Starting phenix.real_space_refine on Sat Aug 8 07:37:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.cif Found real_map, /net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22et_68219/08_2026/22et_68219.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.047 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 119 5.49 5 S 83 5.16 5 C 16105 2.51 5 N 4636 2.21 5 O 5222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26167 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "D" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "C" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4439 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "M" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1511 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 799 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 20, 'rna3p': 17} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2550 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1730 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 204} Chain: "F" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1730 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 204} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22966 SG CYS H 43 98.358 120.043 47.079 1.00128.98 S ATOM 23004 SG CYS H 48 93.942 119.791 47.241 1.00166.34 S ATOM 23251 SG CYS H 78 95.610 121.098 49.767 1.00149.60 S ATOM 24696 SG CYS F 43 61.116 47.096 130.880 1.00 30.00 S ATOM 24719 SG CYS F 46 60.175 44.469 127.326 1.00135.29 S ATOM 24981 SG CYS F 78 61.493 47.487 128.927 1.00202.31 S ATOM 25069 SG CYS F 90 58.407 47.411 128.124 1.00166.20 S Time building chain proxies: 6.25, per 1000 atoms: 0.24 Number of scatterers: 26167 At special positions: 0 Unit cell: (133.44, 156.48, 159.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 119 15.00 O 5222 8.00 N 4636 7.00 C 16105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 90 " distance=2.01 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: 2.30 Conformation dependent library (CDL) restraints added in 931.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 78 " Number of angles added : 6 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5618 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 20 sheets defined 55.6% alpha, 12.4% beta 22 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 13 through 31 Processing helix chain 'E' and resid 34 through 48 Processing helix chain 'E' and resid 97 through 120 removed outlier: 3.690A pdb=" N THR E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.738A pdb=" N ARG E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 219 through 224' Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.946A pdb=" N ALA E 229 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 230 " --> pdb=" O PHE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 256 Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 282 through 308 removed outlier: 3.593A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 327 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 359 through 380 Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.702A pdb=" N GLY E 389 " --> pdb=" O PRO E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 409 through 418 Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'E' and resid 435 through 436 No H-bonds generated for 'chain 'E' and resid 435 through 436' Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'E' and resid 484 through 487 Processing helix chain 'E' and resid 488 through 497 removed outlier: 3.623A pdb=" N ILE E 497 " --> pdb=" O PHE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 523 through 537 Processing helix chain 'E' and resid 540 through 546 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 99 through 120 removed outlier: 3.781A pdb=" N ILE D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.556A pdb=" N ASP D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.528A pdb=" N TYR D 230 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 231 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.734A pdb=" N VAL D 244 " --> pdb=" O PHE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 277 removed outlier: 4.236A pdb=" N GLU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 308 removed outlier: 3.998A pdb=" N GLU D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 359 through 380 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 409 through 418 Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.547A pdb=" N LEU D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 436 No H-bonds generated for 'chain 'D' and resid 435 through 436' Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 484 through 487 Processing helix chain 'D' and resid 488 through 497 Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 523 through 550 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 14 through 29 removed outlier: 4.479A pdb=" N ASN B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.662A pdb=" N GLN B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 120 removed outlier: 3.750A pdb=" N ILE B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.550A pdb=" N ARG B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 239 through 258 removed outlier: 3.705A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 Processing helix chain 'B' and resid 268 through 278 removed outlier: 3.516A pdb=" N LYS B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.501A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 327 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 359 through 380 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.640A pdb=" N GLN B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 418 Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.658A pdb=" N LEU B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 436 No H-bonds generated for 'chain 'B' and resid 435 through 436' Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 484 through 487 Processing helix chain 'B' and resid 488 through 498 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 523 through 551 removed outlier: 3.792A pdb=" N SER B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 13 through 28 Processing helix chain 'C' and resid 33 through 49 Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.646A pdb=" N ILE C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 239 through 256 removed outlier: 3.507A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 279 removed outlier: 3.668A pdb=" N GLY C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 4.291A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 359 through 380 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.503A pdb=" N GLY C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.728A pdb=" N GLN C 408 " --> pdb=" O PRO C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 Processing helix chain 'C' and resid 429 through 434 removed outlier: 3.524A pdb=" N LEU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 436 No H-bonds generated for 'chain 'C' and resid 435 through 436' Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 484 through 487 Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 523 through 551 removed outlier: 3.521A pdb=" N LYS C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.600A pdb=" N VAL A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 86 removed outlier: 3.504A pdb=" N ASN A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.772A pdb=" N ILE A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 125 No H-bonds generated for 'chain 'A' and resid 124 through 125' Processing helix chain 'A' and resid 126 through 136 removed outlier: 4.547A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.676A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.589A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.522A pdb=" N HIS A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 4.147A pdb=" N ILE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'H' and resid 10 through 16 Processing helix chain 'H' and resid 22 through 26 Processing helix chain 'H' and resid 27 through 40 removed outlier: 4.049A pdb=" N ILE H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) Proline residue: H 33 - end of helix Processing helix chain 'H' and resid 64 through 69 removed outlier: 4.320A pdb=" N PHE H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 3.787A pdb=" N ASP H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 removed outlier: 3.614A pdb=" N ASP H 116 " --> pdb=" O ASN H 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 134 through 148 Processing helix chain 'H' and resid 152 through 181 removed outlier: 4.278A pdb=" N GLU H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU H 169 " --> pdb=" O TYR H 165 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU H 178 " --> pdb=" O HIS H 174 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP H 179 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 201 through 210 Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.793A pdb=" N HIS F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 40 removed outlier: 3.785A pdb=" N ILE F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.666A pdb=" N ASP F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.844A pdb=" N LEU F 106 " --> pdb=" O PRO F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 116 Processing helix chain 'F' and resid 133 through 148 removed outlier: 3.568A pdb=" N LEU F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 181 removed outlier: 4.371A pdb=" N GLU F 168 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU F 169 " --> pdb=" O TYR F 165 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU F 178 " --> pdb=" O HIS F 174 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 removed outlier: 3.571A pdb=" N GLY F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing sheet with id=AA1, first strand: chain 'E' and resid 81 through 84 removed outlier: 5.422A pdb=" N LEU E 67 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE E 150 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 69 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE E 151 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LYS E 156 " --> pdb=" O PHE E 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 200 through 204 removed outlier: 6.552A pdb=" N GLY E 391 " --> pdb=" O GLN E 422 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL E 424 " --> pdb=" O GLY E 391 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 393 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR E 426 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE E 395 " --> pdb=" O THR E 426 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR E 90 " --> pdb=" O ILE E 425 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG E 442 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 91 " --> pdb=" O ARG E 442 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE E 444 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE E 93 " --> pdb=" O PHE E 444 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N GLN E 446 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 330 through 335 Processing sheet with id=AA4, first strand: chain 'D' and resid 78 through 84 removed outlier: 6.616A pdb=" N GLN D 80 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 73 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP D 82 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER D 71 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN D 84 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER D 69 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU D 67 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE D 150 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 69 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE D 75 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N PHE D 142 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE D 151 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 200 through 204 removed outlier: 3.675A pdb=" N ALA D 396 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY D 391 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL D 424 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 393 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N THR D 426 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE D 395 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR D 90 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG D 442 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE D 91 " --> pdb=" O ARG D 442 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE D 444 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE D 93 " --> pdb=" O PHE D 444 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N GLN D 446 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 452 " --> pdb=" O ASN D 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 330 through 336 removed outlier: 4.106A pdb=" N ARG D 332 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 165 removed outlier: 4.630A pdb=" N LYS B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE B 151 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 142 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 74 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 144 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 72 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER B 146 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET B 70 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN B 148 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LEU B 453 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN B 80 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 200 through 204 removed outlier: 6.234A pdb=" N THR B 90 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ARG B 442 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 91 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 336 removed outlier: 4.096A pdb=" N ARG B 332 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 84 removed outlier: 6.973A pdb=" N ASN C 148 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET C 70 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER C 146 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE C 72 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP C 144 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP C 74 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 142 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE C 151 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 204 removed outlier: 6.443A pdb=" N GLY C 391 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 424 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 393 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 426 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 395 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR C 90 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG C 442 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE C 91 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE C 444 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE C 93 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N GLN C 446 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 330 through 336 removed outlier: 3.984A pdb=" N ARG C 332 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 35 Processing sheet with id=AB5, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.639A pdb=" N ARG A 218 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AB7, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AB8, first strand: chain 'H' and resid 53 through 57 removed outlier: 3.744A pdb=" N HIS H 54 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 118 through 120 Processing sheet with id=AC1, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AC2, first strand: chain 'F' and resid 118 through 120 1216 hydrogen bonds defined for protein. 3477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8067 1.34 - 1.46: 5326 1.46 - 1.58: 13162 1.58 - 1.70: 230 1.70 - 1.82: 139 Bond restraints: 26924 Sorted by residual: bond pdb=" CA SER A 228 " pdb=" CB SER A 228 " ideal model delta sigma weight residual 1.533 1.470 0.062 1.35e-02 5.49e+03 2.13e+01 bond pdb=" N ASP F 80 " pdb=" CA ASP F 80 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.25e-02 6.40e+03 1.32e+01 bond pdb=" C3' DT M 43 " pdb=" C2' DT M 43 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT M 37 " pdb=" C2' DT M 37 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA M 19 " pdb=" C2' DA M 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 26919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 36844 6.67 - 13.34: 38 13.34 - 20.01: 2 20.01 - 26.68: 0 26.68 - 33.34: 7 Bond angle restraints: 36891 Sorted by residual: angle pdb=" C CYS F 78 " pdb=" CA CYS F 78 " pdb=" CB CYS F 78 " ideal model delta sigma weight residual 109.65 82.89 26.76 1.74e+00 3.30e-01 2.36e+02 angle pdb=" O3' U N 40 " pdb=" P A N 41 " pdb=" OP1 A N 41 " ideal model delta sigma weight residual 108.00 74.66 33.34 3.00e+00 1.11e-01 1.24e+02 angle pdb=" O3' DG M 25 " pdb=" P DG M 26 " pdb=" OP1 DG M 26 " ideal model delta sigma weight residual 108.00 74.97 33.03 3.00e+00 1.11e-01 1.21e+02 angle pdb=" O3' DA M 66 " pdb=" P DT M 67 " pdb=" OP1 DT M 67 " ideal model delta sigma weight residual 108.00 75.72 32.28 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C CYS F 43 " pdb=" CA CYS F 43 " pdb=" CB CYS F 43 " ideal model delta sigma weight residual 109.89 94.35 15.54 1.60e+00 3.91e-01 9.43e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 15058 35.90 - 71.80: 1097 71.80 - 107.70: 74 107.70 - 143.60: 9 143.60 - 179.49: 15 Dihedral angle restraints: 16253 sinusoidal: 7629 harmonic: 8624 Sorted by residual: dihedral pdb=" C CYS F 78 " pdb=" N CYS F 78 " pdb=" CA CYS F 78 " pdb=" CB CYS F 78 " ideal model delta harmonic sigma weight residual -122.60 -93.36 -29.24 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" O4' C N 19 " pdb=" C1' C N 19 " pdb=" N1 C N 19 " pdb=" C2 C N 19 " ideal model delta sinusoidal sigma weight residual 200.00 30.74 169.26 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U N 6 " pdb=" C1' U N 6 " pdb=" N1 U N 6 " pdb=" C2 U N 6 " ideal model delta sinusoidal sigma weight residual -160.00 -13.75 -146.25 1 1.50e+01 4.44e-03 7.81e+01 ... (remaining 16250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 4097 0.256 - 0.512: 8 0.512 - 0.768: 1 0.768 - 1.023: 0 1.023 - 1.279: 3 Chirality restraints: 4109 Sorted by residual: chirality pdb=" P A N 41 " pdb=" OP1 A N 41 " pdb=" OP2 A N 41 " pdb=" O5' A N 41 " both_signs ideal model delta sigma weight residual True 2.41 1.13 1.28 2.00e-01 2.50e+01 4.09e+01 chirality pdb=" P DT M 67 " pdb=" OP1 DT M 67 " pdb=" OP2 DT M 67 " pdb=" O5' DT M 67 " both_signs ideal model delta sigma weight residual True 2.34 1.11 1.23 2.00e-01 2.50e+01 3.77e+01 chirality pdb=" P DG M 26 " pdb=" OP1 DG M 26 " pdb=" OP2 DG M 26 " pdb=" O5' DG M 26 " both_signs ideal model delta sigma weight residual True 2.34 1.12 1.22 2.00e-01 2.50e+01 3.71e+01 ... (remaining 4106 not shown) Planarity restraints: 4367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 89 " -0.710 9.50e-02 1.11e+02 3.18e-01 6.18e+01 pdb=" NE ARG F 89 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 89 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG F 89 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 89 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 134 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C ILE A 134 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE A 134 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU A 135 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 47 " -0.017 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLU F 47 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU F 47 " -0.024 2.00e-02 2.50e+03 pdb=" N CYS F 48 " -0.021 2.00e-02 2.50e+03 ... (remaining 4364 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2690 2.74 - 3.28: 26224 3.28 - 3.82: 45701 3.82 - 4.36: 53296 4.36 - 4.90: 88630 Nonbonded interactions: 216541 Sorted by model distance: nonbonded pdb=" O2' A N 37 " pdb=" O5' C N 38 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP E 499 " pdb=" OG SER E 501 " model vdw 2.239 3.040 nonbonded pdb=" O2' C N 18 " pdb=" O2 C N 19 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN A 89 " pdb=" OG SER A 191 " model vdw 2.251 3.040 nonbonded pdb=" N GLN A 13 " pdb=" OE1 GLN A 13 " model vdw 2.258 3.120 ... (remaining 216536 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 'B' and resid 1 through 551) selection = (chain 'C' and resid 1 through 551) selection = (chain 'D' and resid 1 through 551) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 1.950 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.080 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.006 0.281 26932 Z= 0.387 Angle : 0.961 57.346 36899 Z= 0.542 Chirality : 0.063 1.279 4109 Planarity : 0.006 0.318 4367 Dihedral : 22.385 179.494 10632 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 4.05 % Allowed : 27.77 % Favored : 68.18 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2930 helix: 1.67 (0.14), residues: 1396 sheet: 0.31 (0.25), residues: 391 loop : -0.42 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 534 TYR 0.015 0.001 TYR B 249 PHE 0.035 0.001 PHE D 18 TRP 0.038 0.001 TRP D 39 HIS 0.003 0.001 HIS B 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.38 (26924) covalent geometry : angle 0.89209 / 0.54 (36891) SS BOND : bond 0.02549 / 1.34 ( 1) SS BOND : angle 1.62572 / 0.93 ( 2) hydrogen bonds : bond 0.14235 / 9.68 ( 1258) hydrogen bonds : angle 5.61819 / 4.09 ( 3573) metal coordination : bond 0.11783 / 8.28 ( 7) metal coordination : angle 27.95731 / 13.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 269 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8405 (p90) REVERT: E 511 LEU cc_start: 0.8067 (mt) cc_final: 0.7714 (mp) REVERT: E 537 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8310 (tmm160) REVERT: D 7 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8600 (tmm-80) REVERT: B 505 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8842 (p) REVERT: C 22 GLN cc_start: 0.7766 (pp30) cc_final: 0.6784 (pp30) REVERT: C 170 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8076 (t) REVERT: C 224 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8132 (tp30) REVERT: C 499 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7021 (p0) REVERT: F 16 PHE cc_start: 0.8583 (m-80) cc_final: 0.8371 (m-80) REVERT: F 42 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: F 50 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7819 (pp) REVERT: F 141 GLN cc_start: 0.9133 (mt0) cc_final: 0.8705 (mp10) REVERT: F 193 ILE cc_start: 0.9652 (pp) cc_final: 0.9399 (pp) REVERT: F 211 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.6448 (m-70) outliers start: 107 outliers final: 38 residues processed: 364 average time/residue: 0.6114 time to fit residues: 258.8626 Evaluate side-chains 210 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 HIS E 540 ASN D 22 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN D 540 ASN B 55 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN H 100 ASN F 15 GLN F 88 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058797 restraints weight = 66722.934| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.33 r_work: 0.2740 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 26932 Z= 0.256 Angle : 0.875 69.000 36899 Z= 0.404 Chirality : 0.070 1.913 4109 Planarity : 0.005 0.056 4367 Dihedral : 21.033 179.364 4726 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.96 % Allowed : 27.23 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 2930 helix: 1.79 (0.14), residues: 1402 sheet: 0.08 (0.25), residues: 392 loop : -0.37 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 547 TYR 0.019 0.002 TYR H 202 PHE 0.020 0.002 PHE D 18 TRP 0.026 0.002 TRP D 39 HIS 0.015 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (26924) covalent geometry : angle 0.78604 / 0.40 (36891) SS BOND : bond 0.00865 / 0.46 ( 1) SS BOND : angle 1.35066 / 0.77 ( 2) hydrogen bonds : bond 0.05929 / 3.90 ( 1258) hydrogen bonds : angle 4.76359 / 3.48 ( 3573) metal coordination : bond 0.02233 / 0.95 ( 7) metal coordination : angle 30.23227 / 13.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 154 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8646 (p90) REVERT: E 171 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8751 (tp30) REVERT: D 122 ASP cc_start: 0.9103 (t0) cc_final: 0.8677 (t0) REVERT: D 300 ARG cc_start: 0.7083 (ttt180) cc_final: 0.6769 (ttm170) REVERT: B 58 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8920 (mm) REVERT: B 394 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9021 (mt) REVERT: B 505 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8791 (p) REVERT: C 249 TYR cc_start: 0.8520 (t80) cc_final: 0.8094 (t80) REVERT: C 283 MET cc_start: 0.2619 (mmt) cc_final: 0.2318 (mpm) REVERT: A 247 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8850 (t) REVERT: H 71 TRP cc_start: 0.5501 (OUTLIER) cc_final: 0.4964 (t-100) REVERT: H 177 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.5273 (t80) REVERT: H 188 MET cc_start: 0.9029 (mmm) cc_final: 0.8788 (mmm) REVERT: H 202 TYR cc_start: 0.8748 (t80) cc_final: 0.8519 (t80) REVERT: H 211 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7532 (m-70) REVERT: F 16 PHE cc_start: 0.8483 (m-80) cc_final: 0.8135 (m-80) REVERT: F 42 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (m-10) REVERT: F 141 GLN cc_start: 0.8970 (mt0) cc_final: 0.8713 (mt0) REVERT: F 166 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9252 (tp) REVERT: F 188 MET cc_start: 0.9124 (mmm) cc_final: 0.8778 (mpp) REVERT: F 193 ILE cc_start: 0.9470 (pp) cc_final: 0.9239 (pp) REVERT: F 211 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6183 (m-70) outliers start: 131 outliers final: 39 residues processed: 269 average time/residue: 0.5476 time to fit residues: 172.8756 Evaluate side-chains 180 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 71 TRP Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 211 HIS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 226 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 266 optimal weight: 50.0000 chunk 9 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 HIS D 22 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN H 100 ASN H 212 ASN F 30 ASN F 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.097770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059336 restraints weight = 66743.068| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.35 r_work: 0.2757 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26932 Z= 0.152 Angle : 0.766 47.455 36899 Z= 0.354 Chirality : 0.068 1.947 4109 Planarity : 0.004 0.087 4367 Dihedral : 20.876 179.797 4695 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.94 % Allowed : 27.31 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.16), residues: 2930 helix: 1.96 (0.14), residues: 1405 sheet: 0.20 (0.25), residues: 404 loop : -0.35 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 534 TYR 0.018 0.001 TYR D 21 PHE 0.020 0.001 PHE B 212 TRP 0.011 0.001 TRP D 39 HIS 0.011 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (26924) covalent geometry : angle 0.70932 / 0.35 (36891) SS BOND : bond 0.00467 / 0.25 ( 1) SS BOND : angle 0.66755 / 0.38 ( 2) hydrogen bonds : bond 0.05045 / 3.29 ( 1258) hydrogen bonds : angle 4.45248 / 3.25 ( 3573) metal coordination : bond 0.01151 / 0.37 ( 7) metal coordination : angle 22.74323 / 10.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 149 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8668 (p90) REVERT: E 356 GLU cc_start: 0.9061 (mp0) cc_final: 0.8803 (pm20) REVERT: D 20 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7556 (tm) REVERT: D 122 ASP cc_start: 0.9054 (t0) cc_final: 0.8645 (t0) REVERT: B 187 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.7565 (m-10) REVERT: B 309 MET cc_start: 0.8323 (mmm) cc_final: 0.7874 (mpt) REVERT: B 394 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9077 (mt) REVERT: C 309 MET cc_start: 0.7787 (ptp) cc_final: 0.7425 (pmm) REVERT: A 294 MET cc_start: 0.8932 (mmp) cc_final: 0.8640 (mmp) REVERT: A 308 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7430 (tpp-160) REVERT: H 38 MET cc_start: 0.6384 (tpt) cc_final: 0.6127 (tpt) REVERT: H 71 TRP cc_start: 0.5515 (OUTLIER) cc_final: 0.4907 (t-100) REVERT: H 188 MET cc_start: 0.9144 (mmm) cc_final: 0.8806 (mtp) REVERT: H 202 TYR cc_start: 0.8830 (t80) cc_final: 0.8591 (t80) REVERT: F 16 PHE cc_start: 0.8304 (m-80) cc_final: 0.7947 (m-80) REVERT: F 42 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: F 59 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8179 (mmm-85) REVERT: F 69 PHE cc_start: 0.7167 (m-80) cc_final: 0.6689 (m-80) REVERT: F 141 GLN cc_start: 0.8977 (mt0) cc_final: 0.8730 (mt0) REVERT: F 193 ILE cc_start: 0.9474 (pp) cc_final: 0.9256 (pp) REVERT: F 211 HIS cc_start: 0.6160 (OUTLIER) cc_final: 0.5935 (m-70) outliers start: 104 outliers final: 49 residues processed: 242 average time/residue: 0.5596 time to fit residues: 160.6289 Evaluate side-chains 189 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 71 TRP Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 185 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN H 100 ASN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058173 restraints weight = 65925.974| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.32 r_work: 0.2729 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 26932 Z= 0.177 Angle : 0.725 30.328 36899 Z= 0.347 Chirality : 0.068 1.957 4109 Planarity : 0.004 0.050 4367 Dihedral : 20.819 179.113 4689 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.05 % Allowed : 27.27 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.15), residues: 2930 helix: 2.01 (0.14), residues: 1404 sheet: 0.15 (0.25), residues: 404 loop : -0.36 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 7 TYR 0.017 0.001 TYR H 202 PHE 0.035 0.001 PHE D 18 TRP 0.021 0.001 TRP H 209 HIS 0.006 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (26924) covalent geometry : angle 0.69837 / 0.34 (36891) SS BOND : bond 0.00522 / 0.27 ( 1) SS BOND : angle 0.44154 / 0.25 ( 2) hydrogen bonds : bond 0.05003 / 3.27 ( 1258) hydrogen bonds : angle 4.43560 / 3.24 ( 3573) metal coordination : bond 0.00907 / 0.31 ( 7) metal coordination : angle 15.24152 / 7.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 137 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8998 (tm) REVERT: E 78 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8747 (p90) REVERT: E 356 GLU cc_start: 0.9070 (mp0) cc_final: 0.8807 (pm20) REVERT: D 42 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (pp) REVERT: D 122 ASP cc_start: 0.9101 (t0) cc_final: 0.8707 (t0) REVERT: B 187 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: B 210 HIS cc_start: 0.7212 (p-80) cc_final: 0.6930 (p-80) REVERT: B 394 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9091 (mt) REVERT: B 446 GLN cc_start: 0.7994 (tt0) cc_final: 0.7751 (pm20) REVERT: C 249 TYR cc_start: 0.8479 (t80) cc_final: 0.8078 (t80) REVERT: C 309 MET cc_start: 0.7727 (ptp) cc_final: 0.7391 (pmm) REVERT: A 294 MET cc_start: 0.8966 (mmp) cc_final: 0.8633 (mmp) REVERT: A 308 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7441 (tpp-160) REVERT: H 30 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7395 (p0) REVERT: H 188 MET cc_start: 0.9180 (mmm) cc_final: 0.8808 (mtp) REVERT: H 202 TYR cc_start: 0.8826 (t80) cc_final: 0.8594 (t80) REVERT: F 16 PHE cc_start: 0.8157 (m-80) cc_final: 0.7818 (m-80) REVERT: F 42 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: F 59 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (mmm-85) REVERT: F 69 PHE cc_start: 0.7060 (m-80) cc_final: 0.6590 (m-80) REVERT: F 141 GLN cc_start: 0.8982 (mt0) cc_final: 0.8745 (mt0) REVERT: F 180 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7584 (tm) REVERT: F 188 MET cc_start: 0.9107 (mmm) cc_final: 0.8626 (mpp) REVERT: F 193 ILE cc_start: 0.9491 (pp) cc_final: 0.9274 (pp) outliers start: 107 outliers final: 47 residues processed: 227 average time/residue: 0.5651 time to fit residues: 153.3094 Evaluate side-chains 184 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 71 TRP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 59 ARG Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 180 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 88 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 274 GLN D 536 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.095355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056706 restraints weight = 66051.395| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.31 r_work: 0.2686 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26932 Z= 0.240 Angle : 0.751 26.225 36899 Z= 0.362 Chirality : 0.070 1.952 4109 Planarity : 0.004 0.049 4367 Dihedral : 20.744 179.939 4680 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.37 % Allowed : 27.92 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 2930 helix: 2.02 (0.14), residues: 1400 sheet: 0.09 (0.25), residues: 399 loop : -0.41 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 534 TYR 0.017 0.002 TYR E 105 PHE 0.023 0.002 PHE E 72 TRP 0.015 0.001 TRP H 185 HIS 0.008 0.001 HIS H 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (26924) covalent geometry : angle 0.73033 / 0.36 (36891) SS BOND : bond 0.00671 / 0.35 ( 1) SS BOND : angle 0.43703 / 0.25 ( 2) hydrogen bonds : bond 0.05416 / 3.55 ( 1258) hydrogen bonds : angle 4.45510 / 3.26 ( 3573) metal coordination : bond 0.01125 / 0.41 ( 7) metal coordination : angle 13.76853 / 6.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 137 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8844 (p90) REVERT: E 356 GLU cc_start: 0.9057 (mp0) cc_final: 0.8795 (pm20) REVERT: D 5 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7993 (pt) REVERT: D 20 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7701 (tm) REVERT: D 122 ASP cc_start: 0.9124 (t0) cc_final: 0.8778 (t0) REVERT: B 187 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: B 394 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9118 (mt) REVERT: B 446 GLN cc_start: 0.8006 (tt0) cc_final: 0.7681 (pm20) REVERT: C 64 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: C 309 MET cc_start: 0.7623 (ptp) cc_final: 0.7221 (pmm) REVERT: A 294 MET cc_start: 0.8970 (mmp) cc_final: 0.8688 (mmp) REVERT: A 308 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.7483 (tpp-160) REVERT: H 30 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (p0) REVERT: H 188 MET cc_start: 0.9178 (mmm) cc_final: 0.8898 (mtp) REVERT: H 189 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8063 (ttp-110) REVERT: F 16 PHE cc_start: 0.8083 (m-80) cc_final: 0.7780 (m-80) REVERT: F 42 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: F 69 PHE cc_start: 0.7145 (m-80) cc_final: 0.6754 (m-80) REVERT: F 141 GLN cc_start: 0.8973 (mt0) cc_final: 0.8745 (mt0) REVERT: F 166 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9195 (tp) REVERT: F 188 MET cc_start: 0.9126 (mmm) cc_final: 0.8668 (mpp) REVERT: F 193 ILE cc_start: 0.9483 (pp) cc_final: 0.9275 (pp) REVERT: F 211 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5812 (m-70) outliers start: 89 outliers final: 48 residues processed: 215 average time/residue: 0.5963 time to fit residues: 151.7685 Evaluate side-chains 186 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 128 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 278 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057475 restraints weight = 65844.500| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.32 r_work: 0.2707 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26932 Z= 0.163 Angle : 0.720 26.097 36899 Z= 0.347 Chirality : 0.069 1.977 4109 Planarity : 0.004 0.051 4367 Dihedral : 20.642 179.691 4679 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.99 % Allowed : 28.52 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2930 helix: 2.02 (0.14), residues: 1403 sheet: 0.14 (0.25), residues: 411 loop : -0.42 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 534 TYR 0.016 0.001 TYR B 105 PHE 0.022 0.001 PHE H 120 TRP 0.024 0.001 TRP H 209 HIS 0.011 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (26924) covalent geometry : angle 0.70517 / 0.35 (36891) SS BOND : bond 0.00480 / 0.25 ( 1) SS BOND : angle 0.44125 / 0.26 ( 2) hydrogen bonds : bond 0.04937 / 3.24 ( 1258) hydrogen bonds : angle 4.36083 / 3.19 ( 3573) metal coordination : bond 0.00907 / 0.34 ( 7) metal coordination : angle 11.52262 / 5.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 140 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8885 (p90) REVERT: E 309 MET cc_start: 0.8831 (mtm) cc_final: 0.8535 (mmm) REVERT: E 356 GLU cc_start: 0.9061 (mp0) cc_final: 0.8786 (pm20) REVERT: D 5 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7990 (pp) REVERT: D 20 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7619 (tm) REVERT: D 122 ASP cc_start: 0.9136 (t0) cc_final: 0.8764 (t0) REVERT: D 300 ARG cc_start: 0.7276 (ttt180) cc_final: 0.6901 (ttm-80) REVERT: B 187 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: B 394 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9112 (mt) REVERT: B 446 GLN cc_start: 0.7988 (tt0) cc_final: 0.7651 (pm20) REVERT: C 64 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: C 283 MET cc_start: 0.3684 (OUTLIER) cc_final: 0.3135 (mmp) REVERT: A 294 MET cc_start: 0.8990 (mmp) cc_final: 0.8665 (mmp) REVERT: A 308 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7510 (tpp-160) REVERT: H 30 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7437 (p0) REVERT: H 188 MET cc_start: 0.9149 (mmm) cc_final: 0.8882 (mtp) REVERT: H 189 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8104 (ttp-110) REVERT: F 16 PHE cc_start: 0.7968 (m-80) cc_final: 0.7671 (m-80) REVERT: F 42 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8217 (m-80) REVERT: F 69 PHE cc_start: 0.7172 (m-80) cc_final: 0.6789 (m-80) REVERT: F 141 GLN cc_start: 0.8967 (mt0) cc_final: 0.8740 (mt0) REVERT: F 188 MET cc_start: 0.9187 (mmm) cc_final: 0.8751 (mpp) REVERT: F 193 ILE cc_start: 0.9482 (pp) cc_final: 0.9275 (pp) outliers start: 79 outliers final: 46 residues processed: 208 average time/residue: 0.5639 time to fit residues: 139.4818 Evaluate side-chains 188 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 133 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 134 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 294 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 4 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058622 restraints weight = 65382.783| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.43 r_work: 0.2743 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26932 Z= 0.121 Angle : 0.700 26.286 36899 Z= 0.336 Chirality : 0.068 1.998 4109 Planarity : 0.004 0.062 4367 Dihedral : 20.475 179.673 4678 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.50 % Allowed : 29.17 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2930 helix: 2.05 (0.14), residues: 1401 sheet: 0.32 (0.25), residues: 399 loop : -0.35 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 534 TYR 0.015 0.001 TYR C 105 PHE 0.027 0.001 PHE H 120 TRP 0.027 0.001 TRP H 209 HIS 0.009 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (26924) covalent geometry : angle 0.68925 / 0.34 (36891) SS BOND : bond 0.00383 / 0.20 ( 1) SS BOND : angle 0.51073 / 0.30 ( 2) hydrogen bonds : bond 0.04325 / 2.82 ( 1258) hydrogen bonds : angle 4.24875 / 3.12 ( 3573) metal coordination : bond 0.00672 / 0.26 ( 7) metal coordination : angle 9.77584 / 4.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8841 (p90) REVERT: E 309 MET cc_start: 0.8813 (mtm) cc_final: 0.8492 (mmm) REVERT: E 356 GLU cc_start: 0.9069 (mp0) cc_final: 0.8794 (pm20) REVERT: D 5 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7746 (pp) REVERT: D 20 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7558 (tm) REVERT: D 122 ASP cc_start: 0.9174 (t0) cc_final: 0.8784 (t0) REVERT: B 187 TRP cc_start: 0.8987 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: B 394 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9111 (mt) REVERT: B 446 GLN cc_start: 0.7939 (tt0) cc_final: 0.7644 (pm20) REVERT: C 23 GLN cc_start: 0.8883 (mt0) cc_final: 0.8654 (mm-40) REVERT: C 64 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: C 249 TYR cc_start: 0.8393 (t80) cc_final: 0.8065 (t80) REVERT: C 309 MET cc_start: 0.7539 (ptp) cc_final: 0.7223 (pmm) REVERT: A 294 MET cc_start: 0.8971 (mmp) cc_final: 0.8647 (mmp) REVERT: A 308 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7560 (tpp-160) REVERT: H 188 MET cc_start: 0.9215 (mmm) cc_final: 0.8962 (mtp) REVERT: H 189 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8145 (ttp-110) REVERT: F 16 PHE cc_start: 0.7901 (m-80) cc_final: 0.7596 (m-80) REVERT: F 42 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: F 45 TYR cc_start: 0.8332 (m-80) cc_final: 0.8051 (m-80) REVERT: F 52 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7759 (ptm-80) REVERT: F 69 PHE cc_start: 0.7041 (m-80) cc_final: 0.6530 (m-80) REVERT: F 141 GLN cc_start: 0.8965 (mt0) cc_final: 0.8745 (mt0) REVERT: F 188 MET cc_start: 0.9216 (mmm) cc_final: 0.8831 (mpp) REVERT: F 193 ILE cc_start: 0.9487 (pp) cc_final: 0.9271 (pp) REVERT: F 211 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5542 (m-70) outliers start: 66 outliers final: 37 residues processed: 207 average time/residue: 0.6134 time to fit residues: 149.4328 Evaluate side-chains 184 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 530 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 17 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.095093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056395 restraints weight = 65954.051| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.36 r_work: 0.2682 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26932 Z= 0.229 Angle : 0.762 28.109 36899 Z= 0.364 Chirality : 0.070 1.970 4109 Planarity : 0.004 0.069 4367 Dihedral : 20.525 179.932 4675 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.58 % Allowed : 29.43 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.16), residues: 2930 helix: 2.05 (0.14), residues: 1402 sheet: 0.16 (0.24), residues: 411 loop : -0.41 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 534 TYR 0.018 0.001 TYR B 249 PHE 0.036 0.002 PHE H 120 TRP 0.033 0.001 TRP H 209 HIS 0.009 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (26924) covalent geometry : angle 0.73813 / 0.36 (36891) SS BOND : bond 0.00770 / 0.41 ( 1) SS BOND : angle 0.35902 / 0.21 ( 2) hydrogen bonds : bond 0.05172 / 3.40 ( 1258) hydrogen bonds : angle 4.36205 / 3.20 ( 3573) metal coordination : bond 0.01181 / 0.48 ( 7) metal coordination : angle 14.94379 / 7.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8929 (p90) REVERT: E 309 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8516 (mmm) REVERT: E 356 GLU cc_start: 0.9068 (mp0) cc_final: 0.8817 (pm20) REVERT: E 538 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7690 (tmm) REVERT: D 122 ASP cc_start: 0.9185 (t0) cc_final: 0.8834 (t0) REVERT: B 187 TRP cc_start: 0.9076 (OUTLIER) cc_final: 0.7638 (m-10) REVERT: B 394 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9139 (mt) REVERT: C 23 GLN cc_start: 0.8916 (mt0) cc_final: 0.8677 (mm-40) REVERT: C 64 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: C 249 TYR cc_start: 0.8483 (t80) cc_final: 0.8104 (t80) REVERT: C 283 MET cc_start: 0.3811 (OUTLIER) cc_final: 0.3281 (mmp) REVERT: C 309 MET cc_start: 0.7559 (ptp) cc_final: 0.7193 (pmm) REVERT: A 294 MET cc_start: 0.8984 (mmp) cc_final: 0.8563 (mmp) REVERT: A 308 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7575 (tpp-160) REVERT: H 188 MET cc_start: 0.9240 (mmm) cc_final: 0.9010 (mtp) REVERT: H 189 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8185 (ttp-110) REVERT: F 16 PHE cc_start: 0.7897 (m-80) cc_final: 0.7568 (m-80) REVERT: F 42 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: F 69 PHE cc_start: 0.7230 (m-80) cc_final: 0.6882 (m-80) REVERT: F 188 MET cc_start: 0.9224 (mmm) cc_final: 0.8799 (mpp) REVERT: F 193 ILE cc_start: 0.9492 (pp) cc_final: 0.9283 (pp) REVERT: F 211 HIS cc_start: 0.5891 (OUTLIER) cc_final: 0.5680 (m-70) outliers start: 68 outliers final: 41 residues processed: 193 average time/residue: 0.5768 time to fit residues: 131.8678 Evaluate side-chains 182 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 538 MET Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 283 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 182 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058562 restraints weight = 65525.148| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.39 r_work: 0.2740 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26932 Z= 0.120 Angle : 0.724 26.366 36899 Z= 0.343 Chirality : 0.068 2.014 4109 Planarity : 0.004 0.070 4367 Dihedral : 20.421 179.938 4675 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 30.04 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2930 helix: 2.06 (0.14), residues: 1399 sheet: 0.33 (0.25), residues: 399 loop : -0.37 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 534 TYR 0.016 0.001 TYR H 202 PHE 0.034 0.001 PHE H 120 TRP 0.037 0.001 TRP H 209 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (26924) covalent geometry : angle 0.70625 / 0.34 (36891) SS BOND : bond 0.00382 / 0.20 ( 1) SS BOND : angle 0.72682 / 0.42 ( 2) hydrogen bonds : bond 0.04267 / 2.81 ( 1258) hydrogen bonds : angle 4.21441 / 3.10 ( 3573) metal coordination : bond 0.00556 / 0.20 ( 7) metal coordination : angle 12.58679 / 6.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8873 (p90) REVERT: E 309 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8595 (mmm) REVERT: E 356 GLU cc_start: 0.9069 (mp0) cc_final: 0.8819 (pm20) REVERT: E 538 MET cc_start: 0.7899 (tmm) cc_final: 0.7666 (tmm) REVERT: D 20 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7699 (tm) REVERT: D 122 ASP cc_start: 0.9177 (t0) cc_final: 0.8808 (t0) REVERT: B 187 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.7690 (m-10) REVERT: B 394 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9127 (mt) REVERT: B 446 GLN cc_start: 0.7911 (tt0) cc_final: 0.7632 (pm20) REVERT: C 23 GLN cc_start: 0.8893 (mt0) cc_final: 0.8649 (mm-40) REVERT: C 64 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: C 283 MET cc_start: 0.3723 (OUTLIER) cc_final: 0.3213 (mmp) REVERT: A 294 MET cc_start: 0.8987 (mmp) cc_final: 0.8657 (mmp) REVERT: A 308 ARG cc_start: 0.7917 (tpp-160) cc_final: 0.7660 (tpp-160) REVERT: H 30 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7474 (p0) REVERT: H 189 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8232 (ttp-110) REVERT: F 16 PHE cc_start: 0.7906 (m-80) cc_final: 0.7563 (m-80) REVERT: F 52 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7743 (ptm-80) REVERT: F 69 PHE cc_start: 0.6974 (m-80) cc_final: 0.6509 (m-80) REVERT: F 141 GLN cc_start: 0.9136 (mt0) cc_final: 0.8874 (mp10) REVERT: F 188 MET cc_start: 0.9225 (mmm) cc_final: 0.8784 (mpp) REVERT: F 193 ILE cc_start: 0.9496 (pp) cc_final: 0.9285 (pp) REVERT: F 211 HIS cc_start: 0.5798 (OUTLIER) cc_final: 0.5583 (m-70) outliers start: 58 outliers final: 37 residues processed: 193 average time/residue: 0.5606 time to fit residues: 127.1668 Evaluate side-chains 184 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 45 TYR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 211 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 38 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.096912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058611 restraints weight = 65458.697| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.34 r_work: 0.2707 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26932 Z= 0.128 Angle : 0.719 26.318 36899 Z= 0.344 Chirality : 0.068 2.006 4109 Planarity : 0.004 0.061 4367 Dihedral : 20.385 179.905 4674 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.12 % Allowed : 30.04 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 2930 helix: 2.06 (0.14), residues: 1401 sheet: 0.35 (0.25), residues: 399 loop : -0.36 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 534 TYR 0.021 0.001 TYR H 45 PHE 0.027 0.001 PHE H 120 TRP 0.034 0.001 TRP H 209 HIS 0.008 0.001 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (26924) covalent geometry : angle 0.70774 / 0.34 (36891) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 1.28347 / 0.74 ( 2) hydrogen bonds : bond 0.04266 / 2.82 ( 1258) hydrogen bonds : angle 4.20979 / 3.10 ( 3573) metal coordination : bond 0.00650 / 0.37 ( 7) metal coordination : angle 9.90794 / 5.11 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5860 Ramachandran restraints generated. 2930 Oldfield, 0 Emsley, 2930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8872 (p90) REVERT: E 309 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: E 356 GLU cc_start: 0.9057 (mp0) cc_final: 0.8805 (pm20) REVERT: E 538 MET cc_start: 0.7890 (tmm) cc_final: 0.7667 (tmm) REVERT: D 5 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7821 (pp) REVERT: D 20 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7775 (tm) REVERT: D 122 ASP cc_start: 0.9176 (t0) cc_final: 0.8806 (t0) REVERT: B 187 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: B 394 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9115 (mt) REVERT: B 446 GLN cc_start: 0.7909 (tt0) cc_final: 0.7630 (pm20) REVERT: C 23 GLN cc_start: 0.8889 (mt0) cc_final: 0.8644 (mm-40) REVERT: C 64 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: C 283 MET cc_start: 0.3770 (OUTLIER) cc_final: 0.3182 (mmp) REVERT: A 294 MET cc_start: 0.8957 (mmp) cc_final: 0.8574 (mmp) REVERT: A 308 ARG cc_start: 0.7918 (tpp-160) cc_final: 0.7669 (tpp-160) REVERT: H 30 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7516 (p0) REVERT: H 147 PHE cc_start: 0.8117 (m-80) cc_final: 0.7908 (m-80) REVERT: H 189 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8212 (ttp-110) REVERT: F 16 PHE cc_start: 0.7916 (m-80) cc_final: 0.7559 (m-80) REVERT: F 52 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7771 (ptm-80) REVERT: F 69 PHE cc_start: 0.6923 (m-80) cc_final: 0.6434 (m-80) REVERT: F 188 MET cc_start: 0.9227 (mmm) cc_final: 0.8779 (mpp) REVERT: F 193 ILE cc_start: 0.9493 (pp) cc_final: 0.9285 (pp) outliers start: 56 outliers final: 38 residues processed: 186 average time/residue: 0.5750 time to fit residues: 125.4694 Evaluate side-chains 187 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 187 TRP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 510 ARG Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain H residue 30 ASN Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 213 SER Chi-restraints excluded: chain F residue 42 PHE Chi-restraints excluded: chain F residue 45 TYR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 89 ARG Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 268 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 16 optimal weight: 0.0170 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 263 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 overall best weight: 3.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056056 restraints weight = 65496.824| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.31 r_work: 0.2630 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26932 Z= 0.226 Angle : 0.774 26.258 36899 Z= 0.373 Chirality : 0.070 1.981 4109 Planarity : 0.004 0.068 4367 Dihedral : 20.478 179.749 4674 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.97 % Allowed : 30.30 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.16), residues: 2930 helix: 2.01 (0.14), residues: 1405 sheet: 0.17 (0.25), residues: 399 loop : -0.43 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 534 TYR 0.020 0.001 TYR H 45 PHE 0.040 0.002 PHE H 147 TRP 0.036 0.002 TRP H 209 HIS 0.008 0.001 HIS E 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (26924) covalent geometry : angle 0.75588 / 0.37 (36891) SS BOND : bond 0.00606 / 0.32 ( 1) SS BOND : angle 1.74310 / 0.95 ( 2) hydrogen bonds : bond 0.05277 / 3.50 ( 1258) hydrogen bonds : angle 4.36426 / 3.22 ( 3573) metal coordination : bond 0.01008 / 0.43 ( 7) metal coordination : angle 13.02117 / 6.54 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9488.48 seconds wall clock time: 162 minutes 11.96 seconds (9731.96 seconds total)