Starting phenix.real_space_refine on Thu Mar 5 10:20:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.map" model { file = "/net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k15_9905/03_2026/6k15_9905.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 13701 2.51 5 N 3632 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 14 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3215 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 13, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2510 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 4 Chain: "M" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3058 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1944 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 3 Chain: "G" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1991 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3007 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 22, 'TRANS': 342} Chain breaks: 3 Chain: "J" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1814 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "K" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 347 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "X" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Chain: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 2 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2484 SG CYS H 260 64.277 108.986 63.012 1.00 83.94 S ATOM 2507 SG CYS H 263 61.868 110.525 60.797 1.00 89.19 S ATOM 2693 SG CYS H 286 64.537 113.050 62.273 1.00 78.89 S Time building chain proxies: 4.57, per 1000 atoms: 0.21 Number of scatterers: 21486 At special positions: 0 Unit cell: (136.96, 170.13, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 84 16.00 O 4068 8.00 N 3632 7.00 C 13701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 912.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 286 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 263 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 260 " 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 50.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'F' and resid 319 through 343 removed outlier: 3.831A pdb=" N LYS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 114 through 131 removed outlier: 3.526A pdb=" N LEU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 removed outlier: 3.670A pdb=" N VAL H 142 " --> pdb=" O THR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 163 Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.782A pdb=" N LYS H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.849A pdb=" N ASN H 250 " --> pdb=" O GLU H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 289 removed outlier: 3.562A pdb=" N PHE H 287 " --> pdb=" O CYS H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 Processing helix chain 'H' and resid 333 through 342 removed outlier: 3.993A pdb=" N HIS H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 342 " --> pdb=" O ALA H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 removed outlier: 4.059A pdb=" N GLU H 352 " --> pdb=" O GLU H 348 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 368 Processing helix chain 'H' and resid 388 through 401 Processing helix chain 'H' and resid 403 through 405 No H-bonds generated for 'chain 'H' and resid 403 through 405' Processing helix chain 'H' and resid 406 through 483 removed outlier: 4.144A pdb=" N LYS H 413 " --> pdb=" O LYS H 409 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 419 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU H 431 " --> pdb=" O ALA H 427 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 434 " --> pdb=" O GLN H 430 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET H 437 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS H 439 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS H 446 " --> pdb=" O SER H 442 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 449 " --> pdb=" O THR H 445 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 450 " --> pdb=" O LYS H 446 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU H 455 " --> pdb=" O GLU H 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL H 462 " --> pdb=" O LYS H 458 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 467 " --> pdb=" O LYS H 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 removed outlier: 4.136A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.855A pdb=" N ASN D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.648A pdb=" N TYR D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.668A pdb=" N VAL D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 removed outlier: 4.085A pdb=" N LYS D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 removed outlier: 3.542A pdb=" N MET D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.918A pdb=" N GLU D 366 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 4.480A pdb=" N ASP D 395 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 removed outlier: 3.616A pdb=" N GLU D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 483 removed outlier: 3.884A pdb=" N ILE D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 476 " --> pdb=" O ARG D 472 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D 481 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 482 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 47 removed outlier: 3.814A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL M 47 " --> pdb=" O GLN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 70 removed outlier: 3.534A pdb=" N GLN M 69 " --> pdb=" O ASN M 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER M 70 " --> pdb=" O VAL M 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 66 through 70' Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.548A pdb=" N LEU M 89 " --> pdb=" O MET M 85 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 111 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'M' and resid 123 through 132 removed outlier: 4.433A pdb=" N PHE M 130 " --> pdb=" O LEU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 141 removed outlier: 4.162A pdb=" N ILE M 137 " --> pdb=" O PRO M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 168 removed outlier: 3.663A pdb=" N SER M 154 " --> pdb=" O LYS M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 183 through 201 removed outlier: 3.551A pdb=" N GLY M 201 " --> pdb=" O CYS M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 211 through 230 removed outlier: 4.165A pdb=" N GLU M 217 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU M 218 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 221 " --> pdb=" O GLU M 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 223 " --> pdb=" O THR M 219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 225 " --> pdb=" O TYR M 221 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 228 " --> pdb=" O ASP M 224 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 230 " --> pdb=" O MET M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 240 through 250 removed outlier: 3.714A pdb=" N GLN M 244 " --> pdb=" O ASP M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 270 removed outlier: 3.741A pdb=" N LEU M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 282 Processing helix chain 'M' and resid 288 through 293 removed outlier: 3.609A pdb=" N VAL M 293 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 298 removed outlier: 3.512A pdb=" N LEU M 298 " --> pdb=" O PHE M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 317 Processing helix chain 'M' and resid 322 through 327 Processing helix chain 'M' and resid 331 through 340 removed outlier: 3.601A pdb=" N ILE M 335 " --> pdb=" O GLU M 331 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU M 336 " --> pdb=" O CYS M 332 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU M 337 " --> pdb=" O SER M 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA M 338 " --> pdb=" O LEU M 334 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU M 340 " --> pdb=" O LEU M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 524 through 538 removed outlier: 3.944A pdb=" N LYS M 528 " --> pdb=" O SER M 524 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 529 " --> pdb=" O ASP M 525 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 551 Processing helix chain 'M' and resid 553 through 562 removed outlier: 4.282A pdb=" N HIS M 559 " --> pdb=" O PRO M 555 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS M 560 " --> pdb=" O LEU M 556 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 562 " --> pdb=" O LEU M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 570 removed outlier: 4.164A pdb=" N LEU M 569 " --> pdb=" O PRO M 565 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 570 " --> pdb=" O PRO M 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 565 through 570' Processing helix chain 'M' and resid 572 through 578 Processing helix chain 'I' and resid 29 through 54 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 249 through 263 Processing helix chain 'I' and resid 316 through 324 Processing helix chain 'I' and resid 331 through 342 removed outlier: 3.614A pdb=" N VAL I 339 " --> pdb=" O VAL I 335 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN I 340 " --> pdb=" O VAL I 336 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 341 " --> pdb=" O GLN I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 425 removed outlier: 3.728A pdb=" N PHE I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 removed outlier: 4.333A pdb=" N HIS I 432 " --> pdb=" O GLU I 428 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS I 438 " --> pdb=" O LEU I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 478 removed outlier: 3.575A pdb=" N TYR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 161 through 168 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.509A pdb=" N LYS G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 264 Processing helix chain 'G' and resid 306 through 319 removed outlier: 3.567A pdb=" N ASP G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 345 removed outlier: 3.892A pdb=" N LEU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU G 334 " --> pdb=" O GLN G 330 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR G 335 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.828A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 75 through 82 removed outlier: 4.011A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 4.605A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 removed outlier: 3.578A pdb=" N GLN A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.819A pdb=" N TYR A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.516A pdb=" N ARG A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.947A pdb=" N ASN A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.951A pdb=" N ASN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.527A pdb=" N SER A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 463 removed outlier: 4.037A pdb=" N LYS A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 4.459A pdb=" N MET J 9 " --> pdb=" O GLN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 24 removed outlier: 3.631A pdb=" N LEU J 23 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA J 24 " --> pdb=" O ALA J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 20 through 24' Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'J' and resid 75 through 101 removed outlier: 3.538A pdb=" N ILE J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 127 removed outlier: 4.256A pdb=" N LYS J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.802A pdb=" N ILE J 193 " --> pdb=" O PRO J 189 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG J 194 " --> pdb=" O ASP J 190 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE J 195 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 207 Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.673A pdb=" N GLU J 244 " --> pdb=" O LYS J 240 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 266 removed outlier: 3.524A pdb=" N GLN J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER J 256 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 264 " --> pdb=" O LYS J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 290 removed outlier: 3.522A pdb=" N ALA J 283 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN J 290 " --> pdb=" O GLN J 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.677A pdb=" N ASN E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.523A pdb=" N HIS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 72 Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.861A pdb=" N ASN C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 removed outlier: 3.552A pdb=" N GLU K 176 " --> pdb=" O THR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 173 through 176' Processing helix chain 'K' and resid 177 through 194 removed outlier: 4.165A pdb=" N GLU K 191 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 369 Processing helix chain 'X' and resid 381 through 390 removed outlier: 3.859A pdb=" N LYS X 385 " --> pdb=" O PRO X 381 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE X 388 " --> pdb=" O PHE X 384 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS X 390 " --> pdb=" O LYS X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 489 through 491 No H-bonds generated for 'chain 'X' and resid 489 through 491' Processing helix chain 'L' and resid 863 through 867 removed outlier: 3.860A pdb=" N GLY L 867 " --> pdb=" O PHE L 864 " (cutoff:3.500A) Processing helix chain 'L' and resid 871 through 883 removed outlier: 3.600A pdb=" N THR L 875 " --> pdb=" O SER L 871 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG L 883 " --> pdb=" O LEU L 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AA2, first strand: chain 'H' and resid 186 through 190 Processing sheet with id=AA3, first strand: chain 'H' and resid 80 through 83 removed outlier: 6.334A pdb=" N VAL H 80 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 192 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 82 " --> pdb=" O ASP D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 270 through 274 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'I' and resid 8 through 9 Processing sheet with id=AA7, first strand: chain 'I' and resid 219 through 222 removed outlier: 3.516A pdb=" N ILE I 222 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE I 349 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 233 through 234 Processing sheet with id=AA9, first strand: chain 'G' and resid 203 through 212 removed outlier: 3.717A pdb=" N HIS G 215 " --> pdb=" O HIS G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 279 through 285 removed outlier: 3.521A pdb=" N GLU G 293 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.618A pdb=" N VAL A 189 " --> pdb=" O GLN X 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 192 through 196 removed outlier: 4.253A pdb=" N SER A 192 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 228 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER X 499 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 230 " --> pdb=" O SER X 499 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N MET X 501 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE X 498 " --> pdb=" O TRP X 620 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN X 622 " --> pdb=" O PHE X 498 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE X 500 " --> pdb=" O ASN X 622 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG X 605 " --> pdb=" O LEU X 525 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU X 525 " --> pdb=" O ARG X 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'X' and resid 443 through 444 removed outlier: 3.537A pdb=" N SER X 513 " --> pdb=" O GLU X 589 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU X 589 " --> pdb=" O SER X 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 508 through 510 851 hydrogen bonds defined for protein. 2445 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: 2.91 Time building geometry restraints manager: 1.89 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: 6811 1.34 - 1.46: 3479 1.46 - 1.57: 11455 1.57 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 21882 Sorted by residual: bond pdb=" C ILE G 325 " pdb=" N PRO G 326 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.57e+01 bond pdb=" N GLU X 439 " pdb=" CA GLU X 439 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.27e-02 6.20e+03 7.49e+00 bond pdb=" N GLN X 440 " pdb=" CA GLN X 440 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 bond pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 21877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 28739 2.45 - 4.90: 707 4.90 - 7.35: 103 7.35 - 9.80: 28 9.80 - 12.25: 6 Bond angle restraints: 29583 Sorted by residual: angle pdb=" N PRO J 17 " pdb=" CA PRO J 17 " pdb=" CB PRO J 17 " ideal model delta sigma weight residual 103.25 110.26 -7.01 1.05e+00 9.07e-01 4.45e+01 angle pdb=" N LYS G 338 " pdb=" CA LYS G 338 " pdb=" C LYS G 338 " ideal model delta sigma weight residual 112.04 102.54 9.50 1.44e+00 4.82e-01 4.35e+01 angle pdb=" N ILE M 553 " pdb=" CA ILE M 553 " pdb=" C ILE M 553 " ideal model delta sigma weight residual 113.53 107.52 6.01 9.80e-01 1.04e+00 3.76e+01 angle pdb=" C HIS H 261 " pdb=" N THR H 262 " pdb=" CA THR H 262 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N LYS G 340 " pdb=" CA LYS G 340 " pdb=" C LYS G 340 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.45e+01 ... (remaining 29578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 12742 15.98 - 31.95: 531 31.95 - 47.93: 137 47.93 - 63.90: 8 63.90 - 79.88: 13 Dihedral angle restraints: 13431 sinusoidal: 5563 harmonic: 7868 Sorted by residual: dihedral pdb=" CA THR H 452 " pdb=" C THR H 452 " pdb=" N GLN H 453 " pdb=" CA GLN H 453 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU H 464 " pdb=" C GLU H 464 " pdb=" N SER H 465 " pdb=" CA SER H 465 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER G 275 " pdb=" C SER G 275 " pdb=" N ASP G 276 " pdb=" CA ASP G 276 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 13428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2607 0.060 - 0.119: 661 0.119 - 0.179: 93 0.179 - 0.239: 15 0.239 - 0.298: 5 Chirality restraints: 3381 Sorted by residual: chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE M 115 " pdb=" CA ILE M 115 " pdb=" CG1 ILE M 115 " pdb=" CG2 ILE M 115 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO J 17 " pdb=" N PRO J 17 " pdb=" C PRO J 17 " pdb=" CB PRO J 17 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3378 not shown) Planarity restraints: 3775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 256 " -0.063 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO A 257 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 270 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 271 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 862 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO L 863 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 863 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 863 " -0.040 5.00e-02 4.00e+02 ... (remaining 3772 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 11 2.29 - 2.94: 8647 2.94 - 3.60: 29652 3.60 - 4.25: 45812 4.25 - 4.90: 76680 Nonbonded interactions: 160802 Sorted by model distance: nonbonded pdb=" OE1 GLU X 439 " pdb=" CG GLU X 490 " model vdw 1.639 3.440 nonbonded pdb=" OE2 GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 1.706 3.120 nonbonded pdb=" OE1 GLU X 439 " pdb=" CD GLU X 490 " model vdw 2.087 3.270 nonbonded pdb=" CD GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 2.182 3.350 nonbonded pdb=" OG SER D 316 " pdb=" OE1 GLU D 319 " model vdw 2.225 3.040 ... (remaining 160797 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.236 21885 Z= 0.254 Angle : 0.959 12.252 29583 Z= 0.531 Chirality : 0.054 0.298 3381 Planarity : 0.007 0.096 3775 Dihedral : 10.227 79.881 8277 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 0.33 % Allowed : 3.17 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.13), residues: 2581 helix: -2.49 (0.11), residues: 1286 sheet: -3.31 (0.34), residues: 150 loop : -3.00 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 338 TYR 0.026 0.002 TYR F 410 PHE 0.034 0.002 PHE J 83 TRP 0.030 0.003 TRP F 371 HIS 0.013 0.002 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00499 (21882) covalent geometry : angle 0.95864 (29583) hydrogen bonds : bond 0.17069 ( 851) hydrogen bonds : angle 6.66560 ( 2445) metal coordination : bond 0.20702 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 658 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7881 (ttm170) REVERT: F 395 LEU cc_start: 0.8091 (tp) cc_final: 0.7723 (tt) REVERT: F 409 ILE cc_start: 0.8925 (mm) cc_final: 0.8646 (mt) REVERT: H 349 ASP cc_start: 0.8325 (t70) cc_final: 0.7653 (t0) REVERT: D 226 VAL cc_start: 0.7957 (t) cc_final: 0.7449 (m) REVERT: D 438 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8206 (mt-10) REVERT: M 150 LYS cc_start: 0.8616 (tmtp) cc_final: 0.8036 (tptm) REVERT: I 36 LEU cc_start: 0.9219 (mt) cc_final: 0.8980 (mt) REVERT: I 415 LYS cc_start: 0.8831 (mttt) cc_final: 0.8591 (mtpt) REVERT: I 456 ARG cc_start: 0.8714 (mtp85) cc_final: 0.8116 (mtp85) REVERT: G 29 ILE cc_start: 0.7934 (mm) cc_final: 0.7711 (mm) REVERT: G 259 LYS cc_start: 0.8287 (mptm) cc_final: 0.8047 (tptp) REVERT: G 263 LYS cc_start: 0.7992 (tttt) cc_final: 0.7548 (ttpt) REVERT: G 291 PHE cc_start: 0.7745 (m-80) cc_final: 0.7509 (m-10) REVERT: A 470 ILE cc_start: 0.7494 (mt) cc_final: 0.7180 (pt) REVERT: J 100 LEU cc_start: 0.8640 (tm) cc_final: 0.8380 (tp) REVERT: J 223 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7587 (mt-10) REVERT: E 50 ASN cc_start: 0.8409 (t0) cc_final: 0.8072 (t0) REVERT: E 67 LYS cc_start: 0.8628 (tmmm) cc_final: 0.8372 (mmmt) REVERT: C 217 LYS cc_start: 0.6989 (mttt) cc_final: 0.6664 (mtmt) REVERT: K 186 LYS cc_start: 0.7266 (mttt) cc_final: 0.6765 (mmtp) REVERT: X 532 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6607 (Cg_exo) REVERT: X 605 ARG cc_start: 0.7170 (ptm160) cc_final: 0.6962 (ptm160) REVERT: L 757 LYS cc_start: 0.8631 (mttp) cc_final: 0.8277 (mtmm) REVERT: L 860 LEU cc_start: 0.7920 (pt) cc_final: 0.6589 (pt) outliers start: 8 outliers final: 2 residues processed: 665 average time/residue: 0.1641 time to fit residues: 160.9494 Evaluate side-chains 310 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain X residue 438 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN H 167 ASN H 186 HIS H 195 GLN H 239 GLN H 250 ASN H 281 ASN H 318 GLN H 470 ASN D 145 ASN D 167 ASN D 242 ASN M 359 HIS I 245 GLN I 432 HIS I 463 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 GLN G 352 HIS A 112 GLN A 392 ASN A 471 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN J 123 GLN J 259 GLN J 263 ASN K 160 GLN K 174 GLN X 380 ASN X 493 GLN X 494 ASN X 600 ASN L 800 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.117918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089921 restraints weight = 55800.080| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.18 r_work: 0.3304 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21885 Z= 0.129 Angle : 0.633 9.377 29583 Z= 0.328 Chirality : 0.043 0.167 3381 Planarity : 0.005 0.074 3775 Dihedral : 5.469 44.161 2837 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.02 % Allowed : 10.16 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 2581 helix: -0.79 (0.14), residues: 1292 sheet: -3.00 (0.35), residues: 149 loop : -2.68 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 764 TYR 0.026 0.001 TYR X 368 PHE 0.015 0.001 PHE J 83 TRP 0.018 0.002 TRP D 334 HIS 0.006 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00280 (21882) covalent geometry : angle 0.63345 (29583) hydrogen bonds : bond 0.04458 ( 851) hydrogen bonds : angle 4.57593 ( 2445) metal coordination : bond 0.00744 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 365 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8319 (mmm160) cc_final: 0.7815 (ttm170) REVERT: F 347 GLN cc_start: 0.7957 (tt0) cc_final: 0.7501 (tm-30) REVERT: H 324 LEU cc_start: 0.9052 (mp) cc_final: 0.8626 (mp) REVERT: H 328 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7599 (mt-10) REVERT: H 349 ASP cc_start: 0.8520 (t70) cc_final: 0.8145 (t0) REVERT: H 390 MET cc_start: 0.7990 (mpp) cc_final: 0.7378 (mmt) REVERT: H 451 GLU cc_start: 0.5805 (mt-10) cc_final: 0.5565 (mt-10) REVERT: H 468 MET cc_start: 0.8670 (tpp) cc_final: 0.8378 (tpp) REVERT: D 320 MET cc_start: 0.8790 (tpp) cc_final: 0.8388 (tpp) REVERT: D 420 LYS cc_start: 0.6478 (tmtm) cc_final: 0.6070 (mmtm) REVERT: D 437 MET cc_start: 0.8427 (tmm) cc_final: 0.8071 (tmm) REVERT: D 438 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8029 (mm-30) REVERT: G 259 LYS cc_start: 0.8430 (mptm) cc_final: 0.8014 (tptp) REVERT: G 263 LYS cc_start: 0.8192 (tttt) cc_final: 0.7626 (ttpt) REVERT: G 291 PHE cc_start: 0.7994 (m-80) cc_final: 0.7791 (m-10) REVERT: G 330 GLN cc_start: 0.8627 (mt0) cc_final: 0.8311 (mt0) REVERT: G 366 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: A 258 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 265 MET cc_start: 0.7595 (mmm) cc_final: 0.7389 (mtt) REVERT: J 244 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8156 (mt-10) REVERT: E 50 ASN cc_start: 0.8282 (t0) cc_final: 0.7652 (m110) REVERT: C 217 LYS cc_start: 0.6999 (mttt) cc_final: 0.6583 (mtmt) REVERT: K 174 GLN cc_start: 0.8751 (tt0) cc_final: 0.8211 (tm-30) REVERT: K 186 LYS cc_start: 0.7147 (mttt) cc_final: 0.6750 (mmtt) REVERT: X 368 TYR cc_start: 0.7445 (t80) cc_final: 0.6806 (t80) REVERT: X 435 GLN cc_start: 0.8430 (pm20) cc_final: 0.8057 (pm20) REVERT: X 440 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6610 (mt0) REVERT: X 481 TRP cc_start: 0.7897 (m-10) cc_final: 0.7685 (m-10) REVERT: L 757 LYS cc_start: 0.8373 (mttp) cc_final: 0.8082 (mtmm) REVERT: L 860 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6946 (pt) outliers start: 49 outliers final: 19 residues processed: 401 average time/residue: 0.1470 time to fit residues: 91.2805 Evaluate side-chains 297 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 438 SER Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 860 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 243 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 239 GLN I 329 HIS I 465 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.116274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088064 restraints weight = 55970.576| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.25 r_work: 0.3266 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21885 Z= 0.171 Angle : 0.626 11.271 29583 Z= 0.321 Chirality : 0.043 0.152 3381 Planarity : 0.005 0.067 3775 Dihedral : 5.077 34.434 2836 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.59 % Allowed : 11.68 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2581 helix: 0.03 (0.14), residues: 1293 sheet: -2.82 (0.35), residues: 155 loop : -2.42 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 77 TYR 0.022 0.002 TYR H 272 PHE 0.017 0.002 PHE G 359 TRP 0.028 0.002 TRP L 791 HIS 0.005 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00397 (21882) covalent geometry : angle 0.62613 (29583) hydrogen bonds : bond 0.04233 ( 851) hydrogen bonds : angle 4.31626 ( 2445) metal coordination : bond 0.00224 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8302 (mmm160) cc_final: 0.7557 (ttm170) REVERT: H 239 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7804 (tp40) REVERT: H 349 ASP cc_start: 0.8674 (t70) cc_final: 0.8275 (t0) REVERT: H 363 TYR cc_start: 0.8441 (m-80) cc_final: 0.8241 (m-10) REVERT: H 390 MET cc_start: 0.8227 (mpp) cc_final: 0.7498 (mmt) REVERT: H 451 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5488 (mt-10) REVERT: D 168 TYR cc_start: 0.8707 (t80) cc_final: 0.8233 (t80) REVERT: D 320 MET cc_start: 0.8877 (tpp) cc_final: 0.8666 (tpp) REVERT: D 437 MET cc_start: 0.8539 (tmm) cc_final: 0.8297 (ppp) REVERT: D 438 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8152 (mm-30) REVERT: D 456 MET cc_start: 0.8803 (ppp) cc_final: 0.8297 (ppp) REVERT: M 523 LEU cc_start: 0.8421 (mt) cc_final: 0.8217 (mt) REVERT: I 333 MET cc_start: 0.8397 (tmm) cc_final: 0.7975 (tmm) REVERT: G 259 LYS cc_start: 0.8458 (mptm) cc_final: 0.8037 (tptp) REVERT: G 263 LYS cc_start: 0.8142 (tttt) cc_final: 0.7725 (tptp) REVERT: G 291 PHE cc_start: 0.8305 (m-80) cc_final: 0.8073 (m-80) REVERT: G 330 GLN cc_start: 0.8566 (mt0) cc_final: 0.8239 (mt0) REVERT: G 366 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7851 (mmm-85) REVERT: G 379 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7639 (ptp-170) REVERT: A 132 LEU cc_start: 0.8615 (tp) cc_final: 0.8365 (tp) REVERT: A 258 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7018 (p) REVERT: A 265 MET cc_start: 0.7511 (mmm) cc_final: 0.7245 (mtt) REVERT: A 470 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7744 (tp) REVERT: A 474 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6996 (mmt180) REVERT: J 204 ASN cc_start: 0.8855 (t0) cc_final: 0.8580 (t0) REVERT: E 50 ASN cc_start: 0.8410 (t0) cc_final: 0.7732 (m110) REVERT: E 67 LYS cc_start: 0.8671 (tmtt) cc_final: 0.8187 (mmmm) REVERT: K 174 GLN cc_start: 0.8789 (tt0) cc_final: 0.8177 (tm-30) REVERT: K 186 LYS cc_start: 0.7309 (mttt) cc_final: 0.6898 (mmtt) REVERT: X 368 TYR cc_start: 0.7356 (t80) cc_final: 0.6875 (t80) REVERT: X 435 GLN cc_start: 0.8421 (pm20) cc_final: 0.8079 (pm20) REVERT: X 440 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6593 (mt0) REVERT: X 481 TRP cc_start: 0.7917 (m-10) cc_final: 0.7647 (m-10) REVERT: L 757 LYS cc_start: 0.8322 (mttp) cc_final: 0.8035 (mtmm) REVERT: L 761 VAL cc_start: 0.8224 (p) cc_final: 0.8008 (m) REVERT: L 801 GLU cc_start: 0.7544 (pt0) cc_final: 0.7287 (pt0) REVERT: L 860 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7184 (pt) REVERT: L 869 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7519 (mtt180) REVERT: L 877 HIS cc_start: 0.7692 (t-90) cc_final: 0.7275 (t-90) outliers start: 63 outliers final: 30 residues processed: 344 average time/residue: 0.1476 time to fit residues: 78.6289 Evaluate side-chains 293 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 239 GLN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 438 SER Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 860 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 198 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 0.0010 chunk 69 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 242 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN H 123 ASN H 239 GLN H 288 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089192 restraints weight = 56174.696| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.23 r_work: 0.3290 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21885 Z= 0.117 Angle : 0.565 9.322 29583 Z= 0.290 Chirality : 0.041 0.151 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.743 24.585 2836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.34 % Allowed : 12.96 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2581 helix: 0.55 (0.15), residues: 1271 sheet: -2.57 (0.36), residues: 155 loop : -2.28 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 172 TYR 0.017 0.001 TYR G 361 PHE 0.010 0.001 PHE J 83 TRP 0.009 0.001 TRP A 396 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00265 (21882) covalent geometry : angle 0.56545 (29583) hydrogen bonds : bond 0.03675 ( 851) hydrogen bonds : angle 4.06734 ( 2445) metal coordination : bond 0.00126 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7742 (ttm170) REVERT: H 349 ASP cc_start: 0.8577 (t70) cc_final: 0.8092 (t0) REVERT: H 451 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5501 (mt-10) REVERT: D 168 TYR cc_start: 0.8764 (t80) cc_final: 0.8451 (t80) REVERT: D 320 MET cc_start: 0.8788 (tpp) cc_final: 0.8563 (tpp) REVERT: D 438 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8219 (mt-10) REVERT: D 475 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7582 (mp) REVERT: M 32 MET cc_start: 0.5608 (ttt) cc_final: 0.5189 (ttt) REVERT: I 333 MET cc_start: 0.8476 (tmm) cc_final: 0.8014 (tmm) REVERT: G 259 LYS cc_start: 0.8447 (mptm) cc_final: 0.8007 (tptp) REVERT: G 263 LYS cc_start: 0.8157 (tttt) cc_final: 0.7738 (tptp) REVERT: G 291 PHE cc_start: 0.8395 (m-80) cc_final: 0.8141 (m-80) REVERT: G 330 GLN cc_start: 0.8551 (mt0) cc_final: 0.8205 (mt0) REVERT: G 366 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7888 (mmm-85) REVERT: A 185 MET cc_start: 0.7402 (tpp) cc_final: 0.7201 (tpp) REVERT: A 258 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.6959 (p) REVERT: A 474 ARG cc_start: 0.7301 (mmt180) cc_final: 0.7019 (mmt180) REVERT: J 62 TYR cc_start: 0.8112 (t80) cc_final: 0.7677 (m-80) REVERT: J 204 ASN cc_start: 0.8783 (t0) cc_final: 0.8576 (t0) REVERT: J 229 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: E 50 ASN cc_start: 0.8377 (t0) cc_final: 0.7744 (m110) REVERT: K 174 GLN cc_start: 0.8750 (tt0) cc_final: 0.8189 (tm-30) REVERT: K 186 LYS cc_start: 0.7362 (mttt) cc_final: 0.6959 (mmtt) REVERT: X 368 TYR cc_start: 0.7456 (t80) cc_final: 0.6966 (t80) REVERT: X 434 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7279 (ppp) REVERT: X 435 GLN cc_start: 0.8462 (pm20) cc_final: 0.8035 (pm20) REVERT: X 481 TRP cc_start: 0.7880 (m-10) cc_final: 0.7622 (m-10) REVERT: L 757 LYS cc_start: 0.8238 (mttp) cc_final: 0.7929 (mtmm) REVERT: L 801 GLU cc_start: 0.7766 (pt0) cc_final: 0.7522 (pt0) outliers start: 57 outliers final: 37 residues processed: 332 average time/residue: 0.1482 time to fit residues: 76.7937 Evaluate side-chains 295 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain H residue 466 GLU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 434 MET Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 217 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 288 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 877 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087106 restraints weight = 56266.858| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.23 r_work: 0.3247 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21885 Z= 0.166 Angle : 0.602 9.166 29583 Z= 0.308 Chirality : 0.043 0.185 3381 Planarity : 0.004 0.061 3775 Dihedral : 4.713 26.246 2835 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.09 % Allowed : 13.74 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.17), residues: 2581 helix: 0.68 (0.15), residues: 1289 sheet: -2.33 (0.38), residues: 152 loop : -2.15 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 77 TYR 0.019 0.002 TYR H 272 PHE 0.025 0.002 PHE G 359 TRP 0.031 0.002 TRP L 791 HIS 0.013 0.001 HIS L 877 Details of bonding type rmsd covalent geometry : bond 0.00391 (21882) covalent geometry : angle 0.60190 (29583) hydrogen bonds : bond 0.03892 ( 851) hydrogen bonds : angle 4.07913 ( 2445) metal coordination : bond 0.00244 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 272 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7727 (ttm170) REVERT: F 361 GLU cc_start: 0.8309 (tp30) cc_final: 0.8089 (tp30) REVERT: F 410 TYR cc_start: 0.6592 (p90) cc_final: 0.6012 (p90) REVERT: H 297 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: H 349 ASP cc_start: 0.8598 (t70) cc_final: 0.8176 (t0) REVERT: H 390 MET cc_start: 0.8342 (mpp) cc_final: 0.8101 (pmm) REVERT: H 451 GLU cc_start: 0.5868 (mt-10) cc_final: 0.5448 (mt-10) REVERT: H 459 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8130 (mm) REVERT: D 168 TYR cc_start: 0.8783 (t80) cc_final: 0.8452 (t80) REVERT: D 320 MET cc_start: 0.8836 (tpp) cc_final: 0.8580 (tpp) REVERT: D 437 MET cc_start: 0.8346 (ppp) cc_final: 0.8125 (ppp) REVERT: M 32 MET cc_start: 0.6323 (ttt) cc_final: 0.5998 (ttm) REVERT: I 333 MET cc_start: 0.8491 (tmm) cc_final: 0.8009 (tmm) REVERT: I 461 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: G 259 LYS cc_start: 0.8499 (mptm) cc_final: 0.8093 (tptp) REVERT: G 263 LYS cc_start: 0.8231 (tttt) cc_final: 0.7825 (tptp) REVERT: G 291 PHE cc_start: 0.8440 (m-80) cc_final: 0.8202 (m-80) REVERT: G 330 GLN cc_start: 0.8525 (mt0) cc_final: 0.8167 (mt0) REVERT: G 379 ARG cc_start: 0.7922 (ptp-170) cc_final: 0.7610 (ptp-170) REVERT: A 240 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 314 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7860 (mp) REVERT: J 62 TYR cc_start: 0.8127 (t80) cc_final: 0.7712 (m-80) REVERT: J 204 ASN cc_start: 0.8817 (t0) cc_final: 0.8612 (t0) REVERT: J 205 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8244 (tm-30) REVERT: J 229 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: J 244 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8170 (mt-10) REVERT: E 50 ASN cc_start: 0.8466 (t0) cc_final: 0.7821 (m110) REVERT: K 174 GLN cc_start: 0.8768 (tt0) cc_final: 0.8168 (tm-30) REVERT: K 186 LYS cc_start: 0.7417 (mttt) cc_final: 0.6946 (mmtt) REVERT: X 368 TYR cc_start: 0.7454 (t80) cc_final: 0.6833 (t80) REVERT: X 434 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7261 (ppp) REVERT: X 435 GLN cc_start: 0.8506 (pm20) cc_final: 0.8065 (pm20) REVERT: L 757 LYS cc_start: 0.8265 (mttp) cc_final: 0.7961 (mtmm) outliers start: 75 outliers final: 46 residues processed: 330 average time/residue: 0.1488 time to fit residues: 77.1771 Evaluate side-chains 304 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 454 LEU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 285 CYS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 201 ASN Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 434 MET Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 231 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 186 optimal weight: 0.0980 chunk 159 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 288 GLN H 470 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN A 97 HIS A 193 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 800 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089137 restraints weight = 56191.664| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.29 r_work: 0.3288 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21885 Z= 0.108 Angle : 0.573 11.311 29583 Z= 0.286 Chirality : 0.041 0.210 3381 Planarity : 0.004 0.058 3775 Dihedral : 4.440 26.586 2835 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.39 % Allowed : 14.97 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2581 helix: 0.99 (0.15), residues: 1272 sheet: -2.10 (0.40), residues: 154 loop : -2.00 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 482 TYR 0.014 0.001 TYR D 330 PHE 0.024 0.001 PHE X 384 TRP 0.009 0.001 TRP L 791 HIS 0.009 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00242 (21882) covalent geometry : angle 0.57328 (29583) hydrogen bonds : bond 0.03398 ( 851) hydrogen bonds : angle 3.86269 ( 2445) metal coordination : bond 0.00125 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7775 (ttm170) REVERT: F 361 GLU cc_start: 0.8260 (tp30) cc_final: 0.8006 (tp30) REVERT: F 408 GLU cc_start: 0.8638 (pp20) cc_final: 0.8342 (pp20) REVERT: F 410 TYR cc_start: 0.6481 (p90) cc_final: 0.6218 (p90) REVERT: H 349 ASP cc_start: 0.8488 (t70) cc_final: 0.8061 (t0) REVERT: H 451 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5639 (mt-10) REVERT: H 459 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8135 (mm) REVERT: D 320 MET cc_start: 0.8892 (tpp) cc_final: 0.8650 (tpp) REVERT: D 331 GLU cc_start: 0.6898 (tp30) cc_final: 0.6647 (tp30) REVERT: D 437 MET cc_start: 0.8400 (ppp) cc_final: 0.8135 (ppp) REVERT: D 438 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8210 (mm-30) REVERT: D 468 MET cc_start: 0.7924 (tmm) cc_final: 0.7665 (ppp) REVERT: M 32 MET cc_start: 0.6103 (ttt) cc_final: 0.5889 (ttm) REVERT: M 316 ILE cc_start: 0.8475 (tp) cc_final: 0.8270 (tp) REVERT: I 333 MET cc_start: 0.8476 (tmm) cc_final: 0.8075 (tmm) REVERT: I 461 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.6079 (m-80) REVERT: G 259 LYS cc_start: 0.8487 (mptm) cc_final: 0.8078 (tptp) REVERT: G 263 LYS cc_start: 0.8243 (tttt) cc_final: 0.7812 (tptp) REVERT: G 330 GLN cc_start: 0.8556 (mt0) cc_final: 0.8184 (mt0) REVERT: A 240 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7366 (mm-30) REVERT: A 258 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6933 (p) REVERT: A 314 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7806 (mp) REVERT: J 62 TYR cc_start: 0.8086 (t80) cc_final: 0.7665 (m-80) REVERT: J 100 LEU cc_start: 0.8559 (tt) cc_final: 0.8180 (tp) REVERT: J 205 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8288 (tm-30) REVERT: J 229 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: E 50 ASN cc_start: 0.8336 (t0) cc_final: 0.7756 (m110) REVERT: E 67 LYS cc_start: 0.8770 (tptp) cc_final: 0.8187 (mmmm) REVERT: K 174 GLN cc_start: 0.8766 (tt0) cc_final: 0.8164 (tm-30) REVERT: K 186 LYS cc_start: 0.7370 (mttt) cc_final: 0.6933 (mmtt) REVERT: X 435 GLN cc_start: 0.8490 (pm20) cc_final: 0.8038 (pm20) REVERT: L 757 LYS cc_start: 0.8194 (mttp) cc_final: 0.7920 (mtmm) REVERT: L 801 GLU cc_start: 0.7593 (pt0) cc_final: 0.7362 (pt0) REVERT: L 808 ASP cc_start: 0.6602 (t0) cc_final: 0.6195 (t0) outliers start: 58 outliers final: 35 residues processed: 335 average time/residue: 0.1431 time to fit residues: 75.3778 Evaluate side-chains 303 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 19 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN H 288 GLN H 470 ASN I 425 HIS A 484 ASN J 254 GLN E 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.114612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086279 restraints weight = 56465.748| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.23 r_work: 0.3237 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21885 Z= 0.181 Angle : 0.624 10.780 29583 Z= 0.317 Chirality : 0.043 0.190 3381 Planarity : 0.004 0.061 3775 Dihedral : 4.600 27.177 2835 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.63 % Allowed : 15.96 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2581 helix: 1.00 (0.15), residues: 1273 sheet: -1.96 (0.42), residues: 148 loop : -1.97 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 482 TYR 0.022 0.002 TYR D 168 PHE 0.024 0.002 PHE F 330 TRP 0.016 0.002 TRP D 315 HIS 0.007 0.001 HIS J 118 Details of bonding type rmsd covalent geometry : bond 0.00429 (21882) covalent geometry : angle 0.62449 (29583) hydrogen bonds : bond 0.03920 ( 851) hydrogen bonds : angle 4.07639 ( 2445) metal coordination : bond 0.00277 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7769 (ttm170) REVERT: F 361 GLU cc_start: 0.8307 (tp30) cc_final: 0.8093 (tp30) REVERT: F 408 GLU cc_start: 0.8743 (pp20) cc_final: 0.8478 (pp20) REVERT: F 410 TYR cc_start: 0.6686 (p90) cc_final: 0.6439 (p90) REVERT: F 419 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7389 (tt) REVERT: H 169 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8087 (mm110) REVERT: H 349 ASP cc_start: 0.8620 (t70) cc_final: 0.8215 (t0) REVERT: H 451 GLU cc_start: 0.6103 (mt-10) cc_final: 0.5620 (mt-10) REVERT: H 459 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8144 (mm) REVERT: D 320 MET cc_start: 0.8858 (tpp) cc_final: 0.8569 (tpp) REVERT: D 331 GLU cc_start: 0.7042 (tp30) cc_final: 0.6733 (tp30) REVERT: D 438 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8346 (mm-30) REVERT: I 333 MET cc_start: 0.8576 (tmm) cc_final: 0.8129 (tmm) REVERT: I 461 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: G 259 LYS cc_start: 0.8503 (mptm) cc_final: 0.8098 (tptp) REVERT: G 263 LYS cc_start: 0.8310 (tttt) cc_final: 0.7879 (tptp) REVERT: G 330 GLN cc_start: 0.8529 (mt0) cc_final: 0.8152 (mt0) REVERT: G 379 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.7639 (ptp-170) REVERT: A 202 MET cc_start: 0.7735 (tpp) cc_final: 0.7404 (tpp) REVERT: A 240 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7196 (mm-30) REVERT: A 258 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.6909 (p) REVERT: A 314 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 447 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: J 62 TYR cc_start: 0.8086 (t80) cc_final: 0.7657 (m-80) REVERT: J 100 LEU cc_start: 0.8537 (tt) cc_final: 0.8132 (tp) REVERT: J 205 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8262 (tm-30) REVERT: J 229 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: E 50 ASN cc_start: 0.8317 (t0) cc_final: 0.7819 (m-40) REVERT: K 174 GLN cc_start: 0.8782 (tt0) cc_final: 0.8180 (tm-30) REVERT: K 186 LYS cc_start: 0.7317 (mttt) cc_final: 0.6986 (mmtt) REVERT: X 435 GLN cc_start: 0.8689 (pm20) cc_final: 0.8255 (pm20) REVERT: L 757 LYS cc_start: 0.8263 (mttp) cc_final: 0.7952 (mtmm) REVERT: L 801 GLU cc_start: 0.7685 (pt0) cc_final: 0.7476 (pt0) REVERT: L 808 ASP cc_start: 0.6726 (t0) cc_final: 0.6241 (t0) REVERT: L 860 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6830 (pt) outliers start: 64 outliers final: 44 residues processed: 313 average time/residue: 0.1478 time to fit residues: 73.3400 Evaluate side-chains 309 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 169 GLN Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 201 ASN Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 860 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 215 optimal weight: 2.9990 chunk 178 optimal weight: 0.0170 chunk 123 optimal weight: 7.9990 chunk 251 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 470 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.116477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088365 restraints weight = 56036.883| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.23 r_work: 0.3275 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21885 Z= 0.117 Angle : 0.594 11.769 29583 Z= 0.296 Chirality : 0.041 0.219 3381 Planarity : 0.004 0.058 3775 Dihedral : 4.423 28.559 2835 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.76 % Allowed : 16.21 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2581 helix: 1.20 (0.15), residues: 1273 sheet: -1.82 (0.45), residues: 136 loop : -1.90 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 482 TYR 0.015 0.001 TYR J 275 PHE 0.021 0.001 PHE F 330 TRP 0.016 0.001 TRP D 315 HIS 0.009 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00267 (21882) covalent geometry : angle 0.59383 (29583) hydrogen bonds : bond 0.03476 ( 851) hydrogen bonds : angle 3.87626 ( 2445) metal coordination : bond 0.00140 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7831 (ttm170) REVERT: F 330 PHE cc_start: 0.8962 (t80) cc_final: 0.8643 (t80) REVERT: F 361 GLU cc_start: 0.8178 (tp30) cc_final: 0.7948 (tp30) REVERT: F 408 GLU cc_start: 0.8796 (pp20) cc_final: 0.8542 (pp20) REVERT: H 349 ASP cc_start: 0.8507 (t70) cc_final: 0.7964 (t0) REVERT: H 451 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5648 (mt-10) REVERT: D 168 TYR cc_start: 0.8524 (t80) cc_final: 0.8266 (t80) REVERT: D 320 MET cc_start: 0.8866 (tpp) cc_final: 0.8613 (tpp) REVERT: D 331 GLU cc_start: 0.7018 (tp30) cc_final: 0.6764 (tp30) REVERT: D 352 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 438 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8219 (mm-30) REVERT: M 316 ILE cc_start: 0.8510 (tp) cc_final: 0.8279 (tp) REVERT: I 333 MET cc_start: 0.8500 (tmm) cc_final: 0.8051 (tmm) REVERT: I 461 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: G 32 MET cc_start: 0.6814 (tpp) cc_final: 0.5581 (mpp) REVERT: G 259 LYS cc_start: 0.8472 (mptm) cc_final: 0.8074 (tptp) REVERT: G 263 LYS cc_start: 0.8255 (tttt) cc_final: 0.7837 (tptp) REVERT: G 330 GLN cc_start: 0.8504 (mt0) cc_final: 0.8132 (mt0) REVERT: G 366 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.6400 (mtp180) REVERT: G 379 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7594 (ptp-170) REVERT: A 101 LEU cc_start: 0.8152 (tp) cc_final: 0.7863 (tp) REVERT: A 202 MET cc_start: 0.7719 (tpp) cc_final: 0.7232 (tpp) REVERT: A 258 THR cc_start: 0.7277 (OUTLIER) cc_final: 0.6932 (p) REVERT: A 314 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 447 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: J 62 TYR cc_start: 0.8056 (t80) cc_final: 0.7661 (m-80) REVERT: J 100 LEU cc_start: 0.8496 (tt) cc_final: 0.8088 (tp) REVERT: J 205 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8243 (tm-30) REVERT: J 229 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: E 50 ASN cc_start: 0.8372 (t0) cc_final: 0.7766 (m110) REVERT: E 67 LYS cc_start: 0.8759 (tptp) cc_final: 0.8153 (mmmm) REVERT: C 196 PHE cc_start: 0.8573 (m-80) cc_final: 0.8302 (m-80) REVERT: K 174 GLN cc_start: 0.8788 (tt0) cc_final: 0.8395 (tp40) REVERT: K 186 LYS cc_start: 0.7320 (mttt) cc_final: 0.7076 (mmtp) REVERT: X 435 GLN cc_start: 0.8705 (pm20) cc_final: 0.8246 (pm20) REVERT: X 440 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5918 (mt0) REVERT: L 757 LYS cc_start: 0.8212 (mttp) cc_final: 0.7950 (mtmm) REVERT: L 808 ASP cc_start: 0.6425 (t0) cc_final: 0.5992 (t0) outliers start: 67 outliers final: 45 residues processed: 328 average time/residue: 0.1423 time to fit residues: 73.9342 Evaluate side-chains 308 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 240 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 318 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.116505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088190 restraints weight = 55758.381| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.28 r_work: 0.3268 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21885 Z= 0.123 Angle : 0.602 12.386 29583 Z= 0.300 Chirality : 0.042 0.307 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.341 26.280 2835 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.55 % Allowed : 16.13 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2581 helix: 1.19 (0.15), residues: 1282 sheet: -1.70 (0.46), residues: 134 loop : -1.83 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 482 TYR 0.013 0.001 TYR D 330 PHE 0.020 0.001 PHE F 330 TRP 0.015 0.001 TRP X 481 HIS 0.008 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00282 (21882) covalent geometry : angle 0.60194 (29583) hydrogen bonds : bond 0.03466 ( 851) hydrogen bonds : angle 3.86863 ( 2445) metal coordination : bond 0.00160 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7833 (ttm170) REVERT: F 330 PHE cc_start: 0.8877 (t80) cc_final: 0.8588 (t80) REVERT: F 361 GLU cc_start: 0.8186 (tp30) cc_final: 0.7957 (tp30) REVERT: F 408 GLU cc_start: 0.8745 (pp20) cc_final: 0.8513 (pp20) REVERT: F 410 TYR cc_start: 0.6653 (p90) cc_final: 0.6291 (p90) REVERT: H 331 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: H 349 ASP cc_start: 0.8509 (t70) cc_final: 0.8077 (t0) REVERT: H 451 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5844 (mt-10) REVERT: D 168 TYR cc_start: 0.8533 (t80) cc_final: 0.8281 (t80) REVERT: D 320 MET cc_start: 0.8896 (tpp) cc_final: 0.8626 (tpp) REVERT: D 331 GLU cc_start: 0.7051 (tp30) cc_final: 0.6749 (tp30) REVERT: D 352 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7781 (mm-30) REVERT: D 438 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8378 (mm-30) REVERT: M 32 MET cc_start: 0.6144 (ttm) cc_final: 0.5873 (ttm) REVERT: I 333 MET cc_start: 0.8521 (tmm) cc_final: 0.8089 (tmm) REVERT: I 461 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: G 32 MET cc_start: 0.6826 (tpp) cc_final: 0.5599 (mpp) REVERT: G 259 LYS cc_start: 0.8481 (mptm) cc_final: 0.8072 (tptp) REVERT: G 263 LYS cc_start: 0.8255 (tttt) cc_final: 0.7828 (tptp) REVERT: G 330 GLN cc_start: 0.8500 (mt0) cc_final: 0.8124 (mt0) REVERT: G 366 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.6771 (mtp180) REVERT: G 379 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.7584 (ptp-170) REVERT: A 101 LEU cc_start: 0.8197 (tp) cc_final: 0.7891 (tp) REVERT: A 202 MET cc_start: 0.7732 (tpp) cc_final: 0.7291 (tpp) REVERT: A 258 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6821 (p) REVERT: A 314 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 447 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: J 62 TYR cc_start: 0.8048 (t80) cc_final: 0.7650 (m-80) REVERT: J 205 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8225 (tm-30) REVERT: J 229 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: E 50 ASN cc_start: 0.8344 (t0) cc_final: 0.7836 (m110) REVERT: C 196 PHE cc_start: 0.8604 (m-80) cc_final: 0.8341 (m-80) REVERT: K 174 GLN cc_start: 0.8779 (tt0) cc_final: 0.8381 (tp40) REVERT: X 435 GLN cc_start: 0.8715 (pm20) cc_final: 0.8258 (pm20) REVERT: X 440 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5946 (mt0) REVERT: L 757 LYS cc_start: 0.8215 (mttp) cc_final: 0.7939 (mtmm) REVERT: L 808 ASP cc_start: 0.6480 (t0) cc_final: 0.6036 (t0) REVERT: L 869 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7770 (mtt90) outliers start: 62 outliers final: 44 residues processed: 309 average time/residue: 0.1421 time to fit residues: 69.4060 Evaluate side-chains 305 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 29 optimal weight: 0.7980 chunk 226 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 253 optimal weight: 0.1980 chunk 242 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN I 264 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.117239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089082 restraints weight = 55950.001| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.24 r_work: 0.3300 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21885 Z= 0.113 Angle : 0.601 12.885 29583 Z= 0.298 Chirality : 0.042 0.289 3381 Planarity : 0.004 0.057 3775 Dihedral : 4.290 27.702 2835 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.39 % Allowed : 16.04 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2581 helix: 1.30 (0.15), residues: 1280 sheet: -1.70 (0.45), residues: 135 loop : -1.80 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 482 TYR 0.014 0.001 TYR D 330 PHE 0.019 0.001 PHE F 330 TRP 0.014 0.001 TRP D 315 HIS 0.008 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00258 (21882) covalent geometry : angle 0.60080 (29583) hydrogen bonds : bond 0.03333 ( 851) hydrogen bonds : angle 3.80753 ( 2445) metal coordination : bond 0.00112 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7822 (ttm170) REVERT: F 330 PHE cc_start: 0.8870 (t80) cc_final: 0.8536 (t80) REVERT: F 361 GLU cc_start: 0.8160 (tp30) cc_final: 0.7910 (tp30) REVERT: F 410 TYR cc_start: 0.7009 (p90) cc_final: 0.6737 (p90) REVERT: H 331 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: H 349 ASP cc_start: 0.8455 (t70) cc_final: 0.8013 (t0) REVERT: H 451 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5882 (mt-10) REVERT: D 320 MET cc_start: 0.8922 (tpp) cc_final: 0.8658 (tpp) REVERT: D 331 GLU cc_start: 0.6981 (tp30) cc_final: 0.6705 (tp30) REVERT: D 352 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7795 (mm-30) REVERT: D 437 MET cc_start: 0.8255 (ppp) cc_final: 0.8037 (ppp) REVERT: D 438 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8360 (mm-30) REVERT: M 32 MET cc_start: 0.6184 (ttm) cc_final: 0.5835 (ttm) REVERT: I 264 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7521 (t0) REVERT: I 333 MET cc_start: 0.8449 (tmm) cc_final: 0.8037 (tmm) REVERT: I 461 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.5624 (m-80) REVERT: G 259 LYS cc_start: 0.8466 (mptm) cc_final: 0.8066 (tptp) REVERT: G 263 LYS cc_start: 0.8259 (tttt) cc_final: 0.7841 (tptp) REVERT: G 283 LEU cc_start: 0.8801 (tt) cc_final: 0.8588 (tt) REVERT: G 330 GLN cc_start: 0.8513 (mt0) cc_final: 0.8129 (mt0) REVERT: G 366 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.6821 (mtp180) REVERT: G 379 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7560 (ptp-170) REVERT: A 101 LEU cc_start: 0.8194 (tp) cc_final: 0.7905 (tp) REVERT: A 258 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.6960 (p) REVERT: A 314 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7790 (mp) REVERT: J 62 TYR cc_start: 0.7979 (t80) cc_final: 0.7590 (m-80) REVERT: J 205 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8204 (tm-30) REVERT: J 229 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7215 (m-30) REVERT: E 50 ASN cc_start: 0.8319 (t0) cc_final: 0.7833 (m110) REVERT: C 196 PHE cc_start: 0.8627 (m-80) cc_final: 0.8365 (m-80) REVERT: K 174 GLN cc_start: 0.8776 (tt0) cc_final: 0.8392 (tp40) REVERT: X 435 GLN cc_start: 0.8673 (pm20) cc_final: 0.8225 (pm20) REVERT: X 440 GLN cc_start: 0.6006 (OUTLIER) cc_final: 0.5802 (mt0) REVERT: L 757 LYS cc_start: 0.8184 (mttp) cc_final: 0.7909 (mtmm) REVERT: L 808 ASP cc_start: 0.6371 (t0) cc_final: 0.5986 (t70) REVERT: L 869 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7735 (mtt90) outliers start: 58 outliers final: 45 residues processed: 311 average time/residue: 0.1444 time to fit residues: 71.2434 Evaluate side-chains 313 residues out of total 2458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 261 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 368 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain M residue 104 TYR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 264 ASN Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 461 TYR Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain G residue 215 HIS Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 254 GLN Chi-restraints excluded: chain J residue 259 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 440 GLN Chi-restraints excluded: chain X residue 485 ILE Chi-restraints excluded: chain L residue 755 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 157 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 HIS H 470 ASN I 264 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** X 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.117147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088934 restraints weight = 56123.908| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.24 r_work: 0.3289 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 21885 Z= 0.181 Angle : 0.765 59.194 29583 Z= 0.424 Chirality : 0.042 0.291 3381 Planarity : 0.004 0.058 3775 Dihedral : 4.316 27.561 2835 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.26 % Allowed : 16.41 % Favored : 81.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2581 helix: 1.29 (0.15), residues: 1280 sheet: -1.70 (0.45), residues: 135 loop : -1.80 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 482 TYR 0.025 0.001 TYR G 361 PHE 0.018 0.001 PHE F 330 TRP 0.012 0.001 TRP D 315 HIS 0.007 0.001 HIS A 270 Details of bonding type rmsd covalent geometry : bond 0.00415 (21882) covalent geometry : angle 0.76485 (29583) hydrogen bonds : bond 0.03359 ( 851) hydrogen bonds : angle 3.81003 ( 2445) metal coordination : bond 0.00944 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5569.40 seconds wall clock time: 96 minutes 2.25 seconds (5762.25 seconds total)