 38 GLU cc_start: 0.7917 (tp30) cc_final: 0.7684 (tp30) REVERT: V 44 ILE cc_start: 0.8515 (mt) cc_final: 0.7793 (mm) REVERT: V 71 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7949 (mt-10) REVERT: V 190 ASP cc_start: 0.8327 (m-30) cc_final: 0.8022 (m-30) REVERT: V 321 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: W 52 PHE cc_start: 0.7743 (m-10) cc_final: 0.7345 (m-80) REVERT: W 116 THR cc_start: 0.8042 (t) cc_final: 0.7677 (m) REVERT: W 158 ASN cc_start: 0.8086 (m-40) cc_final: 0.7825 (m-40) REVERT: W 168 PHE cc_start: 0.7985 (t80) cc_final: 0.7610 (t80) REVERT: W 193 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7709 (ttpp) REVERT: W 336 VAL cc_start: 0.7478 (t) cc_final: 0.7257 (t) REVERT: J 86 ASN cc_start: 0.7994 (m-40) cc_final: 0.7603 (m-40) REVERT: J 87 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: J 115 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7796 (ptp90) REVERT: J 158 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (mt) REVERT: J 172 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7851 (mmmm) REVERT: J 189 ASN cc_start: 0.8399 (t0) cc_final: 0.7971 (t0) REVERT: J 236 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: J 310 VAL cc_start: 0.8492 (m) cc_final: 0.8094 (p) REVERT: J 367 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7250 (tpp) REVERT: J 408 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6695 (tt) REVERT: J 414 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: J 431 GLU cc_start: 0.6745 (tt0) cc_final: 0.6471 (tp30) REVERT: J 446 TYR cc_start: 0.7684 (m-80) cc_final: 0.7116 (m-80) outliers start: 78 outliers final: 58 residues processed: 643 average time/residue: 0.4246 time to fit residues: 402.8304 Evaluate side-chains 664 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 589 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 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 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 246 SER Chi-restraints excluded: chain S residue 264 VAL 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 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 310 LEU Chi-restraints excluded: chain V residue 321 GLU 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 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 81 PHE Chi-restraints excluded: chain J residue 87 ARG Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain J residue 94 MET Chi-restraints excluded: chain J residue 115 ARG Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 199 LYS Chi-restraints excluded: chain J residue 236 GLU Chi-restraints excluded: chain J residue 255 LYS Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 276 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 367 MET Chi-restraints excluded: chain J residue 390 SER Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 408 ILE Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 106 optimal weight: 0.3980 chunk 155 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 199 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 GLN T 323 GLN U 328 GLN ** W 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN J 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.119833 restraints weight = 36074.285| |-----------------------------------------------------------------------------| 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: 4.27 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25280 Z= 0.149 Angle : 0.544 8.364 34625 Z= 0.289 Chirality : 0.040 0.204 3879 Planarity : 0.004 0.052 4117 Dihedral : 16.972 87.323 4270 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.31 % Allowed : 28.37 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.13), residues: 1637 sheet: -1.10 (0.41), residues: 186 loop : -0.11 (0.22), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J 284 HIS 0.006 0.001 HIS Q 30 PHE 0.029 0.001 PHE J 323 TYR 0.012 0.001 TYR J 9 ARG 0.006 0.000 ARG S 231 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 1289) hydrogen bonds : angle 3.82295 ( 3530) metal coordination : bond 0.00282 ( 8) metal coordination : angle 2.96767 ( 9) covalent geometry : bond 0.00345 (25272) covalent geometry : angle 0.54168 (34616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16044.80 seconds wall clock time: 277 minutes 29.35 seconds (16649.35 seconds total)