Starting phenix.real_space_refine on Sat Jun 21 04:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh6_34753/06_2025/8hh6_34753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh6_34753/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh6_34753/06_2025/8hh6_34753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh6_34753/06_2025/8hh6_34753.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh6_34753/06_2025/8hh6_34753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh6_34753/06_2025/8hh6_34753.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.26, per 1000 atoms: 0.67 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: 6.13 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.80 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: 8.61 Time building geometry restraints manager: 7.22 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.050 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (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 HIS 0.007 0.001 HIS G 65 PHE 0.011 0.001 PHE D 125 TYR 0.013 0.001 TYR B 248 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.15218 ( 1182) hydrogen bonds : angle 6.06933 ( 3351) covalent geometry : bond 0.00251 (24684) covalent geometry : angle 0.57981 (33479) *********************** 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 : 2.767 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7598 (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: 0.7313 (tp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.4854 time to fit residues: 403.2520 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 : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 7.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.090456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.069027 restraints weight = 46586.572| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.44 r_work: 0.2763 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24684 Z= 0.219 Angle : 0.603 10.920 33479 Z= 0.318 Chirality : 0.048 0.166 3856 Planarity : 0.005 0.060 4363 Dihedral : 8.783 150.650 3580 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.36 % Allowed : 7.71 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.15), residues: 3115 helix: 1.55 (0.15), residues: 1263 sheet: 0.84 (0.22), residues: 538 loop : 0.23 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 470 PHE 0.023 0.002 PHE F 125 TYR 0.012 0.001 TYR G 262 ARG 0.008 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 1182) hydrogen bonds : angle 5.04102 ( 3351) covalent geometry : bond 0.00537 (24684) covalent geometry : angle 0.60290 (33479) *********************** 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 199 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 2.746 Fit side-chains revert: symmetry clash REVERT: A 401 ASP cc_start: 0.8220 (m-30) cc_final: 0.7591 (t0) REVERT: B 181 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8645 (m-30) REVERT: B 407 GLN cc_start: 0.8614 (tp-100) cc_final: 0.7966 (mm-40) REVERT: D 56 ASP cc_start: 0.8609 (t0) cc_final: 0.8252 (t0) REVERT: D 201 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8282 (tp30) REVERT: D 311 ASP cc_start: 0.8888 (t70) cc_final: 0.8339 (t0) REVERT: E 397 LYS cc_start: 0.8332 (tptp) cc_final: 0.7982 (mmpt) REVERT: F 389 MET cc_start: 0.8608 (tpp) cc_final: 0.8378 (tpp) REVERT: G 187 LYS cc_start: 0.4994 (tmtt) cc_final: 0.4451 (tptp) REVERT: G 189 LEU cc_start: 0.7978 (mm) cc_final: 0.7707 (tp) outliers start: 35 outliers final: 8 residues processed: 184 average time/residue: 1.3952 time to fit residues: 296.5475 Evaluate side-chains 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 469 MET 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 129 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.070029 restraints weight = 46654.909| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.45 r_work: 0.2792 rms_B_bonded: 2.90 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: 0.8843 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24684 Z= 0.130 Angle : 0.519 10.627 33479 Z= 0.271 Chirality : 0.045 0.152 3856 Planarity : 0.004 0.052 4363 Dihedral : 8.104 142.231 3580 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.67 % Allowed : 9.89 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 3115 helix: 1.67 (0.15), residues: 1277 sheet: 0.84 (0.22), residues: 539 loop : 0.19 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.015 0.001 PHE F 125 TYR 0.011 0.001 TYR G 220 ARG 0.005 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 1182) hydrogen bonds : angle 4.75574 ( 3351) covalent geometry : bond 0.00305 (24684) covalent geometry : angle 0.51852 (33479) *********************** 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 211 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 7.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 ASP cc_start: 0.8239 (m-30) cc_final: 0.7622 (t0) REVERT: B 89 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8152 (ptp90) REVERT: B 172 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: B 347 ASP cc_start: 0.8804 (m-30) cc_final: 0.8593 (p0) REVERT: B 407 GLN cc_start: 0.8598 (tp-100) cc_final: 0.7930 (mm-40) REVERT: D 56 ASP cc_start: 0.8576 (t0) cc_final: 0.8171 (t0) REVERT: D 201 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 253 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8406 (m-40) REVERT: D 311 ASP cc_start: 0.8969 (t70) cc_final: 0.8342 (t0) REVERT: F 389 MET cc_start: 0.8593 (tpp) cc_final: 0.8338 (tpp) REVERT: G 189 LEU cc_start: 0.7965 (mm) cc_final: 0.7759 (tp) outliers start: 43 outliers final: 15 residues processed: 199 average time/residue: 1.5231 time to fit residues: 352.7111 Evaluate side-chains 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 253 ASN 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 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 130 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.088935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.067582 restraints weight = 47039.445| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.44 r_work: 0.2736 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24684 Z= 0.253 Angle : 0.600 8.623 33479 Z= 0.316 Chirality : 0.049 0.165 3856 Planarity : 0.005 0.054 4363 Dihedral : 8.394 139.407 3580 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.26 % Allowed : 11.02 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1263 sheet: 0.55 (0.22), residues: 537 loop : -0.02 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 470 PHE 0.022 0.002 PHE F 125 TYR 0.013 0.001 TYR G 262 ARG 0.006 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1182) hydrogen bonds : angle 4.90758 ( 3351) covalent geometry : bond 0.00623 (24684) covalent geometry : angle 0.59958 (33479) *********************** 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 218 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 2.734 Fit side-chains REVERT: A 401 ASP cc_start: 0.8313 (m-30) cc_final: 0.7650 (t0) REVERT: A 402 LEU cc_start: 0.7743 (mp) cc_final: 0.7527 (tt) REVERT: B 172 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: B 347 ASP cc_start: 0.8895 (m-30) cc_final: 0.8655 (p0) REVERT: D 56 ASP cc_start: 0.8767 (t0) cc_final: 0.8403 (t0) REVERT: D 201 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8618 (tm-30) REVERT: D 311 ASP cc_start: 0.9019 (t70) cc_final: 0.8394 (t0) REVERT: F 389 MET cc_start: 0.8610 (tpp) cc_final: 0.8344 (tpp) REVERT: G 187 LYS cc_start: 0.5413 (tmtt) cc_final: 0.5167 (tptp) outliers start: 58 outliers final: 26 residues processed: 205 average time/residue: 1.3727 time to fit residues: 329.3567 Evaluate side-chains 173 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 4.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 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 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 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 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 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 276 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 247 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.092509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071146 restraints weight = 46547.979| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.44 r_work: 0.2806 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24684 Z= 0.106 Angle : 0.497 8.805 33479 Z= 0.261 Chirality : 0.044 0.148 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.713 138.666 3580 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.83 % Allowed : 12.54 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3115 helix: 1.83 (0.15), residues: 1269 sheet: 0.71 (0.22), residues: 525 loop : 0.15 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 363 PHE 0.011 0.001 PHE F 125 TYR 0.011 0.001 TYR G 220 ARG 0.003 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1182) hydrogen bonds : angle 4.59389 ( 3351) covalent geometry : bond 0.00234 (24684) covalent geometry : angle 0.49675 (33479) *********************** 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 214 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7745 (ptm160) REVERT: A 401 ASP cc_start: 0.8234 (m-30) cc_final: 0.7606 (t0) REVERT: A 402 LEU cc_start: 0.7784 (mp) cc_final: 0.7570 (tt) REVERT: B 89 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.8102 (ptt-90) REVERT: B 172 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: B 347 ASP cc_start: 0.8823 (m-30) cc_final: 0.8525 (p0) REVERT: B 407 GLN cc_start: 0.8723 (tm130) cc_final: 0.7906 (mm-40) REVERT: C 67 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: D 56 ASP cc_start: 0.8581 (t0) cc_final: 0.8188 (t0) REVERT: D 201 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 311 ASP cc_start: 0.9022 (t70) cc_final: 0.8388 (t0) REVERT: E 379 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7393 (mt-10) REVERT: E 384 ILE cc_start: 0.6489 (mm) cc_final: 0.6267 (mm) REVERT: E 397 LYS cc_start: 0.8015 (tptp) cc_final: 0.7691 (mmpt) REVERT: F 389 MET cc_start: 0.8585 (tpp) cc_final: 0.8266 (tpp) REVERT: G 24 MET cc_start: 0.7073 (mmt) cc_final: 0.6845 (mmp) REVERT: G 187 LYS cc_start: 0.5407 (tmtt) cc_final: 0.5127 (tptp) REVERT: G 241 MET cc_start: 0.6757 (ttt) cc_final: 0.6422 (ttt) outliers start: 47 outliers final: 17 residues processed: 200 average time/residue: 1.5716 time to fit residues: 361.8630 Evaluate side-chains 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 389 MET 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 166 ASP Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 265 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 330 ASN ** 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 = 0.3269 r_free = 0.3269 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.069039 restraints weight = 46547.538| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.44 r_work: 0.2767 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24684 Z= 0.171 Angle : 0.539 8.050 33479 Z= 0.283 Chirality : 0.046 0.261 3856 Planarity : 0.005 0.053 4363 Dihedral : 7.855 144.338 3580 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.26 % Allowed : 12.97 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3115 helix: 1.78 (0.15), residues: 1266 sheet: 0.61 (0.22), residues: 529 loop : 0.04 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 65 PHE 0.019 0.001 PHE F 125 TYR 0.019 0.001 TYR G 262 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1182) hydrogen bonds : angle 4.66234 ( 3351) covalent geometry : bond 0.00418 (24684) covalent geometry : angle 0.53854 (33479) *********************** 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: 58 poor density : 162 time to evaluate : 3.754 Fit side-chains REVERT: A 171 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7835 (ptm160) REVERT: A 401 ASP cc_start: 0.8242 (m-30) cc_final: 0.7591 (t0) REVERT: A 402 LEU cc_start: 0.7843 (mp) cc_final: 0.7620 (tt) REVERT: B 172 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: B 347 ASP cc_start: 0.8853 (m-30) cc_final: 0.8625 (p0) REVERT: C 67 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: D 56 ASP cc_start: 0.8599 (t0) cc_final: 0.8214 (t0) REVERT: D 201 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8611 (tm-30) REVERT: D 311 ASP cc_start: 0.9046 (t70) cc_final: 0.8433 (t0) REVERT: G 148 ASP cc_start: 0.8614 (m-30) cc_final: 0.7915 (p0) REVERT: G 167 GLU cc_start: 0.5786 (pt0) cc_final: 0.5344 (pm20) REVERT: G 187 LYS cc_start: 0.5651 (tmtt) cc_final: 0.4675 (tttp) outliers start: 58 outliers final: 34 residues processed: 207 average time/residue: 1.5852 time to fit residues: 384.9127 Evaluate side-chains 186 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 4.049 ------------------------------------------------------------------------------- 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 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 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 363 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 VAL 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 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 130 ASN Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 244 MET Chi-restraints excluded: chain G residue 257 THR 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 281 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 200 optimal weight: 0.0470 chunk 182 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.089100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.067905 restraints weight = 46962.838| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.43 r_work: 0.2745 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24684 Z= 0.217 Angle : 0.579 9.683 33479 Z= 0.304 Chirality : 0.047 0.235 3856 Planarity : 0.005 0.052 4363 Dihedral : 8.106 150.069 3580 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.49 % Allowed : 12.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3115 helix: 1.64 (0.15), residues: 1263 sheet: 0.49 (0.22), residues: 529 loop : -0.06 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 65 PHE 0.020 0.002 PHE F 125 TYR 0.017 0.001 TYR G 262 ARG 0.005 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 1182) hydrogen bonds : angle 4.77599 ( 3351) covalent geometry : bond 0.00535 (24684) covalent geometry : angle 0.57893 (33479) *********************** 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 220 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 2.800 Fit side-chains REVERT: A 171 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7861 (ptm160) REVERT: A 200 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6761 (mt0) REVERT: A 392 LEU cc_start: 0.7357 (mt) cc_final: 0.7084 (tp) REVERT: A 401 ASP cc_start: 0.8277 (m-30) cc_final: 0.7617 (t0) REVERT: B 172 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: B 181 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8777 (m-30) REVERT: B 347 ASP cc_start: 0.8844 (m-30) cc_final: 0.8633 (p0) REVERT: B 409 LYS cc_start: 0.8570 (ttpp) cc_final: 0.7988 (tptt) REVERT: C 67 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: D 56 ASP cc_start: 0.8677 (t0) cc_final: 0.8359 (t0) REVERT: D 201 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8617 (tm-30) REVERT: D 306 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9015 (mm) REVERT: D 311 ASP cc_start: 0.9105 (t70) cc_final: 0.8490 (t0) REVERT: E 344 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8138 (t) REVERT: G 24 MET cc_start: 0.7001 (mmt) cc_final: 0.6791 (mmp) REVERT: G 167 GLU cc_start: 0.5809 (pt0) cc_final: 0.5359 (pm20) REVERT: G 187 LYS cc_start: 0.5744 (tmtt) cc_final: 0.4798 (tttp) outliers start: 64 outliers final: 36 residues processed: 206 average time/residue: 1.8707 time to fit residues: 452.6320 Evaluate side-chains 190 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 7.154 ------------------------------------------------------------------------------- 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 200 GLN 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 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 323 SER 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 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 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 256 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 274 optimal weight: 0.0980 chunk 306 optimal weight: 0.8980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.090811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.069702 restraints weight = 46663.002| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.43 r_work: 0.2781 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24684 Z= 0.134 Angle : 0.523 8.426 33479 Z= 0.276 Chirality : 0.045 0.216 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.795 152.354 3580 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.10 % Allowed : 13.63 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 3115 helix: 1.76 (0.15), residues: 1267 sheet: 0.57 (0.22), residues: 528 loop : 0.02 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 65 PHE 0.015 0.001 PHE F 125 TYR 0.016 0.001 TYR G 262 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1182) hydrogen bonds : angle 4.61704 ( 3351) covalent geometry : bond 0.00317 (24684) covalent geometry : angle 0.52330 (33479) *********************** 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 216 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 4.489 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7789 (ptm160) REVERT: A 401 ASP cc_start: 0.8233 (m-30) cc_final: 0.7587 (t0) REVERT: B 172 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: B 347 ASP cc_start: 0.8823 (m-30) cc_final: 0.8617 (p0) REVERT: B 407 GLN cc_start: 0.8715 (tp40) cc_final: 0.8032 (mm-40) REVERT: B 409 LYS cc_start: 0.8561 (ttpp) cc_final: 0.7982 (tptt) REVERT: C 67 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: D 56 ASP cc_start: 0.8504 (t0) cc_final: 0.8126 (t0) REVERT: D 201 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8614 (tm-30) REVERT: D 306 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8993 (mm) REVERT: D 311 ASP cc_start: 0.9084 (t70) cc_final: 0.8486 (t0) REVERT: E 332 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8099 (mm-30) REVERT: E 344 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7971 (t) REVERT: E 379 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7494 (mt-10) REVERT: G 3 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.7227 (p) REVERT: G 148 ASP cc_start: 0.8609 (m-30) cc_final: 0.7893 (p0) REVERT: G 167 GLU cc_start: 0.5735 (pt0) cc_final: 0.5268 (pm20) REVERT: G 187 LYS cc_start: 0.5815 (tmtt) cc_final: 0.4775 (tttp) REVERT: G 244 MET cc_start: 0.7888 (mmt) cc_final: 0.7678 (mmt) outliers start: 54 outliers final: 31 residues processed: 209 average time/residue: 1.5561 time to fit residues: 386.5938 Evaluate side-chains 188 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 3.092 ------------------------------------------------------------------------------- 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 314 THR 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 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 34 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 497 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 306 ILE 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 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 166 ASP Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.090905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.069709 restraints weight = 46847.711| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.44 r_work: 0.2779 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24684 Z= 0.136 Angle : 0.531 9.435 33479 Z= 0.278 Chirality : 0.045 0.211 3856 Planarity : 0.004 0.056 4363 Dihedral : 7.705 156.330 3580 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.75 % Allowed : 14.10 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3115 helix: 1.78 (0.15), residues: 1277 sheet: 0.68 (0.22), residues: 516 loop : 0.02 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 65 PHE 0.016 0.001 PHE F 125 TYR 0.016 0.001 TYR G 262 ARG 0.003 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1182) hydrogen bonds : angle 4.60217 ( 3351) covalent geometry : bond 0.00325 (24684) covalent geometry : angle 0.53096 (33479) *********************** 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 204 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (ptm160) REVERT: A 401 ASP cc_start: 0.8238 (m-30) cc_final: 0.7584 (t0) REVERT: B 172 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: B 347 ASP cc_start: 0.8853 (m-30) cc_final: 0.8641 (p0) REVERT: B 407 GLN cc_start: 0.8759 (tp40) cc_final: 0.8064 (mm-40) REVERT: B 409 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8017 (tptt) REVERT: C 67 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: D 56 ASP cc_start: 0.8516 (t0) cc_final: 0.8138 (t0) REVERT: D 201 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8621 (tm-30) REVERT: D 306 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8999 (mm) REVERT: D 311 ASP cc_start: 0.9099 (t70) cc_final: 0.8514 (t0) REVERT: E 344 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (t) REVERT: E 379 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7506 (mt-10) REVERT: G 3 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6874 (p) REVERT: G 87 LEU cc_start: 0.8634 (mp) cc_final: 0.8410 (mm) REVERT: G 167 GLU cc_start: 0.5753 (pt0) cc_final: 0.5278 (pm20) REVERT: G 187 LYS cc_start: 0.5898 (tmtt) cc_final: 0.4903 (tttp) outliers start: 45 outliers final: 33 residues processed: 200 average time/residue: 1.5241 time to fit residues: 362.0895 Evaluate side-chains 191 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 5.971 ------------------------------------------------------------------------------- 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 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 236 PHE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 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 87 VAL Chi-restraints excluded: chain D residue 306 ILE 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 3 SER Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 220 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 chunk 179 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.092804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.071505 restraints weight = 46494.848| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.47 r_work: 0.2815 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24684 Z= 0.102 Angle : 0.503 8.314 33479 Z= 0.263 Chirality : 0.044 0.197 3856 Planarity : 0.004 0.059 4363 Dihedral : 7.407 158.208 3580 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.75 % Allowed : 14.17 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3115 helix: 1.90 (0.15), residues: 1281 sheet: 0.77 (0.22), residues: 521 loop : 0.11 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 65 PHE 0.012 0.001 PHE C 463 TYR 0.015 0.001 TYR G 262 ARG 0.004 0.000 ARG E 376 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1182) hydrogen bonds : angle 4.50698 ( 3351) covalent geometry : bond 0.00229 (24684) covalent geometry : angle 0.50266 (33479) ********************** 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 214 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: B 89 ARG cc_start: 0.8633 (ptp-110) cc_final: 0.8078 (ptt-90) REVERT: B 172 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: B 173 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 407 GLN cc_start: 0.8706 (tp40) cc_final: 0.8046 (mm-40) REVERT: B 409 LYS cc_start: 0.8579 (ttpp) cc_final: 0.7971 (tptt) REVERT: C 67 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: D 56 ASP cc_start: 0.8583 (t0) cc_final: 0.8197 (t0) REVERT: D 201 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 306 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8976 (mm) REVERT: D 311 ASP cc_start: 0.9052 (t70) cc_final: 0.8478 (t0) REVERT: D 379 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: E 149 ILE cc_start: 0.9165 (mt) cc_final: 0.8820 (mm) REVERT: E 344 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7571 (t) REVERT: E 379 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7373 (mt-10) REVERT: G 3 SER cc_start: 0.7182 (OUTLIER) cc_final: 0.6902 (p) REVERT: G 24 MET cc_start: 0.6787 (mmt) cc_final: 0.6555 (mmp) REVERT: G 87 LEU cc_start: 0.8560 (mp) cc_final: 0.8335 (mm) REVERT: G 148 ASP cc_start: 0.8595 (m-30) cc_final: 0.8011 (p0) REVERT: G 167 GLU cc_start: 0.5717 (pt0) cc_final: 0.5223 (pm20) REVERT: G 187 LYS cc_start: 0.5980 (tmtt) cc_final: 0.5049 (tttp) outliers start: 45 outliers final: 24 residues processed: 207 average time/residue: 1.2918 time to fit residues: 312.5633 Evaluate side-chains 191 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 386 LEU 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 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 67 GLU 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 87 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 GLU 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 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 166 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 239 optimal weight: 0.0060 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.1802 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.089262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.068113 restraints weight = 46736.806| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.43 r_work: 0.2750 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24684 Z= 0.214 Angle : 0.582 8.569 33479 Z= 0.305 Chirality : 0.047 0.207 3856 Planarity : 0.005 0.058 4363 Dihedral : 7.903 166.437 3580 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.87 % Allowed : 14.29 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1265 sheet: 0.51 (0.22), residues: 540 loop : -0.03 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 470 PHE 0.021 0.002 PHE F 125 TYR 0.015 0.001 TYR G 262 ARG 0.004 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 1182) hydrogen bonds : angle 4.72476 ( 3351) covalent geometry : bond 0.00524 (24684) covalent geometry : angle 0.58172 (33479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15935.03 seconds wall clock time: 283 minutes 9.60 seconds (16989.60 seconds total)