Starting phenix.real_space_refine on Mon Aug 25 01:51:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh6_34753/08_2025/8hh6_34753.map" } resolution = 2.9 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= -0.000 sd= 0.001 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 P 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24277 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.74, per 1000 atoms: 0.24 Number of scatterers: 24277 At special positions: 0 Unit cell: (124.08, 124.08, 153.12, 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) S 77 16.00 P 18 15.00 Mg 6 11.99 O 4670 8.00 N 4219 7.00 C 15287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 21 sheets defined 48.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.112A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.588A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.502A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.706A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.535A pdb=" N ALA A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.530A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.910A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 removed outlier: 4.126A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.501A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.723A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.556A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.615A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.735A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.720A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.635A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 396 Processing helix chain 'B' and resid 402 through 412 removed outlier: 3.529A pdb=" N LEU B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.788A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.516A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 498 removed outlier: 3.580A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.311A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.583A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.558A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.641A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.575A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.742A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 396 No H-bonds generated for 'chain 'C' and resid 394 through 396' Processing helix chain 'C' and resid 403 through 421 Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.952A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.655A pdb=" N ASP C 465 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 180 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 5.195A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.786A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.809A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.524A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.658A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.818A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.526A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 4.945A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 removed outlier: 3.568A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.625A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 388 removed outlier: 3.973A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.724A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.553A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 4.866A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.069A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 removed outlier: 3.586A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.707A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.913A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.938A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.830A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 5.415A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA G 57 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.902A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.583A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 208 through 284 removed outlier: 3.532A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.690A pdb=" N GLN G 267 " --> pdb=" O ASN G 263 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.920A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.939A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.379A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.335A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.723A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.349A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.402A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 54 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.786A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.538A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.424A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 4.373A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.486A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.698A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.478A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.529A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.452A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.576A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3351 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8230 1.34 - 1.46: 4668 1.46 - 1.58: 11609 1.58 - 1.70: 23 1.70 - 1.82: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" O2 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O1 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C VAL G 43 " pdb=" N PRO G 44 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.12e+00 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 33240 2.80 - 5.60: 231 5.60 - 8.40: 6 8.40 - 11.20: 1 11.20 - 14.00: 1 Bond angle restraints: 33479 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 112.83 107.40 5.43 9.90e-01 1.02e+00 3.00e+01 angle pdb=" C ARG A 390 " pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 121.92 114.70 7.22 1.73e+00 3.34e-01 1.74e+01 angle pdb=" CA LEU G 68 " pdb=" CB LEU G 68 " pdb=" CG LEU G 68 " ideal model delta sigma weight residual 116.30 130.30 -14.00 3.50e+00 8.16e-02 1.60e+01 angle pdb=" N ILE F 340 " pdb=" CA ILE F 340 " pdb=" C ILE F 340 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N VAL A 378 " pdb=" CA VAL A 378 " pdb=" C VAL A 378 " ideal model delta sigma weight residual 113.71 110.11 3.60 9.50e-01 1.11e+00 1.44e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 14803 35.42 - 70.84: 262 70.84 - 106.27: 26 106.27 - 141.69: 0 141.69 - 177.11: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 117.11 -177.11 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 102.65 -162.65 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" CA LYS G 187 " pdb=" C LYS G 187 " pdb=" N LEU G 188 " pdb=" CA LEU G 188 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2514 0.035 - 0.069: 897 0.069 - 0.104: 285 0.104 - 0.139: 153 0.139 - 0.174: 7 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CB THR F 130 " pdb=" CA THR F 130 " pdb=" OG1 THR F 130 " pdb=" CG2 THR F 130 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU G 68 " pdb=" CB LEU G 68 " pdb=" CD1 LEU G 68 " pdb=" CD2 LEU G 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA LYS G 74 " pdb=" N LYS G 74 " pdb=" C LYS G 74 " pdb=" CB LYS G 74 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 140 " -0.049 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO G 141 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 354 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO A 355 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO C 110 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.026 5.00e-02 4.00e+02 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 143 2.58 - 3.16: 19908 3.16 - 3.74: 37008 3.74 - 4.32: 51982 4.32 - 4.90: 88772 Nonbonded interactions: 197813 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.002 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP B 602 " model vdw 2.020 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 603 " model vdw 2.021 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.032 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.037 2.170 ... (remaining 197808 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 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.880 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24684 Z= 0.129 Angle : 0.580 14.000 33479 Z= 0.329 Chirality : 0.044 0.174 3856 Planarity : 0.004 0.075 4363 Dihedral : 13.715 177.112 9381 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.15), residues: 3115 helix: 1.71 (0.15), residues: 1261 sheet: 1.12 (0.23), residues: 533 loop : 0.42 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.013 0.001 TYR B 248 PHE 0.011 0.001 PHE D 125 HIS 0.007 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00251 (24684) covalent geometry : angle 0.57981 (33479) hydrogen bonds : bond 0.15218 ( 1182) hydrogen bonds : angle 6.06933 ( 3351) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 401 ASP cc_start: 0.8318 (m-30) cc_final: 0.7960 (t0) REVERT: D 201 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 311 ASP cc_start: 0.8072 (t0) cc_final: 0.7657 (t0) REVERT: E 149 ILE cc_start: 0.9021 (mt) cc_final: 0.8715 (mm) REVERT: F 389 MET cc_start: 0.8857 (tpp) cc_final: 0.8560 (tpp) REVERT: G 40 LYS cc_start: 0.6963 (mmpt) cc_final: 0.6522 (mmpt) REVERT: G 187 LYS cc_start: 0.4656 (tmtt) cc_final: 0.4067 (tptp) REVERT: G 189 LEU cc_start: 0.7614 (mm) cc_final: 0.7314 (tp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.7344 time to fit residues: 198.6738 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN E 423 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.090379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069121 restraints weight = 47189.892| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.46 r_work: 0.2777 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24684 Z= 0.185 Angle : 0.575 10.753 33479 Z= 0.303 Chirality : 0.047 0.160 3856 Planarity : 0.005 0.060 4363 Dihedral : 8.703 150.346 3580 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.21 % Allowed : 7.79 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.15), residues: 3115 helix: 1.58 (0.15), residues: 1271 sheet: 0.91 (0.22), residues: 538 loop : 0.29 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 404 TYR 0.011 0.001 TYR B 248 PHE 0.022 0.001 PHE F 125 HIS 0.004 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00452 (24684) covalent geometry : angle 0.57538 (33479) hydrogen bonds : bond 0.04939 ( 1182) hydrogen bonds : angle 4.99617 ( 3351) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 401 ASP cc_start: 0.8199 (m-30) cc_final: 0.7578 (t0) REVERT: B 181 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8628 (m-30) REVERT: B 407 GLN cc_start: 0.8597 (tp-100) cc_final: 0.7927 (mm-40) REVERT: C 191 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (mtt) REVERT: D 56 ASP cc_start: 0.8523 (t0) cc_final: 0.8146 (t0) REVERT: D 201 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8281 (tp30) REVERT: D 311 ASP cc_start: 0.8851 (t70) cc_final: 0.8302 (t0) REVERT: E 397 LYS cc_start: 0.8314 (tptp) cc_final: 0.7994 (mmpt) REVERT: F 389 MET cc_start: 0.8602 (tpp) cc_final: 0.8370 (tpp) REVERT: G 187 LYS cc_start: 0.4949 (tmtt) cc_final: 0.4419 (tptp) REVERT: G 189 LEU cc_start: 0.7954 (mm) cc_final: 0.7677 (tp) outliers start: 31 outliers final: 8 residues processed: 182 average time/residue: 0.7373 time to fit residues: 154.0466 Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 176 optimal weight: 0.0000 chunk 23 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN E 8 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.071924 restraints weight = 46934.658| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.50 r_work: 0.2828 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24684 Z= 0.100 Angle : 0.494 10.865 33479 Z= 0.257 Chirality : 0.043 0.149 3856 Planarity : 0.004 0.051 4363 Dihedral : 7.845 140.372 3580 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.21 % Allowed : 9.77 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.15), residues: 3115 helix: 1.80 (0.15), residues: 1277 sheet: 0.94 (0.22), residues: 537 loop : 0.34 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 404 TYR 0.011 0.001 TYR G 220 PHE 0.013 0.001 PHE G 126 HIS 0.003 0.000 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00216 (24684) covalent geometry : angle 0.49401 (33479) hydrogen bonds : bond 0.03720 ( 1182) hydrogen bonds : angle 4.66392 ( 3351) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 ASP cc_start: 0.8142 (m-30) cc_final: 0.7540 (t0) REVERT: B 89 ARG cc_start: 0.8603 (ptp-110) cc_final: 0.8136 (ptp90) REVERT: B 188 ASP cc_start: 0.8650 (m-30) cc_final: 0.8423 (OUTLIER) REVERT: B 347 ASP cc_start: 0.8756 (m-30) cc_final: 0.8555 (p0) REVERT: B 407 GLN cc_start: 0.8544 (tp-100) cc_final: 0.7952 (mm-40) REVERT: C 95 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: D 56 ASP cc_start: 0.8529 (t0) cc_final: 0.8133 (t0) REVERT: D 201 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8550 (tm-30) REVERT: D 253 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8455 (m-40) REVERT: D 311 ASP cc_start: 0.8916 (t70) cc_final: 0.8610 (t0) REVERT: E 2 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7897 (m) REVERT: E 149 ILE cc_start: 0.9118 (mt) cc_final: 0.8789 (mm) REVERT: E 379 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 384 ILE cc_start: 0.6354 (mm) cc_final: 0.6132 (mm) REVERT: E 397 LYS cc_start: 0.8336 (tptp) cc_final: 0.8039 (mmpt) REVERT: F 365 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: F 389 MET cc_start: 0.8569 (tpp) cc_final: 0.8323 (tpp) REVERT: G 187 LYS cc_start: 0.5180 (tmtt) cc_final: 0.4888 (tptp) REVERT: G 189 LEU cc_start: 0.7920 (mm) cc_final: 0.7706 (tp) outliers start: 31 outliers final: 9 residues processed: 197 average time/residue: 0.6770 time to fit residues: 154.6644 Evaluate side-chains 165 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 365 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 245 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN ** G 65 HIS ** 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 = 0.3286 r_free = 0.3286 target = 0.091420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070025 restraints weight = 46608.924| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.45 r_work: 0.2786 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24684 Z= 0.163 Angle : 0.529 9.035 33479 Z= 0.278 Chirality : 0.045 0.161 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.858 139.331 3580 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.02 % Allowed : 10.83 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.15), residues: 3115 helix: 1.79 (0.15), residues: 1271 sheet: 0.78 (0.22), residues: 529 loop : 0.22 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 300 TYR 0.010 0.001 TYR G 220 PHE 0.019 0.001 PHE F 125 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00397 (24684) covalent geometry : angle 0.52886 (33479) hydrogen bonds : bond 0.04489 ( 1182) hydrogen bonds : angle 4.70122 ( 3351) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 ASP cc_start: 0.8201 (m-30) cc_final: 0.7570 (t0) REVERT: B 89 ARG cc_start: 0.8668 (ptp-110) cc_final: 0.8121 (ptt-90) REVERT: B 172 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: B 173 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8852 (p) REVERT: B 347 ASP cc_start: 0.8861 (m-30) cc_final: 0.8595 (p0) REVERT: C 67 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: D 56 ASP cc_start: 0.8613 (t0) cc_final: 0.8232 (t0) REVERT: D 201 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8583 (tm-30) REVERT: D 311 ASP cc_start: 0.8973 (t70) cc_final: 0.8337 (t0) REVERT: E 149 ILE cc_start: 0.9161 (mt) cc_final: 0.8805 (mm) REVERT: E 397 LYS cc_start: 0.8239 (tptp) cc_final: 0.7887 (mmpt) REVERT: E 464 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: F 389 MET cc_start: 0.8581 (tpp) cc_final: 0.8307 (tpp) REVERT: G 148 ASP cc_start: 0.8666 (m-30) cc_final: 0.7843 (p0) REVERT: G 187 LYS cc_start: 0.5320 (tmtt) cc_final: 0.5085 (tptp) outliers start: 52 outliers final: 19 residues processed: 204 average time/residue: 0.6601 time to fit residues: 156.5770 Evaluate side-chains 173 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 267 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 77 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3289 r_free = 0.3289 target = 0.091645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.070201 restraints weight = 46375.367| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.47 r_work: 0.2792 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24684 Z= 0.138 Angle : 0.525 15.060 33479 Z= 0.272 Chirality : 0.045 0.152 3856 Planarity : 0.004 0.052 4363 Dihedral : 7.717 139.714 3580 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.02 % Allowed : 11.53 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.15), residues: 3115 helix: 1.81 (0.15), residues: 1278 sheet: 0.74 (0.22), residues: 529 loop : 0.20 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 266 TYR 0.017 0.001 TYR G 262 PHE 0.016 0.001 PHE F 125 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00331 (24684) covalent geometry : angle 0.52516 (33479) hydrogen bonds : bond 0.04193 ( 1182) hydrogen bonds : angle 4.62954 ( 3351) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7801 (ptm160) REVERT: A 401 ASP cc_start: 0.8205 (m-30) cc_final: 0.7596 (t0) REVERT: B 89 ARG cc_start: 0.8655 (ptp-110) cc_final: 0.8089 (ptt-90) REVERT: B 172 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: B 173 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 347 ASP cc_start: 0.8863 (m-30) cc_final: 0.8594 (p0) REVERT: B 407 GLN cc_start: 0.8719 (tm130) cc_final: 0.7889 (mm-40) REVERT: C 67 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 56 ASP cc_start: 0.8597 (t0) cc_final: 0.8236 (t0) REVERT: D 201 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8601 (tm-30) REVERT: D 311 ASP cc_start: 0.8990 (t70) cc_final: 0.8383 (t0) REVERT: E 1 MET cc_start: 0.6496 (tpp) cc_final: 0.6216 (tpp) REVERT: E 149 ILE cc_start: 0.9153 (mt) cc_final: 0.8794 (mm) REVERT: E 333 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7854 (ttp-170) REVERT: E 379 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7424 (mt-10) REVERT: E 397 LYS cc_start: 0.8228 (tptp) cc_final: 0.7870 (mmpt) REVERT: F 389 MET cc_start: 0.8576 (tpp) cc_final: 0.8293 (tpp) REVERT: G 148 ASP cc_start: 0.8692 (m-30) cc_final: 0.7913 (p0) REVERT: G 187 LYS cc_start: 0.5439 (tmtt) cc_final: 0.4702 (tptp) outliers start: 52 outliers final: 23 residues processed: 198 average time/residue: 0.6900 time to fit residues: 159.4818 Evaluate side-chains 179 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 333 ARG Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 165 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 273 optimal weight: 7.9990 chunk 278 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3251 r_free = 0.3251 target = 0.089298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.067846 restraints weight = 46964.694| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.45 r_work: 0.2748 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24684 Z= 0.226 Angle : 0.590 15.951 33479 Z= 0.308 Chirality : 0.048 0.163 3856 Planarity : 0.005 0.051 4363 Dihedral : 8.121 143.096 3580 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 12.19 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1266 sheet: 0.54 (0.22), residues: 529 loop : 0.02 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 300 TYR 0.017 0.001 TYR G 262 PHE 0.021 0.002 PHE F 125 HIS 0.005 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00558 (24684) covalent geometry : angle 0.59010 (33479) hydrogen bonds : bond 0.05182 ( 1182) hydrogen bonds : angle 4.78523 ( 3351) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 1.058 Fit side-chains REVERT: A 171 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7855 (ptm160) REVERT: A 401 ASP cc_start: 0.8232 (m-30) cc_final: 0.7581 (t0) REVERT: B 172 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: B 247 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8729 (mt-10) REVERT: C 67 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: D 56 ASP cc_start: 0.8738 (t0) cc_final: 0.8382 (t0) REVERT: D 201 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8627 (tm-30) REVERT: D 311 ASP cc_start: 0.9038 (t70) cc_final: 0.8461 (t0) REVERT: E 1 MET cc_start: 0.6828 (tpp) cc_final: 0.6592 (tpp) REVERT: F 389 MET cc_start: 0.8523 (tpp) cc_final: 0.8260 (tpp) REVERT: G 46 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6611 (tpt) REVERT: G 187 LYS cc_start: 0.5646 (tmtt) cc_final: 0.5366 (tptp) outliers start: 57 outliers final: 32 residues processed: 204 average time/residue: 0.6493 time to fit residues: 155.2195 Evaluate side-chains 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 296 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 HIS ** G 65 HIS ** 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 = 0.3235 r_free = 0.3235 target = 0.088342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.067183 restraints weight = 46936.000| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.42 r_work: 0.2730 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24684 Z= 0.261 Angle : 0.618 13.973 33479 Z= 0.324 Chirality : 0.049 0.177 3856 Planarity : 0.005 0.050 4363 Dihedral : 8.374 148.046 3580 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.26 % Allowed : 12.89 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1262 sheet: 0.41 (0.22), residues: 529 loop : -0.13 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 300 TYR 0.016 0.002 TYR G 262 PHE 0.022 0.002 PHE F 125 HIS 0.006 0.001 HIS E 200 Details of bonding type rmsd covalent geometry : bond 0.00645 (24684) covalent geometry : angle 0.61842 (33479) hydrogen bonds : bond 0.05484 ( 1182) hydrogen bonds : angle 4.86977 ( 3351) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 1.014 Fit side-chains REVERT: A 171 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: A 401 ASP cc_start: 0.8297 (m-30) cc_final: 0.7605 (t0) REVERT: B 172 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: B 181 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: B 409 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8040 (tptt) REVERT: C 67 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: D 56 ASP cc_start: 0.8670 (t0) cc_final: 0.8366 (t0) REVERT: D 201 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8629 (tm-30) REVERT: D 311 ASP cc_start: 0.9109 (t70) cc_final: 0.8489 (t0) REVERT: F 389 MET cc_start: 0.8521 (tpp) cc_final: 0.8264 (tpp) REVERT: G 3 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7332 (p) REVERT: G 46 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6547 (tpt) REVERT: G 148 ASP cc_start: 0.8633 (m-30) cc_final: 0.7840 (p0) REVERT: G 187 LYS cc_start: 0.5685 (tmtt) cc_final: 0.5443 (tptp) REVERT: G 241 MET cc_start: 0.6728 (ttt) cc_final: 0.6508 (ttm) outliers start: 58 outliers final: 36 residues processed: 205 average time/residue: 0.6561 time to fit residues: 157.5714 Evaluate side-chains 189 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 70 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 282 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3265 r_free = 0.3265 target = 0.090220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.069065 restraints weight = 46706.614| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.43 r_work: 0.2767 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24684 Z= 0.154 Angle : 0.551 13.634 33479 Z= 0.288 Chirality : 0.045 0.154 3856 Planarity : 0.005 0.052 4363 Dihedral : 8.017 149.522 3580 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.95 % Allowed : 13.32 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 3115 helix: 1.69 (0.15), residues: 1263 sheet: 0.52 (0.22), residues: 525 loop : -0.05 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 300 TYR 0.015 0.001 TYR G 262 PHE 0.016 0.001 PHE F 125 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00370 (24684) covalent geometry : angle 0.55064 (33479) hydrogen bonds : bond 0.04554 ( 1182) hydrogen bonds : angle 4.70379 ( 3351) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 1.040 Fit side-chains REVERT: A 171 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7823 (ptm160) REVERT: A 401 ASP cc_start: 0.8269 (m-30) cc_final: 0.7583 (t0) REVERT: B 172 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: B 407 GLN cc_start: 0.8741 (tp40) cc_final: 0.8029 (mm-40) REVERT: B 409 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8013 (tptt) REVERT: C 67 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: D 56 ASP cc_start: 0.8664 (t0) cc_final: 0.8282 (t0) REVERT: D 201 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8624 (tm-30) REVERT: D 311 ASP cc_start: 0.9100 (t70) cc_final: 0.8500 (t0) REVERT: E 332 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8133 (mm-30) REVERT: E 344 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8119 (t) REVERT: F 389 MET cc_start: 0.8486 (tpp) cc_final: 0.8197 (tpp) REVERT: G 46 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6553 (tpt) REVERT: G 167 GLU cc_start: 0.5796 (pt0) cc_final: 0.5319 (pm20) REVERT: G 187 LYS cc_start: 0.5783 (tmtt) cc_final: 0.4752 (tttp) outliers start: 50 outliers final: 31 residues processed: 197 average time/residue: 0.6205 time to fit residues: 142.9136 Evaluate side-chains 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 154 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3270 r_free = 0.3270 target = 0.090535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.069226 restraints weight = 46911.524| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.45 r_work: 0.2773 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24684 Z= 0.151 Angle : 0.551 13.141 33479 Z= 0.287 Chirality : 0.045 0.310 3856 Planarity : 0.004 0.055 4363 Dihedral : 7.877 153.463 3580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.91 % Allowed : 13.43 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1268 sheet: 0.60 (0.22), residues: 508 loop : -0.04 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 300 TYR 0.014 0.001 TYR G 262 PHE 0.017 0.001 PHE F 125 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00364 (24684) covalent geometry : angle 0.55118 (33479) hydrogen bonds : bond 0.04431 ( 1182) hydrogen bonds : angle 4.65883 ( 3351) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7788 (ptm160) REVERT: B 172 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: B 407 GLN cc_start: 0.8764 (tp40) cc_final: 0.8042 (mm-40) REVERT: B 409 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8034 (tptt) REVERT: C 67 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: D 56 ASP cc_start: 0.8520 (t0) cc_final: 0.8161 (t0) REVERT: D 201 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8624 (tm-30) REVERT: D 311 ASP cc_start: 0.9105 (t70) cc_final: 0.8510 (t0) REVERT: E 332 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8135 (mm-30) REVERT: E 344 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8008 (t) REVERT: E 379 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 389 MET cc_start: 0.8442 (tpp) cc_final: 0.8141 (tpp) REVERT: G 46 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6565 (tpt) REVERT: G 148 ASP cc_start: 0.8615 (m-30) cc_final: 0.7817 (p0) REVERT: G 167 GLU cc_start: 0.5867 (pt0) cc_final: 0.5332 (pm20) REVERT: G 187 LYS cc_start: 0.5786 (tmtt) cc_final: 0.4763 (tttp) REVERT: G 244 MET cc_start: 0.8019 (mmt) cc_final: 0.7809 (mmp) outliers start: 49 outliers final: 34 residues processed: 192 average time/residue: 0.5284 time to fit residues: 119.1382 Evaluate side-chains 187 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 166 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 149 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 273 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3269 r_free = 0.3269 target = 0.090423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.069109 restraints weight = 46872.098| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.44 r_work: 0.2770 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24684 Z= 0.159 Angle : 0.557 12.962 33479 Z= 0.291 Chirality : 0.046 0.290 3856 Planarity : 0.005 0.058 4363 Dihedral : 7.867 156.683 3580 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.64 % Allowed : 13.86 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.15), residues: 3115 helix: 1.74 (0.15), residues: 1268 sheet: 0.58 (0.22), residues: 526 loop : -0.08 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 300 TYR 0.014 0.001 TYR G 262 PHE 0.017 0.001 PHE F 125 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00387 (24684) covalent geometry : angle 0.55683 (33479) hydrogen bonds : bond 0.04478 ( 1182) hydrogen bonds : angle 4.69315 ( 3351) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7783 (ptm160) REVERT: B 172 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: B 407 GLN cc_start: 0.8761 (tp40) cc_final: 0.8037 (mm-40) REVERT: D 56 ASP cc_start: 0.8548 (t0) cc_final: 0.8180 (t0) REVERT: D 201 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8640 (tm-30) REVERT: D 311 ASP cc_start: 0.9095 (t70) cc_final: 0.8505 (t0) REVERT: E 332 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8125 (mm-30) REVERT: E 344 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8011 (t) REVERT: E 379 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7436 (mt-10) REVERT: F 389 MET cc_start: 0.8429 (tpp) cc_final: 0.8128 (tpp) REVERT: G 46 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6568 (tpt) REVERT: G 167 GLU cc_start: 0.5812 (pt0) cc_final: 0.5281 (pm20) REVERT: G 187 LYS cc_start: 0.5853 (tmtt) cc_final: 0.4850 (tttp) outliers start: 42 outliers final: 35 residues processed: 189 average time/residue: 0.5852 time to fit residues: 130.2915 Evaluate side-chains 187 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 298 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 287 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 132 optimal weight: 8.9990 chunk 222 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** 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 = 0.3282 r_free = 0.3282 target = 0.091224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.070029 restraints weight = 46679.682| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.43 r_work: 0.2786 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24684 Z= 0.133 Angle : 0.534 12.737 33479 Z= 0.278 Chirality : 0.045 0.278 3856 Planarity : 0.004 0.058 4363 Dihedral : 7.699 159.475 3580 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.60 % Allowed : 14.02 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.15), residues: 3115 helix: 1.82 (0.15), residues: 1275 sheet: 0.62 (0.22), residues: 518 loop : 0.01 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 376 TYR 0.013 0.001 TYR G 262 PHE 0.015 0.001 PHE F 125 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00317 (24684) covalent geometry : angle 0.53366 (33479) hydrogen bonds : bond 0.04144 ( 1182) hydrogen bonds : angle 4.62031 ( 3351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7206.30 seconds wall clock time: 123 minutes 56.37 seconds (7436.37 seconds total)