Starting phenix.real_space_refine on Wed Mar 4 22:49:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogp_12885/03_2026/7ogp_12885.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 87 5.16 5 C 10927 2.51 5 N 2975 2.21 5 O 3181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17171 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2932 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 3 Chain: "B" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1619 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5482 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 41, 'TRANS': 651} Chain breaks: 1 Chain: "D" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4110 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 22, 'TRANS': 487} Chain breaks: 1 Chain: "E" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3027 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 360} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" 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 12397 SG CYS D 288 27.168 82.638 18.330 1.00114.84 S ATOM 12831 SG CYS D 341 26.654 81.151 21.553 1.00112.95 S ATOM 12897 SG CYS D 350 30.298 83.034 19.593 1.00107.75 S ATOM 12918 SG CYS D 353 28.107 83.820 21.262 1.00104.38 S Time building chain proxies: 3.64, per 1000 atoms: 0.21 Number of scatterers: 17171 At special positions: 0 Unit cell: (119.85, 137.7, 114.75, 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 87 16.00 O 3181 8.00 N 2975 7.00 C 10927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 632.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 341 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 350 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 353 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 288 " Number of angles added : 6 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 41.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.652A pdb=" N HIS A 14 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 4.375A pdb=" N GLY A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.847A pdb=" N ASN A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.559A pdb=" N CYS A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.819A pdb=" N ASN A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.745A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.570A pdb=" N ASN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.578A pdb=" N ALA A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 408 through 412 removed outlier: 4.131A pdb=" N LYS A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.520A pdb=" N LEU A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.833A pdb=" N THR A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.718A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.831A pdb=" N ALA B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.860A pdb=" N CYS B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.596A pdb=" N VAL B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.720A pdb=" N VAL B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 removed outlier: 3.960A pdb=" N SER B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 380 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.655A pdb=" N HIS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.813A pdb=" N MET B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 460 through 474 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.873A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.639A pdb=" N LEU C 19 " --> pdb=" O HIS C 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 20 " --> pdb=" O THR C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 20' Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.520A pdb=" N VAL C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.658A pdb=" N ALA C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.776A pdb=" N GLU C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.619A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 299 through 327 removed outlier: 3.938A pdb=" N VAL C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 Processing helix chain 'C' and resid 422 through 428 removed outlier: 4.049A pdb=" N ARG C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.643A pdb=" N TYR C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 440 " --> pdb=" O HIS C 436 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.693A pdb=" N SER C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 504 through 515 removed outlier: 3.523A pdb=" N VAL C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 514 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 Processing helix chain 'C' and resid 618 through 628 Processing helix chain 'C' and resid 632 through 643 removed outlier: 3.935A pdb=" N GLU C 636 " --> pdb=" O GLY C 632 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 638 " --> pdb=" O THR C 634 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 641 " --> pdb=" O ILE C 637 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 657 removed outlier: 3.770A pdb=" N ILE C 651 " --> pdb=" O HIS C 647 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 689 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.037A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.980A pdb=" N TRP D 20 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 4.090A pdb=" N LEU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.610A pdb=" N HIS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 77 through 81 removed outlier: 4.028A pdb=" N ASP D 80 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 81 " --> pdb=" O PRO D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.982A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 removed outlier: 3.631A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.592A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.705A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.572A pdb=" N LYS D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.652A pdb=" N ARG D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 278 removed outlier: 4.147A pdb=" N LEU D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 366 through 384 removed outlier: 3.944A pdb=" N VAL D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA D 371 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 Processing helix chain 'D' and resid 579 through 588 Processing helix chain 'D' and resid 594 through 604 removed outlier: 3.647A pdb=" N CYS D 598 " --> pdb=" O ASN D 594 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 600 " --> pdb=" O SER D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.714A pdb=" N ARG D 613 " --> pdb=" O ALA D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.740A pdb=" N PHE D 657 " --> pdb=" O PRO D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 removed outlier: 3.663A pdb=" N LYS D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.625A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.676A pdb=" N ASP E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.034A pdb=" N VAL E 55 " --> pdb=" O ILE E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 79 removed outlier: 3.594A pdb=" N GLU E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 325 removed outlier: 4.054A pdb=" N GLU E 325 " --> pdb=" O GLY E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 326 through 338 removed outlier: 3.605A pdb=" N SER E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 356 through 367 removed outlier: 3.521A pdb=" N MET E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 4.010A pdb=" N LEU E 372 " --> pdb=" O ALA E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.585A pdb=" N TYR E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 400 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET E 407 " --> pdb=" O MET E 403 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 429 removed outlier: 3.558A pdb=" N GLU E 423 " --> pdb=" O GLN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 495 removed outlier: 3.558A pdb=" N VAL E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 522 removed outlier: 4.007A pdb=" N GLY E 521 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 538 removed outlier: 3.907A pdb=" N LEU E 538 " --> pdb=" O ASP E 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.337A pdb=" N LEU A 310 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 395 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 312 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 372 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 424 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.468A pdb=" N THR A 299 " --> pdb=" O MET A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.200A pdb=" N ILE C 519 " --> pdb=" O LEU C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.185A pdb=" N GLU C 102 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL C 75 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU C 144 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 174 removed outlier: 3.567A pdb=" N VAL C 186 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE C 185 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 400 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA C 187 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.387A pdb=" N LYS C 376 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL C 278 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 211 through 212 Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 360 Processing sheet with id=AB3, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.806A pdb=" N TYR D 6 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'D' and resid 310 through 311 Processing sheet with id=AB7, first strand: chain 'E' and resid 61 through 63 Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 145 535 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.77 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: 5572 1.34 - 1.46: 3041 1.46 - 1.58: 8799 1.58 - 1.69: 1 1.69 - 1.81: 153 Bond restraints: 17566 Sorted by residual: bond pdb=" C ASN C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.82e+00 bond pdb=" CA GLU C 8 " pdb=" CB GLU C 8 " ideal model delta sigma weight residual 1.527 1.581 -0.054 2.48e-02 1.63e+03 4.67e+00 bond pdb=" N PHE C 240 " pdb=" CA PHE C 240 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.30e+00 bond pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.23e+00 bond pdb=" C ASN A 379 " pdb=" N PRO A 380 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.85e+00 ... (remaining 17561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 23310 2.09 - 4.18: 398 4.18 - 6.27: 49 6.27 - 8.37: 21 8.37 - 10.46: 7 Bond angle restraints: 23785 Sorted by residual: angle pdb=" N VAL E 389 " pdb=" CA VAL E 389 " pdb=" C VAL E 389 " ideal model delta sigma weight residual 113.53 107.76 5.77 9.80e-01 1.04e+00 3.47e+01 angle pdb=" CA GLU C 8 " pdb=" CB GLU C 8 " pdb=" CG GLU C 8 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" C PRO E 519 " pdb=" N THR E 520 " pdb=" CA THR E 520 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" N LYS A 224 " pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 angle pdb=" C LYS E 162 " pdb=" N GLN E 163 " pdb=" CA GLN E 163 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 ... (remaining 23780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 9210 16.36 - 32.72: 1071 32.72 - 49.08: 241 49.08 - 65.44: 47 65.44 - 81.81: 12 Dihedral angle restraints: 10581 sinusoidal: 4324 harmonic: 6257 Sorted by residual: dihedral pdb=" CA LYS A 277 " pdb=" C LYS A 277 " pdb=" N PRO A 278 " pdb=" CA PRO A 278 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA A 413 " pdb=" C ALA A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N PRO E 117 " pdb=" CA PRO E 117 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 10578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2165 0.061 - 0.121: 361 0.121 - 0.182: 76 0.182 - 0.242: 2 0.242 - 0.303: 1 Chirality restraints: 2605 Sorted by residual: chirality pdb=" CB ILE D 292 " pdb=" CA ILE D 292 " pdb=" CG1 ILE D 292 " pdb=" CG2 ILE D 292 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 290 " pdb=" N ASN C 290 " pdb=" C ASN C 290 " pdb=" CB ASN C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS A 224 " pdb=" N LYS A 224 " pdb=" C LYS A 224 " pdb=" CB LYS A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2602 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 665 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 666 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 666 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 666 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 304 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 234 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 235 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.028 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4747 2.81 - 3.33: 14086 3.33 - 3.85: 27184 3.85 - 4.38: 31212 4.38 - 4.90: 54194 Nonbonded interactions: 131423 Sorted by model distance: nonbonded pdb=" O LEU A 433 " pdb=" OG1 THR A 437 " model vdw 2.287 3.040 nonbonded pdb=" O HIS A 443 " pdb=" OG SER D 119 " model vdw 2.294 3.040 nonbonded pdb=" O PRO B 312 " pdb=" OG SER C 587 " model vdw 2.302 3.040 nonbonded pdb=" O GLU C 652 " pdb=" OG1 THR C 656 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR B 494 " pdb=" O ASN B 496 " model vdw 2.323 3.040 ... (remaining 131418 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.970 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17570 Z= 0.157 Angle : 0.814 44.035 23791 Z= 0.390 Chirality : 0.049 0.303 2605 Planarity : 0.005 0.054 3068 Dihedral : 14.591 81.806 6551 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.13), residues: 2118 helix: -3.73 (0.10), residues: 798 sheet: -1.92 (0.36), residues: 160 loop : -2.96 (0.14), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 510 TYR 0.014 0.001 TYR D 243 PHE 0.020 0.001 PHE C 240 TRP 0.011 0.001 TRP D 320 HIS 0.006 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00297 (17566) covalent geometry : angle 0.68510 (23785) hydrogen bonds : bond 0.19539 ( 535) hydrogen bonds : angle 7.61557 ( 1500) metal coordination : bond 0.00823 ( 4) metal coordination : angle 27.70622 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 497 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4056 (tp30) REVERT: A 256 MET cc_start: 0.6174 (mpp) cc_final: 0.4927 (tpt) REVERT: A 282 ARG cc_start: 0.7241 (mtm180) cc_final: 0.7018 (ttm170) REVERT: A 421 ASP cc_start: 0.7266 (t0) cc_final: 0.5720 (p0) REVERT: B 343 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 410 VAL cc_start: 0.8279 (t) cc_final: 0.8014 (m) REVERT: B 412 LEU cc_start: 0.7505 (tt) cc_final: 0.7212 (tp) REVERT: C 109 LYS cc_start: 0.6207 (mptt) cc_final: 0.5171 (mmmt) REVERT: C 336 GLU cc_start: 0.7673 (tt0) cc_final: 0.7382 (tp30) REVERT: C 478 TYR cc_start: 0.5976 (t80) cc_final: 0.5041 (t80) REVERT: C 562 LYS cc_start: 0.7245 (mmtm) cc_final: 0.6945 (pttp) REVERT: C 615 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.7208 (ttt90) REVERT: C 658 GLU cc_start: 0.7883 (pm20) cc_final: 0.7423 (pm20) REVERT: D 157 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7566 (mttp) REVERT: D 205 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6240 (mptt) REVERT: D 251 SER cc_start: 0.9176 (t) cc_final: 0.8645 (p) REVERT: D 267 GLU cc_start: 0.6714 (tp30) cc_final: 0.6297 (pt0) REVERT: D 268 TYR cc_start: 0.6500 (t80) cc_final: 0.6168 (t80) REVERT: D 321 ILE cc_start: 0.7636 (mt) cc_final: 0.7377 (mt) REVERT: D 325 GLU cc_start: 0.7368 (mp0) cc_final: 0.7142 (mp0) REVERT: D 607 ILE cc_start: 0.6821 (mm) cc_final: 0.6354 (mm) REVERT: D 631 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6870 (mtt-85) REVERT: D 649 GLU cc_start: 0.6633 (mp0) cc_final: 0.6061 (mt-10) REVERT: D 658 LEU cc_start: 0.7064 (pp) cc_final: 0.6642 (pp) REVERT: D 661 MET cc_start: 0.4373 (mmm) cc_final: 0.3288 (mtp) REVERT: E 11 ARG cc_start: 0.7029 (tpm170) cc_final: 0.6240 (ttm170) REVERT: E 51 ASP cc_start: 0.6620 (p0) cc_final: 0.6302 (m-30) REVERT: E 56 LEU cc_start: 0.7596 (mp) cc_final: 0.7183 (tt) REVERT: E 63 TYR cc_start: 0.6714 (t80) cc_final: 0.6328 (t80) REVERT: E 94 ASP cc_start: 0.7467 (m-30) cc_final: 0.7246 (m-30) REVERT: E 342 MET cc_start: 0.3957 (tpt) cc_final: 0.3608 (mmm) REVERT: E 356 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.5964 (p) REVERT: E 409 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 412 ARG cc_start: 0.5047 (ptp90) cc_final: 0.4695 (mmm160) REVERT: E 416 TRP cc_start: 0.6707 (m100) cc_final: 0.6479 (m100) REVERT: E 436 LYS cc_start: 0.7732 (pttm) cc_final: 0.7163 (pttt) REVERT: E 437 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6847 (mmm-85) outliers start: 5 outliers final: 0 residues processed: 499 average time/residue: 0.1471 time to fit residues: 105.5255 Evaluate side-chains 307 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 356 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 25 ASN A 193 GLN A 252 GLN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 311 HIS A 319 GLN A 324 HIS A 347 ASN A 350 GLN A 388 GLN A 415 ASN A 453 HIS B 369 HIS B 386 ASN B 481 HIS B 515 HIS C 154 GLN C 429 ASN C 538 ASN D 71 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 665 HIS E 36 ASN E 74 HIS E 371 HIS E 398 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128474 restraints weight = 25223.396| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.81 r_work: 0.3356 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 17570 Z= 0.183 Angle : 0.646 9.357 23791 Z= 0.333 Chirality : 0.045 0.200 2605 Planarity : 0.005 0.045 3068 Dihedral : 4.858 31.224 2343 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.25 % Allowed : 14.57 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.15), residues: 2118 helix: -1.73 (0.16), residues: 797 sheet: -1.19 (0.41), residues: 149 loop : -2.56 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 427 TYR 0.016 0.002 TYR C 108 PHE 0.025 0.002 PHE C 240 TRP 0.013 0.002 TRP D 103 HIS 0.007 0.001 HIS C 495 Details of bonding type rmsd covalent geometry : bond 0.00431 (17566) covalent geometry : angle 0.63746 (23785) hydrogen bonds : bond 0.04012 ( 535) hydrogen bonds : angle 4.98145 ( 1500) metal coordination : bond 0.01656 ( 4) metal coordination : angle 6.81240 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 0.511 Fit side-chains REVERT: A 224 LYS cc_start: 0.7305 (pttm) cc_final: 0.6661 (tptt) REVERT: A 227 GLU cc_start: 0.5370 (mm-30) cc_final: 0.5060 (pp20) REVERT: A 256 MET cc_start: 0.7056 (mpp) cc_final: 0.5755 (tpt) REVERT: B 308 GLN cc_start: 0.5957 (mp10) cc_final: 0.4788 (tp-100) REVERT: B 343 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 107 LYS cc_start: 0.7476 (tttp) cc_final: 0.7187 (tttt) REVERT: C 196 MET cc_start: 0.8881 (ttm) cc_final: 0.8646 (ttm) REVERT: C 551 TYR cc_start: 0.8574 (p90) cc_final: 0.8025 (p90) REVERT: D 96 LYS cc_start: 0.8430 (tttm) cc_final: 0.7974 (ttmm) REVERT: D 157 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8336 (mtmt) REVERT: D 163 HIS cc_start: 0.7219 (m-70) cc_final: 0.7018 (m170) REVERT: D 174 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7875 (mtmt) REVERT: D 205 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7749 (mptt) REVERT: D 251 SER cc_start: 0.9032 (t) cc_final: 0.8566 (p) REVERT: D 268 TYR cc_start: 0.7301 (t80) cc_final: 0.6983 (t80) REVERT: D 574 LYS cc_start: 0.7548 (tmtt) cc_final: 0.6925 (mtmt) REVERT: D 607 ILE cc_start: 0.6850 (mm) cc_final: 0.6610 (mm) REVERT: D 631 ARG cc_start: 0.7576 (mtt180) cc_final: 0.7369 (mtt-85) REVERT: D 649 GLU cc_start: 0.7480 (mp0) cc_final: 0.6816 (mt-10) REVERT: D 661 MET cc_start: 0.5844 (mmm) cc_final: 0.4688 (mtp) REVERT: E 148 ASP cc_start: 0.4897 (OUTLIER) cc_final: 0.4175 (t0) REVERT: E 342 MET cc_start: 0.4391 (tpt) cc_final: 0.4011 (mmm) REVERT: E 409 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 412 ARG cc_start: 0.5836 (ptp90) cc_final: 0.5320 (mmm160) outliers start: 42 outliers final: 26 residues processed: 321 average time/residue: 0.1534 time to fit residues: 70.8100 Evaluate side-chains 270 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 464 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 0.0470 chunk 62 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 41 HIS ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS C 429 ASN C 600 ASN D 127 ASN ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN D 327 HIS D 342 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118918 restraints weight = 25377.261| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.66 r_work: 0.3223 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17570 Z= 0.202 Angle : 0.646 9.619 23791 Z= 0.334 Chirality : 0.045 0.180 2605 Planarity : 0.005 0.056 3068 Dihedral : 5.069 32.881 2343 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.59 % Allowed : 16.87 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.16), residues: 2118 helix: -0.94 (0.18), residues: 789 sheet: -0.93 (0.40), residues: 157 loop : -2.42 (0.15), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 510 TYR 0.023 0.002 TYR D 629 PHE 0.032 0.002 PHE C 240 TRP 0.009 0.001 TRP C 22 HIS 0.006 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00489 (17566) covalent geometry : angle 0.63905 (23785) hydrogen bonds : bond 0.04402 ( 535) hydrogen bonds : angle 4.84301 ( 1500) metal coordination : bond 0.01306 ( 4) metal coordination : angle 6.05158 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.7346 (pttm) cc_final: 0.6601 (tptm) REVERT: A 256 MET cc_start: 0.6957 (mpp) cc_final: 0.5761 (tpt) REVERT: A 419 ASP cc_start: 0.7535 (t0) cc_final: 0.7294 (t0) REVERT: A 477 TYR cc_start: 0.6408 (t80) cc_final: 0.6182 (t80) REVERT: B 308 GLN cc_start: 0.6097 (mp10) cc_final: 0.4397 (tp-100) REVERT: C 336 GLU cc_start: 0.8389 (tt0) cc_final: 0.8152 (tp30) REVERT: C 551 TYR cc_start: 0.8840 (p90) cc_final: 0.8480 (p90) REVERT: D 205 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7868 (mmtt) REVERT: D 605 MET cc_start: 0.8649 (mmm) cc_final: 0.8396 (mmm) REVERT: D 607 ILE cc_start: 0.7610 (mm) cc_final: 0.7235 (mm) REVERT: D 649 GLU cc_start: 0.7776 (mp0) cc_final: 0.7114 (mt-10) REVERT: D 661 MET cc_start: 0.6334 (mmm) cc_final: 0.5150 (mtp) REVERT: E 11 ARG cc_start: 0.8119 (tpm170) cc_final: 0.7480 (tpp-160) REVERT: E 82 TYR cc_start: 0.7867 (t80) cc_final: 0.6539 (t80) REVERT: E 150 ILE cc_start: 0.6779 (pt) cc_final: 0.6579 (tt) REVERT: E 342 MET cc_start: 0.4495 (tpt) cc_final: 0.4124 (mmm) REVERT: E 359 GLU cc_start: 0.7145 (mp0) cc_final: 0.6239 (tt0) REVERT: E 412 ARG cc_start: 0.5785 (ptp90) cc_final: 0.5364 (mmm160) REVERT: E 510 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7816 (mmp-170) outliers start: 67 outliers final: 43 residues processed: 288 average time/residue: 0.1418 time to fit residues: 60.4810 Evaluate side-chains 261 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 510 ARG Chi-restraints excluded: chain E residue 522 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 110 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 175 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS D 66 HIS D 189 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN D 343 HIS E 466 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124229 restraints weight = 25113.969| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.67 r_work: 0.3294 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 17570 Z= 0.094 Angle : 0.527 11.849 23791 Z= 0.268 Chirality : 0.042 0.218 2605 Planarity : 0.004 0.039 3068 Dihedral : 4.444 30.138 2343 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.41 % Allowed : 19.12 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 2118 helix: -0.33 (0.18), residues: 792 sheet: -0.65 (0.42), residues: 149 loop : -2.16 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 282 TYR 0.017 0.001 TYR E 63 PHE 0.020 0.001 PHE E 335 TRP 0.011 0.001 TRP D 320 HIS 0.009 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00214 (17566) covalent geometry : angle 0.52021 (23785) hydrogen bonds : bond 0.02759 ( 535) hydrogen bonds : angle 4.31298 ( 1500) metal coordination : bond 0.00758 ( 4) metal coordination : angle 5.22378 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.4593 (OUTLIER) cc_final: 0.4101 (t0) REVERT: A 224 LYS cc_start: 0.7347 (pttm) cc_final: 0.6701 (tptm) REVERT: A 256 MET cc_start: 0.6829 (mpp) cc_final: 0.5673 (tpt) REVERT: A 419 ASP cc_start: 0.7398 (t0) cc_final: 0.7167 (t0) REVERT: B 308 GLN cc_start: 0.5725 (mp10) cc_final: 0.4377 (tp-100) REVERT: C 80 ARG cc_start: 0.7903 (ptp-110) cc_final: 0.7554 (ptp90) REVERT: C 336 GLU cc_start: 0.8381 (tt0) cc_final: 0.8130 (tp30) REVERT: C 535 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8436 (mtmt) REVERT: C 551 TYR cc_start: 0.8824 (p90) cc_final: 0.8554 (p90) REVERT: C 678 ARG cc_start: 0.6930 (ttt180) cc_final: 0.6705 (mtp180) REVERT: D 36 THR cc_start: 0.7878 (t) cc_final: 0.7606 (m) REVERT: D 41 ASP cc_start: 0.8035 (p0) cc_final: 0.7792 (p0) REVERT: D 205 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7716 (mmtp) REVERT: D 282 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.8018 (ttp-110) REVERT: D 649 GLU cc_start: 0.7739 (mp0) cc_final: 0.6974 (mt-10) REVERT: D 661 MET cc_start: 0.6257 (mmm) cc_final: 0.5131 (mtm) REVERT: E 11 ARG cc_start: 0.7989 (tpm170) cc_final: 0.7512 (tpp-160) REVERT: E 50 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6689 (t80) REVERT: E 82 TYR cc_start: 0.7723 (t80) cc_final: 0.6935 (t80) REVERT: E 150 ILE cc_start: 0.6750 (pt) cc_final: 0.6544 (tt) REVERT: E 342 MET cc_start: 0.4507 (tpt) cc_final: 0.4145 (mmm) REVERT: E 359 GLU cc_start: 0.7103 (mp0) cc_final: 0.6263 (tt0) REVERT: E 412 ARG cc_start: 0.5649 (ptp90) cc_final: 0.5263 (mmm160) outliers start: 45 outliers final: 25 residues processed: 280 average time/residue: 0.1413 time to fit residues: 58.0410 Evaluate side-chains 256 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 75 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 169 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN D 343 HIS D 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122959 restraints weight = 24948.900| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.65 r_work: 0.3287 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17570 Z= 0.105 Angle : 0.519 9.260 23791 Z= 0.265 Chirality : 0.042 0.222 2605 Planarity : 0.003 0.034 3068 Dihedral : 4.353 30.950 2343 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.16 % Allowed : 19.01 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2118 helix: -0.05 (0.19), residues: 793 sheet: -0.48 (0.43), residues: 149 loop : -2.06 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.025 0.001 TYR A 477 PHE 0.016 0.001 PHE C 240 TRP 0.010 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00250 (17566) covalent geometry : angle 0.51434 (23785) hydrogen bonds : bond 0.02911 ( 535) hydrogen bonds : angle 4.24816 ( 1500) metal coordination : bond 0.00785 ( 4) metal coordination : angle 4.43285 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.7348 (pttm) cc_final: 0.6670 (tptm) REVERT: A 256 MET cc_start: 0.6727 (mpp) cc_final: 0.5593 (tpt) REVERT: A 419 ASP cc_start: 0.7427 (t0) cc_final: 0.7182 (t0) REVERT: B 308 GLN cc_start: 0.5673 (mp10) cc_final: 0.4274 (tp-100) REVERT: C 80 ARG cc_start: 0.7961 (ptp-110) cc_final: 0.7551 (ptp90) REVERT: C 336 GLU cc_start: 0.8368 (tt0) cc_final: 0.8133 (tp30) REVERT: C 535 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8374 (mtmt) REVERT: C 551 TYR cc_start: 0.8827 (p90) cc_final: 0.8566 (p90) REVERT: C 678 ARG cc_start: 0.6973 (ttt180) cc_final: 0.6742 (mtp180) REVERT: D 36 THR cc_start: 0.7878 (t) cc_final: 0.7591 (m) REVERT: D 205 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7728 (mmtp) REVERT: D 605 MET cc_start: 0.8655 (mmm) cc_final: 0.8427 (mmm) REVERT: D 607 ILE cc_start: 0.7334 (mm) cc_final: 0.6725 (mm) REVERT: D 649 GLU cc_start: 0.7724 (mp0) cc_final: 0.6998 (mt-10) REVERT: D 661 MET cc_start: 0.6319 (mmm) cc_final: 0.5110 (mtm) REVERT: E 11 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7465 (tpp-160) REVERT: E 50 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6674 (t80) REVERT: E 82 TYR cc_start: 0.7768 (t80) cc_final: 0.6973 (t80) REVERT: E 148 ASP cc_start: 0.5197 (OUTLIER) cc_final: 0.4104 (t0) REVERT: E 342 MET cc_start: 0.4521 (tpt) cc_final: 0.4165 (mmm) REVERT: E 359 GLU cc_start: 0.7101 (mp0) cc_final: 0.6359 (tt0) REVERT: E 412 ARG cc_start: 0.5722 (ptp90) cc_final: 0.5327 (mmm160) outliers start: 59 outliers final: 44 residues processed: 278 average time/residue: 0.1442 time to fit residues: 58.8865 Evaluate side-chains 271 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 11 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 501 HIS D 163 HIS D 208 GLN D 274 GLN D 281 GLN D 342 ASN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118922 restraints weight = 25143.997| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.65 r_work: 0.3230 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17570 Z= 0.170 Angle : 0.594 9.969 23791 Z= 0.304 Chirality : 0.044 0.224 2605 Planarity : 0.004 0.050 3068 Dihedral : 4.716 32.665 2343 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.96 % Allowed : 19.76 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2118 helix: -0.04 (0.19), residues: 794 sheet: -0.48 (0.41), residues: 157 loop : -2.08 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 525 TYR 0.023 0.002 TYR A 477 PHE 0.025 0.001 PHE C 240 TRP 0.010 0.001 TRP D 240 HIS 0.005 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00416 (17566) covalent geometry : angle 0.58768 (23785) hydrogen bonds : bond 0.03602 ( 535) hydrogen bonds : angle 4.43712 ( 1500) metal coordination : bond 0.01086 ( 4) metal coordination : angle 5.66204 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 152 LEU cc_start: 0.4342 (OUTLIER) cc_final: 0.4072 (mt) REVERT: A 224 LYS cc_start: 0.7387 (pttm) cc_final: 0.6567 (tptm) REVERT: A 256 MET cc_start: 0.6750 (mpp) cc_final: 0.5586 (tpt) REVERT: A 419 ASP cc_start: 0.7474 (t0) cc_final: 0.7118 (t0) REVERT: B 308 GLN cc_start: 0.6057 (mp10) cc_final: 0.4290 (tp-100) REVERT: C 80 ARG cc_start: 0.8080 (ptp-110) cc_final: 0.7676 (ptp90) REVERT: C 551 TYR cc_start: 0.8832 (p90) cc_final: 0.8554 (p90) REVERT: C 678 ARG cc_start: 0.6854 (ttt180) cc_final: 0.6640 (mtp180) REVERT: D 205 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7754 (mmtp) REVERT: D 574 LYS cc_start: 0.7795 (tmtt) cc_final: 0.7481 (ttmm) REVERT: D 595 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 607 ILE cc_start: 0.7438 (mm) cc_final: 0.7178 (mm) REVERT: D 649 GLU cc_start: 0.7847 (mp0) cc_final: 0.7049 (mt-10) REVERT: D 661 MET cc_start: 0.6443 (mmm) cc_final: 0.5170 (mtp) REVERT: E 11 ARG cc_start: 0.8152 (tpm170) cc_final: 0.7481 (tpp-160) REVERT: E 50 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6760 (t80) REVERT: E 82 TYR cc_start: 0.7926 (t80) cc_final: 0.6417 (t80) REVERT: E 342 MET cc_start: 0.4551 (tpt) cc_final: 0.4177 (mmm) REVERT: E 359 GLU cc_start: 0.7197 (mp0) cc_final: 0.6394 (tt0) REVERT: E 412 ARG cc_start: 0.5755 (ptp90) cc_final: 0.5336 (mmm160) REVERT: E 510 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7339 (mmp-170) outliers start: 74 outliers final: 53 residues processed: 284 average time/residue: 0.1396 time to fit residues: 58.5094 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 193 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 659 ASN D 663 ASN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119450 restraints weight = 25166.803| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.66 r_work: 0.3235 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17570 Z= 0.143 Angle : 0.566 10.426 23791 Z= 0.290 Chirality : 0.043 0.235 2605 Planarity : 0.004 0.051 3068 Dihedral : 4.661 32.257 2343 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.07 % Allowed : 19.55 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.17), residues: 2118 helix: 0.05 (0.19), residues: 795 sheet: -0.43 (0.43), residues: 149 loop : -2.01 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 525 TYR 0.025 0.001 TYR A 477 PHE 0.020 0.001 PHE C 240 TRP 0.009 0.001 TRP D 103 HIS 0.010 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00348 (17566) covalent geometry : angle 0.56032 (23785) hydrogen bonds : bond 0.03328 ( 535) hydrogen bonds : angle 4.37792 ( 1500) metal coordination : bond 0.00717 ( 4) metal coordination : angle 5.05354 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 223 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 152 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4297 (mt) REVERT: A 224 LYS cc_start: 0.7408 (pttm) cc_final: 0.6589 (tptm) REVERT: A 256 MET cc_start: 0.6689 (mpp) cc_final: 0.5550 (tpt) REVERT: A 419 ASP cc_start: 0.7513 (t0) cc_final: 0.7231 (t0) REVERT: B 308 GLN cc_start: 0.6148 (mp10) cc_final: 0.4314 (tp-100) REVERT: C 80 ARG cc_start: 0.8063 (ptp-110) cc_final: 0.7642 (ptp90) REVERT: C 551 TYR cc_start: 0.8811 (p90) cc_final: 0.8528 (p90) REVERT: D 205 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7742 (mmtp) REVERT: D 595 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 607 ILE cc_start: 0.7436 (mm) cc_final: 0.7154 (mm) REVERT: D 642 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6773 (mpp) REVERT: D 649 GLU cc_start: 0.7787 (mp0) cc_final: 0.6980 (mt-10) REVERT: D 659 ASN cc_start: 0.2429 (m-40) cc_final: 0.2059 (m110) REVERT: D 661 MET cc_start: 0.6454 (mmm) cc_final: 0.5154 (mtp) REVERT: E 11 ARG cc_start: 0.8160 (tpm170) cc_final: 0.7468 (tpp-160) REVERT: E 50 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.6694 (t80) REVERT: E 342 MET cc_start: 0.4498 (tpt) cc_final: 0.4183 (mmm) REVERT: E 359 GLU cc_start: 0.7212 (mp0) cc_final: 0.6433 (tt0) REVERT: E 412 ARG cc_start: 0.5715 (ptp90) cc_final: 0.5338 (mmm160) REVERT: E 510 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7440 (mmp-170) outliers start: 76 outliers final: 59 residues processed: 281 average time/residue: 0.1387 time to fit residues: 57.2863 Evaluate side-chains 279 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 653 ASN Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 212 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN C 103 ASN D 342 ASN E 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119230 restraints weight = 25205.184| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.66 r_work: 0.3234 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17570 Z= 0.141 Angle : 0.567 9.880 23791 Z= 0.291 Chirality : 0.043 0.209 2605 Planarity : 0.004 0.037 3068 Dihedral : 4.656 32.046 2343 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.18 % Allowed : 19.82 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2118 helix: 0.13 (0.19), residues: 795 sheet: -0.35 (0.43), residues: 147 loop : -1.99 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 615 TYR 0.025 0.001 TYR A 477 PHE 0.023 0.001 PHE C 240 TRP 0.009 0.001 TRP D 103 HIS 0.005 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00344 (17566) covalent geometry : angle 0.56282 (23785) hydrogen bonds : bond 0.03323 ( 535) hydrogen bonds : angle 4.35441 ( 1500) metal coordination : bond 0.00870 ( 4) metal coordination : angle 4.37125 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 152 LEU cc_start: 0.4467 (OUTLIER) cc_final: 0.4250 (mt) REVERT: A 162 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.4992 (t70) REVERT: A 224 LYS cc_start: 0.7376 (pttm) cc_final: 0.6623 (mmtp) REVERT: A 256 MET cc_start: 0.6650 (mpp) cc_final: 0.5533 (tpt) REVERT: A 419 ASP cc_start: 0.7602 (t0) cc_final: 0.7311 (t0) REVERT: B 308 GLN cc_start: 0.6207 (mp10) cc_final: 0.4360 (tp-100) REVERT: C 80 ARG cc_start: 0.7979 (ptp-110) cc_final: 0.7519 (ptp90) REVERT: C 551 TYR cc_start: 0.8804 (p90) cc_final: 0.8491 (p90) REVERT: D 205 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7758 (mmtp) REVERT: D 595 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8268 (tt) REVERT: D 607 ILE cc_start: 0.7384 (mm) cc_final: 0.7067 (mm) REVERT: D 642 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.6805 (mpp) REVERT: D 661 MET cc_start: 0.6417 (mmm) cc_final: 0.5186 (mtp) REVERT: D 676 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6045 (mt) REVERT: E 11 ARG cc_start: 0.8091 (tpm170) cc_final: 0.7473 (tpp-160) REVERT: E 50 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.6686 (t80) REVERT: E 82 TYR cc_start: 0.8037 (t80) cc_final: 0.7593 (t80) REVERT: E 342 MET cc_start: 0.4482 (tpt) cc_final: 0.4223 (mmm) REVERT: E 359 GLU cc_start: 0.7236 (mp0) cc_final: 0.6431 (tt0) REVERT: E 412 ARG cc_start: 0.5657 (ptp90) cc_final: 0.5372 (mmm160) REVERT: E 510 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7304 (mmp-170) outliers start: 78 outliers final: 63 residues processed: 278 average time/residue: 0.1363 time to fit residues: 56.3279 Evaluate side-chains 282 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 32 optimal weight: 0.0670 chunk 168 optimal weight: 7.9990 chunk 205 optimal weight: 0.0970 chunk 183 optimal weight: 0.4980 chunk 123 optimal weight: 7.9990 chunk 195 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.1318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 GLN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121200 restraints weight = 25099.851| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.65 r_work: 0.3259 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17570 Z= 0.102 Angle : 0.535 10.091 23791 Z= 0.273 Chirality : 0.042 0.213 2605 Planarity : 0.003 0.035 3068 Dihedral : 4.464 31.052 2343 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.59 % Allowed : 20.35 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2118 helix: 0.33 (0.19), residues: 789 sheet: -0.40 (0.43), residues: 149 loop : -1.91 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 615 TYR 0.026 0.001 TYR A 477 PHE 0.018 0.001 PHE C 240 TRP 0.011 0.001 TRP D 320 HIS 0.005 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00241 (17566) covalent geometry : angle 0.53136 (23785) hydrogen bonds : bond 0.02927 ( 535) hydrogen bonds : angle 4.22819 ( 1500) metal coordination : bond 0.00706 ( 4) metal coordination : angle 3.78402 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5832 (OUTLIER) cc_final: 0.4958 (m90) REVERT: A 162 HIS cc_start: 0.5444 (OUTLIER) cc_final: 0.5002 (t70) REVERT: A 256 MET cc_start: 0.6600 (mpp) cc_final: 0.5533 (tpt) REVERT: A 419 ASP cc_start: 0.7461 (t0) cc_final: 0.7176 (t0) REVERT: B 308 GLN cc_start: 0.6115 (mp10) cc_final: 0.4343 (tp-100) REVERT: C 80 ARG cc_start: 0.7933 (ptp-110) cc_final: 0.7459 (mtt90) REVERT: C 368 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: C 551 TYR cc_start: 0.8770 (p90) cc_final: 0.8497 (p90) REVERT: D 58 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8693 (pttt) REVERT: D 205 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7736 (mmtp) REVERT: D 595 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 607 ILE cc_start: 0.7264 (mm) cc_final: 0.6950 (mm) REVERT: D 642 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.6715 (mpp) REVERT: D 661 MET cc_start: 0.6393 (mmm) cc_final: 0.5166 (mtp) REVERT: D 676 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6024 (mt) REVERT: E 11 ARG cc_start: 0.8050 (tpm170) cc_final: 0.7475 (tpp-160) REVERT: E 50 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6696 (t80) REVERT: E 82 TYR cc_start: 0.7963 (t80) cc_final: 0.7561 (t80) REVERT: E 342 MET cc_start: 0.4476 (tpt) cc_final: 0.4227 (mmm) REVERT: E 359 GLU cc_start: 0.7209 (mp0) cc_final: 0.6433 (tt0) REVERT: E 412 ARG cc_start: 0.5644 (ptp90) cc_final: 0.5344 (mmm160) REVERT: E 510 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7271 (mmt180) outliers start: 67 outliers final: 52 residues processed: 277 average time/residue: 0.1356 time to fit residues: 56.2197 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121309 restraints weight = 24991.653| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.64 r_work: 0.3270 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17570 Z= 0.109 Angle : 0.534 9.269 23791 Z= 0.273 Chirality : 0.042 0.202 2605 Planarity : 0.003 0.036 3068 Dihedral : 4.384 30.899 2343 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.16 % Allowed : 20.78 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2118 helix: 0.43 (0.19), residues: 790 sheet: -0.31 (0.44), residues: 143 loop : -1.85 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 615 TYR 0.026 0.001 TYR A 477 PHE 0.018 0.001 PHE C 240 TRP 0.011 0.001 TRP D 320 HIS 0.005 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00259 (17566) covalent geometry : angle 0.53020 (23785) hydrogen bonds : bond 0.02929 ( 535) hydrogen bonds : angle 4.18250 ( 1500) metal coordination : bond 0.00728 ( 4) metal coordination : angle 4.18100 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5851 (OUTLIER) cc_final: 0.4980 (m90) REVERT: A 41 HIS cc_start: 0.6217 (m170) cc_final: 0.5874 (m170) REVERT: A 162 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.5021 (t70) REVERT: A 256 MET cc_start: 0.6620 (mpp) cc_final: 0.5439 (tpp) REVERT: A 419 ASP cc_start: 0.7402 (t0) cc_final: 0.7137 (t0) REVERT: B 308 GLN cc_start: 0.6158 (mp10) cc_final: 0.4332 (tp-100) REVERT: C 80 ARG cc_start: 0.7934 (ptp-110) cc_final: 0.7500 (mtt90) REVERT: C 368 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: C 551 TYR cc_start: 0.8771 (p90) cc_final: 0.8489 (p90) REVERT: C 687 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7879 (mp) REVERT: D 58 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8703 (pttt) REVERT: D 205 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7725 (mmtp) REVERT: D 595 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8271 (tt) REVERT: D 607 ILE cc_start: 0.7226 (mm) cc_final: 0.6903 (mm) REVERT: D 642 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.6707 (mpp) REVERT: D 661 MET cc_start: 0.6328 (mmm) cc_final: 0.5112 (mtm) REVERT: D 676 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6034 (mt) REVERT: E 11 ARG cc_start: 0.8060 (tpm170) cc_final: 0.7507 (tpp-160) REVERT: E 50 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6712 (t80) REVERT: E 82 TYR cc_start: 0.7932 (t80) cc_final: 0.7552 (t80) REVERT: E 342 MET cc_start: 0.4479 (tpt) cc_final: 0.4229 (mmm) REVERT: E 359 GLU cc_start: 0.7170 (mp0) cc_final: 0.6417 (tt0) REVERT: E 412 ARG cc_start: 0.5598 (ptp90) cc_final: 0.5360 (mmm160) REVERT: E 510 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7355 (mmt180) outliers start: 59 outliers final: 49 residues processed: 267 average time/residue: 0.1384 time to fit residues: 54.6718 Evaluate side-chains 274 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 102 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119617 restraints weight = 25125.340| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.66 r_work: 0.3236 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17570 Z= 0.135 Angle : 0.559 9.218 23791 Z= 0.286 Chirality : 0.043 0.181 2605 Planarity : 0.004 0.037 3068 Dihedral : 4.545 31.936 2343 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.48 % Allowed : 20.51 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.18), residues: 2118 helix: 0.39 (0.19), residues: 792 sheet: -0.33 (0.42), residues: 151 loop : -1.87 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 615 TYR 0.024 0.001 TYR A 477 PHE 0.022 0.001 PHE C 240 TRP 0.009 0.001 TRP D 103 HIS 0.005 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00328 (17566) covalent geometry : angle 0.55445 (23785) hydrogen bonds : bond 0.03234 ( 535) hydrogen bonds : angle 4.27350 ( 1500) metal coordination : bond 0.00867 ( 4) metal coordination : angle 4.67217 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.54 seconds wall clock time: 68 minutes 3.41 seconds (4083.41 seconds total)