Starting phenix.real_space_refine on Sun Sep 29 05:37:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_9905.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_9905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_9905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_9905.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/09_2024/6k15_9905.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.66, per 1000 atoms: 0.54 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: 5.27 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.00 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: 5.59 Time building geometry restraints manager: 6.17 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: 2.250 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 48.250 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.970 ------------------------------------------------------------------------------- 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 : 0.005 0.071 21882 Z= 0.317 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.003 TRP F 371 HIS 0.013 0.002 HIS A 270 PHE 0.034 0.002 PHE J 83 TYR 0.026 0.002 TYR F 410 ARG 0.013 0.001 ARG F 338 *********************** 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 fitting. rotamer outliers: 8 poor density : 658 time to evaluate : 2.244 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: 0.7722 (tt) REVERT: F 409 ILE cc_start: 0.8925 (mm) cc_final: 0.8650 (mt) REVERT: H 349 ASP cc_start: 0.8325 (t70) cc_final: 0.7654 (t0) REVERT: D 94 ILE cc_start: 0.7582 (pp) cc_final: 0.7274 (pt) 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: 0.8205 (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: 0.7510 (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: 0.8381 (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: 0.8071 (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: 0.8261 (mtmm) REVERT: L 860 LEU cc_start: 0.7920 (pt) cc_final: 0.7221 (pt) outliers start: 8 outliers final: 2 residues processed: 665 average time/residue: 0.3624 time to fit residues: 354.4288 Evaluate side-chains 310 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 218 optimal weight: 0.0070 chunk 196 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 203 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 235 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 329 HIS I 432 HIS I 463 ASN G 10 GLN 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 494 ASN X 600 ASN L 800 ASN L 810 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21882 Z= 0.167 Angle : 0.630 9.587 29583 Z= 0.327 Chirality : 0.042 0.165 3381 Planarity : 0.005 0.074 3775 Dihedral : 5.460 44.039 2837 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.89 % Allowed : 10.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2581 helix: -0.81 (0.14), residues: 1293 sheet: -2.97 (0.35), residues: 149 loop : -2.67 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 334 HIS 0.006 0.001 HIS A 270 PHE 0.016 0.001 PHE J 83 TYR 0.027 0.001 TYR X 368 ARG 0.012 0.001 ARG L 764 *********************** 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 423 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 377 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7734 (ttm170) REVERT: F 347 GLN cc_start: 0.7831 (tt0) cc_final: 0.7502 (tm-30) REVERT: H 324 LEU cc_start: 0.8780 (mp) cc_final: 0.8334 (mp) REVERT: H 328 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7294 (mt-10) REVERT: H 349 ASP cc_start: 0.8217 (t70) cc_final: 0.7833 (t0) REVERT: H 390 MET cc_start: 0.7485 (mpp) cc_final: 0.7020 (mmt) REVERT: H 468 MET cc_start: 0.8608 (tpp) cc_final: 0.8267 (tpp) REVERT: D 94 ILE cc_start: 0.7573 (pp) cc_final: 0.7315 (pt) REVERT: D 420 LYS cc_start: 0.6336 (tmtm) cc_final: 0.6040 (mmtm) REVERT: D 437 MET cc_start: 0.7645 (tmm) cc_final: 0.7308 (tmm) REVERT: D 438 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7860 (mm-30) REVERT: G 259 LYS cc_start: 0.8366 (mptm) cc_final: 0.7995 (tptp) REVERT: G 263 LYS cc_start: 0.8046 (tttt) cc_final: 0.7573 (ttpt) REVERT: G 330 GLN cc_start: 0.8294 (mt0) cc_final: 0.8009 (mt0) REVERT: A 258 THR cc_start: 0.7437 (OUTLIER) cc_final: 0.7041 (p) REVERT: J 244 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7428 (mt-10) REVERT: E 50 ASN cc_start: 0.8224 (t0) cc_final: 0.7619 (m110) REVERT: C 217 LYS cc_start: 0.7059 (mttt) cc_final: 0.6671 (mtmt) REVERT: K 174 GLN cc_start: 0.8336 (tt0) cc_final: 0.8034 (tm-30) REVERT: K 186 LYS cc_start: 0.7244 (mttt) cc_final: 0.6868 (mmtt) REVERT: X 435 GLN cc_start: 0.8442 (pm20) cc_final: 0.8130 (pm20) REVERT: X 440 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: X 481 TRP cc_start: 0.7764 (m-10) cc_final: 0.7506 (m-10) REVERT: L 755 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7020 (tp) REVERT: L 757 LYS cc_start: 0.8307 (mttp) cc_final: 0.7788 (tptt) outliers start: 46 outliers final: 17 residues processed: 410 average time/residue: 0.3220 time to fit residues: 203.9641 Evaluate side-chains 296 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 394 ASP 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 254 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 233 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 239 GLN I 465 ASN ** 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 X 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21882 Z= 0.178 Angle : 0.590 11.039 29583 Z= 0.302 Chirality : 0.042 0.151 3381 Planarity : 0.004 0.063 3775 Dihedral : 4.914 31.342 2836 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.43 % Allowed : 12.01 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2581 helix: 0.02 (0.14), residues: 1294 sheet: -2.81 (0.34), residues: 153 loop : -2.39 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 791 HIS 0.006 0.001 HIS A 270 PHE 0.012 0.001 PHE J 83 TYR 0.019 0.001 TYR X 368 ARG 0.006 0.000 ARG M 77 *********************** 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 361 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 302 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7498 (ttm170) REVERT: H 349 ASP cc_start: 0.8309 (t70) cc_final: 0.7923 (t0) REVERT: H 390 MET cc_start: 0.7683 (mpp) cc_final: 0.7143 (mmt) REVERT: D 168 TYR cc_start: 0.8470 (t80) cc_final: 0.8059 (t80) REVERT: D 437 MET cc_start: 0.7875 (tmm) cc_final: 0.7592 (tmm) REVERT: D 438 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7904 (mm-30) REVERT: D 456 MET cc_start: 0.8405 (ppp) cc_final: 0.7745 (ppp) REVERT: D 468 MET cc_start: 0.7691 (tmm) cc_final: 0.7491 (tmm) REVERT: D 475 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7566 (mp) REVERT: I 333 MET cc_start: 0.8206 (tmm) cc_final: 0.7800 (tmm) REVERT: G 259 LYS cc_start: 0.8352 (mptm) cc_final: 0.7958 (tptp) REVERT: G 263 LYS cc_start: 0.8043 (tttt) cc_final: 0.7639 (tptp) REVERT: G 330 GLN cc_start: 0.8191 (mt0) cc_final: 0.7816 (mt0) REVERT: A 132 LEU cc_start: 0.8350 (tp) cc_final: 0.8119 (tp) REVERT: A 258 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7083 (p) REVERT: J 62 TYR cc_start: 0.8072 (t80) cc_final: 0.7656 (m-80) REVERT: J 204 ASN cc_start: 0.8591 (t0) cc_final: 0.8208 (t0) REVERT: E 50 ASN cc_start: 0.8207 (t0) cc_final: 0.7622 (m110) REVERT: E 67 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8224 (mmmm) REVERT: C 217 LYS cc_start: 0.6918 (mttt) cc_final: 0.6701 (mtmt) REVERT: K 174 GLN cc_start: 0.8312 (tt0) cc_final: 0.7996 (tm-30) REVERT: K 186 LYS cc_start: 0.7320 (mttt) cc_final: 0.6974 (mmtt) REVERT: X 368 TYR cc_start: 0.6766 (t80) cc_final: 0.6527 (t80) REVERT: X 435 GLN cc_start: 0.8308 (pm20) cc_final: 0.7993 (pm20) REVERT: X 481 TRP cc_start: 0.7634 (m-10) cc_final: 0.7322 (m-10) REVERT: L 757 LYS cc_start: 0.8281 (mttp) cc_final: 0.8049 (mtmm) REVERT: L 801 GLU cc_start: 0.6892 (pt0) cc_final: 0.6670 (pt0) REVERT: L 869 ARG cc_start: 0.7807 (mpt-90) cc_final: 0.7218 (mtt180) REVERT: L 877 HIS cc_start: 0.7546 (t-90) cc_final: 0.7253 (t-90) outliers start: 59 outliers final: 27 residues processed: 350 average time/residue: 0.3300 time to fit residues: 177.7356 Evaluate side-chains 295 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 349 LEU 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 184 THR 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 M residue 326 LEU 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 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 K residue 191 GLU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 485 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 123 ASN I 334 ASN ** 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** ** L 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21882 Z= 0.276 Angle : 0.620 12.862 29583 Z= 0.318 Chirality : 0.043 0.186 3381 Planarity : 0.004 0.061 3775 Dihedral : 4.871 24.428 2835 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.67 % Allowed : 12.55 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2581 helix: 0.45 (0.15), residues: 1273 sheet: -2.42 (0.39), residues: 132 loop : -2.26 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 396 HIS 0.005 0.001 HIS A 270 PHE 0.013 0.002 PHE H 296 TYR 0.022 0.002 TYR H 272 ARG 0.006 0.001 ARG G 172 *********************** 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 346 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 281 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7738 (ttm170) REVERT: H 349 ASP cc_start: 0.8387 (t70) cc_final: 0.7763 (t0) REVERT: D 168 TYR cc_start: 0.8518 (t80) cc_final: 0.8268 (t80) REVERT: D 438 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7698 (mt-10) REVERT: M 32 MET cc_start: 0.5702 (ttt) cc_final: 0.5343 (ttt) REVERT: I 333 MET cc_start: 0.8389 (tmm) cc_final: 0.7943 (tmm) REVERT: I 471 MET cc_start: 0.8314 (mmm) cc_final: 0.7941 (mmm) REVERT: G 259 LYS cc_start: 0.8387 (mptm) cc_final: 0.8032 (tptp) REVERT: G 263 LYS cc_start: 0.7955 (tttt) cc_final: 0.7671 (tptp) REVERT: G 266 GLU cc_start: 0.6946 (pm20) cc_final: 0.6666 (pm20) REVERT: G 330 GLN cc_start: 0.8158 (mt0) cc_final: 0.7746 (mt0) REVERT: A 258 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7065 (p) REVERT: J 62 TYR cc_start: 0.8081 (t80) cc_final: 0.7683 (m-80) REVERT: J 204 ASN cc_start: 0.8591 (t0) cc_final: 0.8368 (t0) REVERT: J 205 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 50 ASN cc_start: 0.8312 (t0) cc_final: 0.7646 (m110) REVERT: E 67 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8190 (mmmm) REVERT: C 217 LYS cc_start: 0.6874 (mttt) cc_final: 0.6664 (mtmt) REVERT: K 174 GLN cc_start: 0.8357 (tt0) cc_final: 0.8025 (tm-30) REVERT: K 186 LYS cc_start: 0.7351 (mttt) cc_final: 0.7014 (mmtt) REVERT: X 435 GLN cc_start: 0.8399 (pm20) cc_final: 0.8016 (pm20) REVERT: X 481 TRP cc_start: 0.7716 (m-10) cc_final: 0.7395 (m-10) REVERT: X 505 MET cc_start: 0.6719 (ttp) cc_final: 0.6405 (tmm) REVERT: L 757 LYS cc_start: 0.8161 (mttp) cc_final: 0.7928 (mtmm) REVERT: L 877 HIS cc_start: 0.7765 (t-90) cc_final: 0.7533 (t-170) outliers start: 65 outliers final: 46 residues processed: 327 average time/residue: 0.3309 time to fit residues: 167.8196 Evaluate side-chains 296 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain F residue 419 LEU Chi-restraints excluded: chain H residue 139 ILE 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 35 ASN 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 25 ASP 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 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 J residue 46 ILE Chi-restraints excluded: chain J residue 215 THR 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.9990 chunk 142 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 186 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 470 ASN G 220 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21882 Z= 0.165 Angle : 0.563 9.639 29583 Z= 0.287 Chirality : 0.041 0.152 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.561 26.004 2835 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.59 % Allowed : 13.78 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2581 helix: 0.82 (0.15), residues: 1274 sheet: -2.38 (0.38), residues: 153 loop : -2.12 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 791 HIS 0.008 0.001 HIS A 270 PHE 0.009 0.001 PHE M 311 TYR 0.017 0.001 TYR G 361 ARG 0.006 0.000 ARG I 482 *********************** 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 353 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 290 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7671 (ttm170) REVERT: H 297 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: H 349 ASP cc_start: 0.8159 (t70) cc_final: 0.7803 (t0) REVERT: H 459 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (mm) REVERT: D 437 MET cc_start: 0.7803 (ppp) cc_final: 0.7492 (ppp) REVERT: D 438 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7936 (mm-30) REVERT: D 475 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (mp) REVERT: M 32 MET cc_start: 0.5906 (ttt) cc_final: 0.5553 (ttt) REVERT: I 333 MET cc_start: 0.8406 (tmm) cc_final: 0.7905 (tmm) REVERT: I 461 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: G 259 LYS cc_start: 0.8373 (mptm) cc_final: 0.8024 (tptp) REVERT: G 330 GLN cc_start: 0.8169 (mt0) cc_final: 0.7789 (mt0) REVERT: G 379 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7418 (ptp-170) REVERT: A 258 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6933 (p) REVERT: A 314 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 474 ARG cc_start: 0.6980 (mmt-90) cc_final: 0.6592 (mmt180) REVERT: J 62 TYR cc_start: 0.8029 (t80) cc_final: 0.7635 (m-80) REVERT: J 204 ASN cc_start: 0.8528 (t0) cc_final: 0.8324 (t0) REVERT: E 50 ASN cc_start: 0.8300 (t0) cc_final: 0.7763 (m110) REVERT: K 174 GLN cc_start: 0.8356 (tt0) cc_final: 0.7996 (tm-30) REVERT: K 186 LYS cc_start: 0.7468 (mttt) cc_final: 0.6978 (mmtt) REVERT: X 435 GLN cc_start: 0.8478 (pm20) cc_final: 0.8042 (pm20) REVERT: X 481 TRP cc_start: 0.7651 (m-10) cc_final: 0.7450 (m-10) REVERT: L 808 ASP cc_start: 0.6368 (t0) cc_final: 0.5973 (t0) outliers start: 63 outliers final: 38 residues processed: 339 average time/residue: 0.3198 time to fit residues: 169.0431 Evaluate side-chains 304 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 2.516 ------------------------------------------------------------------------------- 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 297 GLN Chi-restraints excluded: chain H residue 392 CYS 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 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 115 ILE 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 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 300 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 269 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN X 493 GLN ** L 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21882 Z= 0.171 Angle : 0.570 10.386 29583 Z= 0.288 Chirality : 0.041 0.154 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.413 24.521 2835 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.59 % Allowed : 15.10 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 2581 helix: 1.02 (0.15), residues: 1280 sheet: -2.17 (0.40), residues: 153 loop : -2.01 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 791 HIS 0.008 0.001 HIS A 270 PHE 0.034 0.001 PHE G 359 TYR 0.019 0.001 TYR D 168 ARG 0.009 0.000 ARG X 370 *********************** 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 349 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 286 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7713 (ttm170) REVERT: F 361 GLU cc_start: 0.7854 (tp30) cc_final: 0.7619 (tp30) REVERT: F 408 GLU cc_start: 0.8233 (pp20) cc_final: 0.7926 (pp20) REVERT: F 410 TYR cc_start: 0.6293 (p90) cc_final: 0.5918 (p90) REVERT: H 148 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8181 (mtm) REVERT: H 297 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: H 331 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: H 349 ASP cc_start: 0.8239 (t70) cc_final: 0.7802 (t0) REVERT: H 459 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8158 (mm) REVERT: D 438 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7989 (mm-30) REVERT: D 468 MET cc_start: 0.7903 (tmm) cc_final: 0.7566 (ppp) REVERT: M 89 LEU cc_start: 0.8974 (mt) cc_final: 0.8742 (mp) REVERT: I 333 MET cc_start: 0.8393 (tmm) cc_final: 0.7984 (tmm) REVERT: I 461 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: G 259 LYS cc_start: 0.8391 (mptm) cc_final: 0.7925 (tptp) REVERT: G 263 LYS cc_start: 0.8911 (tptp) cc_final: 0.7883 (mtpt) REVERT: G 330 GLN cc_start: 0.8157 (mt0) cc_final: 0.7758 (mt0) REVERT: A 258 THR cc_start: 0.7316 (OUTLIER) cc_final: 0.6949 (p) REVERT: A 314 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 474 ARG cc_start: 0.7024 (mmt-90) cc_final: 0.6620 (mmt180) REVERT: J 62 TYR cc_start: 0.8023 (t80) cc_final: 0.7621 (m-80) REVERT: J 204 ASN cc_start: 0.8510 (t0) cc_final: 0.8301 (t0) REVERT: J 205 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7796 (tm-30) REVERT: E 50 ASN cc_start: 0.8252 (t0) cc_final: 0.7792 (m-40) REVERT: K 174 GLN cc_start: 0.8346 (tt0) cc_final: 0.7989 (tm-30) REVERT: K 186 LYS cc_start: 0.7466 (mttt) cc_final: 0.7061 (mmtt) REVERT: X 435 GLN cc_start: 0.8496 (pm20) cc_final: 0.8078 (pm20) REVERT: X 481 TRP cc_start: 0.7698 (m-10) cc_final: 0.7286 (m-10) REVERT: L 808 ASP cc_start: 0.6399 (t0) cc_final: 0.5996 (t0) outliers start: 63 outliers final: 42 residues processed: 335 average time/residue: 0.3133 time to fit residues: 163.4257 Evaluate side-chains 309 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 3.159 ------------------------------------------------------------------------------- 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 148 MET Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 331 GLU 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 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 300 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 269 LEU 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 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 K residue 192 LEU Chi-restraints excluded: chain X residue 374 THR Chi-restraints excluded: chain X residue 438 SER 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 241 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN H 314 ASN H 470 ASN M 206 GLN I 425 HIS G 220 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 254 GLN J 259 GLN J 272 ASN E 58 GLN ** X 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 758 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21882 Z= 0.436 Angle : 0.737 16.773 29583 Z= 0.373 Chirality : 0.046 0.188 3381 Planarity : 0.005 0.064 3775 Dihedral : 5.023 25.646 2835 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.13 % Allowed : 15.26 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2581 helix: 0.68 (0.15), residues: 1280 sheet: -2.03 (0.42), residues: 143 loop : -2.09 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 791 HIS 0.008 0.001 HIS F 358 PHE 0.024 0.002 PHE F 330 TYR 0.030 0.002 TYR H 272 ARG 0.007 0.001 ARG G 290 *********************** 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 334 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 258 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7846 (ttm170) REVERT: F 408 GLU cc_start: 0.8399 (pp20) cc_final: 0.8160 (pp20) REVERT: H 148 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: H 169 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7927 (mm110) REVERT: H 297 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: H 349 ASP cc_start: 0.8459 (t70) cc_final: 0.8084 (t0) REVERT: H 459 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8105 (mm) REVERT: D 437 MET cc_start: 0.7933 (ppp) cc_final: 0.7720 (ppp) REVERT: I 333 MET cc_start: 0.8529 (tmm) cc_final: 0.8074 (tmm) REVERT: I 461 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: G 259 LYS cc_start: 0.8501 (mptm) cc_final: 0.8129 (tptp) REVERT: G 330 GLN cc_start: 0.8180 (mt0) cc_final: 0.7742 (mt0) REVERT: G 379 ARG cc_start: 0.7650 (ptp-170) cc_final: 0.7370 (ptp-170) REVERT: A 240 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7091 (mm-30) REVERT: A 314 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7847 (mp) REVERT: A 474 ARG cc_start: 0.7093 (mmt-90) cc_final: 0.6867 (mmt180) REVERT: J 100 LEU cc_start: 0.8575 (tt) cc_final: 0.8216 (tp) REVERT: J 204 ASN cc_start: 0.8621 (t0) cc_final: 0.8252 (t0) REVERT: J 205 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7774 (tm-30) REVERT: E 50 ASN cc_start: 0.8416 (t0) cc_final: 0.7852 (m-40) REVERT: K 174 GLN cc_start: 0.8442 (tt0) cc_final: 0.8056 (tm-30) REVERT: K 186 LYS cc_start: 0.7566 (mttt) cc_final: 0.7305 (mmtt) REVERT: X 435 GLN cc_start: 0.8514 (pm20) cc_final: 0.8090 (pm20) REVERT: X 481 TRP cc_start: 0.7776 (m-10) cc_final: 0.7322 (m-10) REVERT: L 757 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6570 (mmtt) REVERT: L 808 ASP cc_start: 0.6680 (t0) cc_final: 0.6117 (t0) REVERT: L 869 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.7733 (mtt180) outliers start: 76 outliers final: 54 residues processed: 313 average time/residue: 0.3269 time to fit residues: 158.6266 Evaluate side-chains 301 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 241 time to evaluate : 2.553 ------------------------------------------------------------------------------- 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 F residue 425 GLN Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain H residue 148 MET Chi-restraints excluded: chain H residue 169 GLN 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 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 M residue 332 CYS Chi-restraints excluded: chain M residue 536 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 29 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 184 TYR 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 312 THR Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 239 ASN 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 46 ILE Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 LEU 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 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 758 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 470 ASN M 206 GLN G 220 GLN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 800 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21882 Z= 0.224 Angle : 0.634 12.820 29583 Z= 0.316 Chirality : 0.043 0.177 3381 Planarity : 0.004 0.061 3775 Dihedral : 4.716 27.753 2835 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.88 % Allowed : 15.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2581 helix: 0.98 (0.15), residues: 1269 sheet: -2.18 (0.42), residues: 147 loop : -1.96 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 315 HIS 0.009 0.001 HIS A 270 PHE 0.022 0.001 PHE G 359 TYR 0.016 0.001 TYR D 168 ARG 0.017 0.001 ARG M 136 *********************** 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 335 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 265 time to evaluate : 2.677 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7874 (ttm170) REVERT: F 330 PHE cc_start: 0.8915 (t80) cc_final: 0.8562 (t80) REVERT: F 408 GLU cc_start: 0.8443 (pp20) cc_final: 0.8200 (pp20) REVERT: F 410 TYR cc_start: 0.6251 (p90) cc_final: 0.5988 (p90) REVERT: H 297 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: H 349 ASP cc_start: 0.8280 (t70) cc_final: 0.7731 (t0) REVERT: H 459 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8088 (mm) REVERT: D 145 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7890 (p0) REVERT: D 437 MET cc_start: 0.7998 (ppp) cc_final: 0.7711 (ppp) REVERT: D 438 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8229 (mm-30) REVERT: M 32 MET cc_start: 0.6123 (ttm) cc_final: 0.5829 (ttm) REVERT: I 333 MET cc_start: 0.8469 (tmm) cc_final: 0.7988 (tmm) REVERT: I 461 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: G 259 LYS cc_start: 0.8471 (mptm) cc_final: 0.8104 (tptp) REVERT: G 330 GLN cc_start: 0.8140 (mt0) cc_final: 0.7699 (mt0) REVERT: G 366 ARG cc_start: 0.7729 (mmm-85) cc_final: 0.6751 (mtp180) REVERT: G 379 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.7323 (ptp-170) REVERT: A 240 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7008 (mm-30) REVERT: A 258 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.6985 (p) REVERT: A 314 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 474 ARG cc_start: 0.7120 (mmt-90) cc_final: 0.6913 (mmt180) REVERT: J 62 TYR cc_start: 0.7979 (t80) cc_final: 0.7606 (m-80) REVERT: J 100 LEU cc_start: 0.8519 (tt) cc_final: 0.8138 (tp) REVERT: J 204 ASN cc_start: 0.8542 (t0) cc_final: 0.8163 (t0) REVERT: J 205 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 50 ASN cc_start: 0.8325 (t0) cc_final: 0.7846 (m-40) REVERT: C 196 PHE cc_start: 0.8564 (m-80) cc_final: 0.8302 (m-80) REVERT: K 174 GLN cc_start: 0.8433 (tt0) cc_final: 0.8068 (tm-30) REVERT: K 186 LYS cc_start: 0.7480 (mttt) cc_final: 0.7132 (mmtt) REVERT: X 435 GLN cc_start: 0.8646 (pm20) cc_final: 0.8249 (pm20) REVERT: X 481 TRP cc_start: 0.7708 (m-10) cc_final: 0.7401 (m-10) REVERT: L 757 LYS cc_start: 0.7107 (mtmm) cc_final: 0.6353 (mmtt) REVERT: L 800 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6786 (m110) REVERT: L 808 ASP cc_start: 0.6391 (t0) cc_final: 0.5890 (t0) outliers start: 70 outliers final: 46 residues processed: 316 average time/residue: 0.3192 time to fit residues: 157.2902 Evaluate side-chains 307 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 F residue 425 GLN Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 435 LEU Chi-restraints excluded: chain H residue 459 LEU Chi-restraints excluded: chain D residue 145 ASN 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 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 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 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 J residue 215 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 254 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 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 758 ASN Chi-restraints excluded: chain L residue 800 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 0.0980 chunk 239 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 182 optimal weight: 0.0270 chunk 71 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21882 Z= 0.162 Angle : 0.617 12.578 29583 Z= 0.305 Chirality : 0.042 0.232 3381 Planarity : 0.004 0.060 3775 Dihedral : 4.482 25.484 2835 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.39 % Allowed : 16.25 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2581 helix: 1.24 (0.15), residues: 1259 sheet: -2.11 (0.41), residues: 149 loop : -1.83 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 315 HIS 0.010 0.001 HIS A 270 PHE 0.032 0.001 PHE X 384 TYR 0.019 0.001 TYR G 361 ARG 0.012 0.000 ARG M 136 *********************** 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 330 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7870 (ttm170) REVERT: H 297 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: H 331 GLU cc_start: 0.7462 (mp0) cc_final: 0.7154 (pm20) REVERT: H 349 ASP cc_start: 0.8172 (t70) cc_final: 0.7848 (t0) REVERT: D 437 MET cc_start: 0.7995 (ppp) cc_final: 0.7728 (ppp) REVERT: M 32 MET cc_start: 0.6112 (ttm) cc_final: 0.5835 (ttm) REVERT: I 333 MET cc_start: 0.8439 (tmm) cc_final: 0.8006 (tmm) REVERT: I 461 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: G 32 MET cc_start: 0.6490 (tpp) cc_final: 0.5558 (mpp) REVERT: G 259 LYS cc_start: 0.8404 (mptm) cc_final: 0.8074 (tptp) REVERT: G 330 GLN cc_start: 0.8137 (mt0) cc_final: 0.7713 (mt0) REVERT: G 366 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.6938 (mtp180) REVERT: G 379 ARG cc_start: 0.7558 (ptp-170) cc_final: 0.7325 (ptp-170) REVERT: A 203 ASP cc_start: 0.7649 (t0) cc_final: 0.7184 (t0) REVERT: A 240 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7159 (mm-30) REVERT: A 258 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6848 (p) REVERT: A 314 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7806 (mp) REVERT: J 62 TYR cc_start: 0.7944 (t80) cc_final: 0.7580 (m-80) REVERT: J 100 LEU cc_start: 0.8425 (tt) cc_final: 0.8014 (tp) REVERT: J 204 ASN cc_start: 0.8488 (t0) cc_final: 0.8097 (t0) REVERT: J 205 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7770 (tm-30) REVERT: J 229 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: E 50 ASN cc_start: 0.8311 (t0) cc_final: 0.7853 (m-40) REVERT: E 67 LYS cc_start: 0.8747 (tptp) cc_final: 0.8129 (mmmm) REVERT: C 196 PHE cc_start: 0.8604 (m-80) cc_final: 0.8351 (m-80) REVERT: K 186 LYS cc_start: 0.7323 (mttt) cc_final: 0.7118 (mmtp) REVERT: X 435 GLN cc_start: 0.8612 (pm20) cc_final: 0.8247 (pm20) REVERT: X 481 TRP cc_start: 0.7737 (m-10) cc_final: 0.7230 (m-10) REVERT: X 482 VAL cc_start: 0.8812 (t) cc_final: 0.8487 (p) REVERT: L 757 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6402 (mmtt) REVERT: L 800 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7202 (m110) REVERT: L 808 ASP cc_start: 0.6249 (t0) cc_final: 0.5765 (t0) outliers start: 58 outliers final: 43 residues processed: 318 average time/residue: 0.3161 time to fit residues: 157.2570 Evaluate side-chains 301 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 F residue 425 GLN Chi-restraints excluded: chain H residue 297 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 226 VAL 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 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 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 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 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 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 800 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.7980 chunk 245 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 116 optimal weight: 0.0070 chunk 171 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 205 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.5614 ------------------------------------------------------------------------------- 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 ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21882 Z= 0.169 Angle : 0.625 13.325 29583 Z= 0.307 Chirality : 0.042 0.218 3381 Planarity : 0.004 0.055 3775 Dihedral : 4.420 27.703 2835 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.26 % Allowed : 16.58 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2581 helix: 1.34 (0.15), residues: 1257 sheet: -2.05 (0.41), residues: 154 loop : -1.77 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.009 0.001 HIS A 270 PHE 0.034 0.001 PHE F 330 TYR 0.015 0.001 TYR D 168 ARG 0.007 0.000 ARG M 136 ********************** 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 322 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 267 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: F 329 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7866 (ttm170) REVERT: H 297 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: H 331 GLU cc_start: 0.7418 (mp0) cc_final: 0.7178 (pm20) REVERT: H 349 ASP cc_start: 0.8223 (t70) cc_final: 0.7796 (t0) REVERT: H 459 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8121 (mm) REVERT: M 32 MET cc_start: 0.6133 (ttm) cc_final: 0.5825 (ttm) REVERT: I 333 MET cc_start: 0.8419 (tmm) cc_final: 0.8014 (tmm) REVERT: I 461 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: G 32 MET cc_start: 0.6688 (tpp) cc_final: 0.5666 (mpp) REVERT: G 259 LYS cc_start: 0.8406 (mptm) cc_final: 0.8074 (tptp) REVERT: G 330 GLN cc_start: 0.8149 (mt0) cc_final: 0.7732 (mt0) REVERT: G 366 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.6849 (mtp180) REVERT: G 379 ARG cc_start: 0.7579 (ptp-170) cc_final: 0.7342 (ptp-170) REVERT: A 101 LEU cc_start: 0.8098 (tp) cc_final: 0.7750 (tp) REVERT: A 203 ASP cc_start: 0.7622 (t0) cc_final: 0.7295 (t0) REVERT: A 240 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7185 (mm-30) REVERT: A 258 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.6924 (p) REVERT: A 314 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7830 (mp) REVERT: J 62 TYR cc_start: 0.7914 (t80) cc_final: 0.7568 (m-80) REVERT: J 100 LEU cc_start: 0.8411 (tt) cc_final: 0.7964 (tp) REVERT: J 204 ASN cc_start: 0.8458 (t0) cc_final: 0.8072 (t0) REVERT: J 205 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7735 (tm-30) REVERT: J 229 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: E 50 ASN cc_start: 0.8325 (t0) cc_final: 0.7867 (m-40) REVERT: C 196 PHE cc_start: 0.8605 (m-80) cc_final: 0.8362 (m-80) REVERT: K 174 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7821 (tm-30) REVERT: K 186 LYS cc_start: 0.7311 (mttt) cc_final: 0.7111 (mmtp) REVERT: X 435 GLN cc_start: 0.8581 (pm20) cc_final: 0.8237 (pm20) REVERT: X 481 TRP cc_start: 0.7749 (m-10) cc_final: 0.7293 (m-10) REVERT: X 482 VAL cc_start: 0.8805 (t) cc_final: 0.8481 (p) REVERT: L 757 LYS cc_start: 0.7134 (mtmm) cc_final: 0.6373 (mmtt) REVERT: L 800 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7216 (m110) REVERT: L 808 ASP cc_start: 0.6060 (t0) cc_final: 0.5635 (t70) outliers start: 55 outliers final: 42 residues processed: 309 average time/residue: 0.3400 time to fit residues: 164.2802 Evaluate side-chains 304 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 255 time to evaluate : 2.550 ------------------------------------------------------------------------------- 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 F residue 425 GLN Chi-restraints excluded: chain H residue 297 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 226 VAL Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 422 ILE 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 258 THR Chi-restraints excluded: chain A residue 263 GLU 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 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 E residue 30 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 485 ILE Chi-restraints excluded: chain L residue 755 ILE Chi-restraints excluded: chain L residue 800 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.4980 chunk 218 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN H 470 ASN ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.117177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.089007 restraints weight = 56204.924| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.22 r_work: 0.3288 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21882 Z= 0.167 Angle : 0.620 12.946 29583 Z= 0.304 Chirality : 0.041 0.232 3381 Planarity : 0.004 0.055 3775 Dihedral : 4.337 31.632 2835 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.10 % Allowed : 16.62 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2581 helix: 1.39 (0.15), residues: 1261 sheet: -1.86 (0.41), residues: 154 loop : -1.73 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.009 0.001 HIS A 270 PHE 0.032 0.001 PHE X 384 TYR 0.020 0.001 TYR G 361 ARG 0.007 0.000 ARG I 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4958.98 seconds wall clock time: 88 minutes 59.00 seconds (5339.00 seconds total)