Starting phenix.real_space_refine on Sun Jun 15 06:21:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_12885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_12885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_12885.map" model { file = "/net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_12885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ogp_12885/06_2025/7ogp_12885.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.33, per 1000 atoms: 0.54 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: 3.77 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.70 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: 4.69 Time building geometry restraints manager: 4.53 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 38.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- 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 : 3.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (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 TRP 0.011 0.001 TRP D 320 HIS 0.006 0.001 HIS C 436 PHE 0.020 0.001 PHE C 240 TYR 0.014 0.001 TYR D 243 ARG 0.002 0.000 ARG E 510 Details of bonding type rmsd hydrogen bonds : bond 0.19539 ( 535) hydrogen bonds : angle 7.61557 ( 1500) metal coordination : bond 0.00823 ( 4) metal coordination : angle 27.70622 ( 6) covalent geometry : bond 0.00297 (17566) covalent geometry : angle 0.68510 (23785) *********************** 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 : 1.832 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: 0.7821 (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: 0.7957 (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: 0.6713 (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: 0.3329 time to fit residues: 237.1268 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 : 1.870 ------------------------------------------------------------------------------- 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 179 optimal weight: 0.5980 chunk 161 optimal weight: 0.0670 chunk 89 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- 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 291 ASN A 319 GLN A 350 GLN A 415 ASN A 453 HIS B 386 ASN B 448 GLN C 3 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN C 538 ASN D 71 ASN D 189 GLN D 274 GLN D 284 HIS D 342 ASN D 663 ASN D 665 HIS E 36 ASN E 371 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148515 restraints weight = 25311.313| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.80 r_work: 0.3617 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 17570 Z= 0.100 Angle : 0.509 8.148 23791 Z= 0.262 Chirality : 0.041 0.195 2605 Planarity : 0.004 0.042 3068 Dihedral : 4.113 28.205 2343 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.66 % Allowed : 12.43 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.15), residues: 2118 helix: -1.76 (0.16), residues: 790 sheet: -1.55 (0.37), residues: 160 loop : -2.52 (0.15), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.003 0.001 HIS B 398 PHE 0.020 0.001 PHE C 34 TYR 0.015 0.001 TYR D 81 ARG 0.006 0.000 ARG E 427 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 535) hydrogen bonds : angle 4.69939 ( 1500) metal coordination : bond 0.00989 ( 4) metal coordination : angle 5.07723 ( 6) covalent geometry : bond 0.00226 (17566) covalent geometry : angle 0.50312 (23785) *********************** 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 351 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 320 time to evaluate : 1.858 Fit side-chains REVERT: A 227 GLU cc_start: 0.5279 (mm-30) cc_final: 0.4406 (tp30) REVERT: A 256 MET cc_start: 0.7025 (mpp) cc_final: 0.5739 (tpt) REVERT: A 423 LEU cc_start: 0.8415 (mp) cc_final: 0.8134 (mp) REVERT: B 319 ASN cc_start: 0.9037 (m-40) cc_final: 0.8634 (m110) REVERT: B 381 ASN cc_start: 0.8217 (p0) cc_final: 0.7976 (p0) REVERT: B 412 LEU cc_start: 0.7927 (tt) cc_final: 0.7643 (tp) REVERT: B 413 TYR cc_start: 0.6274 (t80) cc_final: 0.5925 (t80) REVERT: C 107 LYS cc_start: 0.6996 (tttp) cc_final: 0.6680 (tttt) REVERT: C 216 MET cc_start: 0.7436 (mpp) cc_final: 0.7013 (mtt) REVERT: C 380 MET cc_start: 0.8485 (tpt) cc_final: 0.8275 (tpt) REVERT: C 426 ARG cc_start: 0.8468 (mtp180) cc_final: 0.7875 (mtt-85) REVERT: C 478 TYR cc_start: 0.6376 (t80) cc_final: 0.4672 (t80) REVERT: C 658 GLU cc_start: 0.7824 (pm20) cc_final: 0.7584 (pm20) REVERT: D 157 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8223 (mtmt) REVERT: D 163 HIS cc_start: 0.7022 (m-70) cc_final: 0.6720 (m170) REVERT: D 182 GLU cc_start: 0.7863 (pp20) cc_final: 0.7370 (mt-10) REVERT: D 205 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7388 (mptt) REVERT: D 251 SER cc_start: 0.8795 (t) cc_final: 0.8438 (p) REVERT: D 268 TYR cc_start: 0.6993 (t80) cc_final: 0.6666 (t80) REVERT: D 574 LYS cc_start: 0.7462 (tmtt) cc_final: 0.6683 (mtpt) REVERT: D 605 MET cc_start: 0.8423 (mmm) cc_final: 0.8103 (mmm) REVERT: D 631 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7248 (mtt-85) REVERT: D 649 GLU cc_start: 0.7283 (mp0) cc_final: 0.6717 (mt-10) REVERT: D 661 MET cc_start: 0.5301 (mmm) cc_final: 0.4207 (mtp) REVERT: E 342 MET cc_start: 0.4123 (tpt) cc_final: 0.3809 (mmm) REVERT: E 409 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7638 (tm-30) REVERT: E 412 ARG cc_start: 0.5394 (ptp90) cc_final: 0.5041 (mmm160) outliers start: 31 outliers final: 18 residues processed: 336 average time/residue: 0.3220 time to fit residues: 160.0621 Evaluate side-chains 284 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 527 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 E residue 356 THR Chi-restraints excluded: chain E residue 406 TYR 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 197 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 324 HIS A 347 ASN B 369 HIS B 481 HIS C 429 ASN C 600 ASN D 208 GLN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 ASN E 398 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128610 restraints weight = 25096.458| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.76 r_work: 0.3359 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17570 Z= 0.143 Angle : 0.588 22.995 23791 Z= 0.298 Chirality : 0.043 0.229 2605 Planarity : 0.004 0.044 3068 Dihedral : 4.478 29.889 2343 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.89 % Allowed : 14.41 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2118 helix: -0.72 (0.18), residues: 808 sheet: -0.87 (0.40), residues: 168 loop : -2.31 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 26 HIS 0.024 0.001 HIS D 343 PHE 0.023 0.002 PHE C 240 TYR 0.014 0.001 TYR C 320 ARG 0.008 0.001 ARG E 427 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 535) hydrogen bonds : angle 4.51515 ( 1500) metal coordination : bond 0.01054 ( 4) metal coordination : angle 2.97867 ( 6) covalent geometry : bond 0.00334 (17566) covalent geometry : angle 0.58664 (23785) *********************** 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 337 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 2.035 Fit side-chains REVERT: A 224 LYS cc_start: 0.7190 (pttm) cc_final: 0.6720 (tptm) REVERT: A 227 GLU cc_start: 0.5394 (mm-30) cc_final: 0.5067 (pp20) REVERT: A 256 MET cc_start: 0.7059 (mpp) cc_final: 0.5768 (tpt) REVERT: A 412 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7964 (mttp) REVERT: B 308 GLN cc_start: 0.5874 (mp10) cc_final: 0.4806 (tp-100) REVERT: B 355 ASP cc_start: 0.8430 (m-30) cc_final: 0.8212 (m-30) REVERT: B 412 LEU cc_start: 0.7973 (tt) cc_final: 0.7467 (tp) REVERT: C 107 LYS cc_start: 0.7315 (tttp) cc_final: 0.6979 (tttt) REVERT: C 216 MET cc_start: 0.7788 (mpp) cc_final: 0.7388 (mtt) REVERT: C 551 TYR cc_start: 0.8618 (p90) cc_final: 0.7976 (p90) REVERT: C 621 GLU cc_start: 0.8367 (mp0) cc_final: 0.8131 (mp0) REVERT: D 96 LYS cc_start: 0.8378 (tttm) cc_final: 0.7956 (ttmm) REVERT: D 157 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8518 (mmtp) REVERT: D 163 HIS cc_start: 0.7209 (m-70) cc_final: 0.6989 (m170) REVERT: D 174 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7931 (mtmt) REVERT: D 205 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7610 (mmtp) REVERT: D 251 SER cc_start: 0.8840 (t) cc_final: 0.8507 (p) REVERT: D 268 TYR cc_start: 0.7336 (t80) cc_final: 0.6967 (t80) REVERT: D 649 GLU cc_start: 0.7621 (mp0) cc_final: 0.6955 (mt-10) REVERT: D 661 MET cc_start: 0.5976 (mmm) cc_final: 0.4800 (mtp) REVERT: E 63 TYR cc_start: 0.7927 (t80) cc_final: 0.7683 (t80) REVERT: E 148 ASP cc_start: 0.5044 (OUTLIER) cc_final: 0.4231 (t0) REVERT: E 342 MET cc_start: 0.4479 (tpt) cc_final: 0.4066 (mmm) REVERT: E 359 GLU cc_start: 0.6713 (mp0) cc_final: 0.6191 (tt0) REVERT: E 412 ARG cc_start: 0.5730 (ptp90) cc_final: 0.5347 (mmm160) outliers start: 54 outliers final: 36 residues processed: 312 average time/residue: 0.3231 time to fit residues: 146.7288 Evaluate side-chains 281 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.960 ------------------------------------------------------------------------------- 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 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 B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU 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 135 GLU Chi-restraints excluded: chain C residue 147 SER 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 373 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 527 VAL 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 307 LYS 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 440 VAL Chi-restraints excluded: chain E residue 464 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 185 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 0.3980 chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 70 optimal weight: 0.0170 chunk 62 optimal weight: 10.0000 overall best weight: 3.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 319 ASN B 379 HIS B 515 HIS ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN ** C 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 208 GLN D 281 GLN D 327 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120348 restraints weight = 25013.191| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.66 r_work: 0.3243 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 17570 Z= 0.189 Angle : 0.622 10.272 23791 Z= 0.320 Chirality : 0.045 0.235 2605 Planarity : 0.004 0.055 3068 Dihedral : 4.904 34.695 2343 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.02 % Allowed : 16.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2118 helix: -0.49 (0.18), residues: 800 sheet: -0.59 (0.43), residues: 148 loop : -2.23 (0.15), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 240 HIS 0.006 0.001 HIS D 97 PHE 0.027 0.002 PHE C 240 TYR 0.017 0.002 TYR D 629 ARG 0.009 0.001 ARG C 426 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 535) hydrogen bonds : angle 4.60373 ( 1500) metal coordination : bond 0.01101 ( 4) metal coordination : angle 6.33796 ( 6) covalent geometry : bond 0.00458 (17566) covalent geometry : angle 0.61413 (23785) *********************** 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 325 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 250 time to evaluate : 3.380 Fit side-chains REVERT: A 14 HIS cc_start: 0.5489 (OUTLIER) cc_final: 0.4888 (m-70) REVERT: A 224 LYS cc_start: 0.7289 (pttm) cc_final: 0.6569 (tptm) REVERT: A 256 MET cc_start: 0.6915 (mpp) cc_final: 0.5756 (tpt) REVERT: A 419 ASP cc_start: 0.7528 (t0) cc_final: 0.7292 (t0) REVERT: B 308 GLN cc_start: 0.6087 (mp10) cc_final: 0.4490 (tp-100) REVERT: C 551 TYR cc_start: 0.8815 (p90) cc_final: 0.8480 (p90) REVERT: C 621 GLU cc_start: 0.8415 (mp0) cc_final: 0.8155 (mp0) REVERT: C 678 ARG cc_start: 0.6944 (ttt180) cc_final: 0.6714 (mtp180) REVERT: D 205 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7750 (mmtp) REVERT: D 267 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: D 607 ILE cc_start: 0.7724 (mm) cc_final: 0.7491 (mm) REVERT: D 631 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7146 (ttm-80) REVERT: D 649 GLU cc_start: 0.7775 (mp0) cc_final: 0.7054 (mt-10) REVERT: D 661 MET cc_start: 0.6240 (mmm) cc_final: 0.5034 (mtp) REVERT: E 11 ARG cc_start: 0.8112 (tpm170) cc_final: 0.7491 (tpp-160) REVERT: E 82 TYR cc_start: 0.7756 (t80) cc_final: 0.7065 (t80) REVERT: E 148 ASP cc_start: 0.5164 (OUTLIER) cc_final: 0.4152 (t0) REVERT: E 335 PHE cc_start: 0.4854 (t80) cc_final: 0.4614 (t80) REVERT: E 342 MET cc_start: 0.4483 (tpt) cc_final: 0.4091 (mmm) REVERT: E 359 GLU cc_start: 0.7113 (mp0) cc_final: 0.6296 (tt0) REVERT: E 412 ARG cc_start: 0.5780 (ptp90) cc_final: 0.5353 (mmm160) REVERT: E 510 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7629 (mmp-170) outliers start: 75 outliers final: 51 residues processed: 301 average time/residue: 0.4293 time to fit residues: 190.4908 Evaluate side-chains 275 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 220 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 17 PHE 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 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 B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU 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 135 GLU Chi-restraints excluded: chain C residue 147 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 366 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 527 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 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE 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 E residue 148 ASP Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Chi-restraints excluded: chain E residue 522 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 191 optimal weight: 0.6980 chunk 91 optimal weight: 0.3980 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN C 458 HIS D 208 GLN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120586 restraints weight = 25247.642| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.66 r_work: 0.3250 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17570 Z= 0.137 Angle : 0.560 8.387 23791 Z= 0.286 Chirality : 0.043 0.169 2605 Planarity : 0.004 0.038 3068 Dihedral : 4.650 32.351 2343 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.02 % Allowed : 17.14 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2118 helix: -0.16 (0.19), residues: 796 sheet: -0.39 (0.43), residues: 144 loop : -2.12 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 320 HIS 0.004 0.001 HIS D 97 PHE 0.020 0.001 PHE E 151 TYR 0.016 0.001 TYR A 43 ARG 0.007 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 535) hydrogen bonds : angle 4.36265 ( 1500) metal coordination : bond 0.01013 ( 4) metal coordination : angle 5.44201 ( 6) covalent geometry : bond 0.00336 (17566) covalent geometry : angle 0.55366 (23785) *********************** 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 309 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.5075 (m-70) REVERT: A 39 ASP cc_start: 0.4588 (OUTLIER) cc_final: 0.4076 (t0) REVERT: A 224 LYS cc_start: 0.7278 (pttm) cc_final: 0.6605 (tptm) REVERT: A 256 MET cc_start: 0.6732 (mpp) cc_final: 0.5586 (tpt) REVERT: A 419 ASP cc_start: 0.7518 (t0) cc_final: 0.7259 (t0) REVERT: B 308 GLN cc_start: 0.5777 (mp10) cc_final: 0.4207 (tp-100) REVERT: C 388 THR cc_start: 0.8951 (m) cc_final: 0.8719 (m) REVERT: C 551 TYR cc_start: 0.8769 (p90) cc_final: 0.8407 (p90) REVERT: C 678 ARG cc_start: 0.6920 (ttt180) cc_final: 0.6682 (mtp180) REVERT: D 205 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7717 (mmtp) REVERT: D 267 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: D 607 ILE cc_start: 0.7582 (mm) cc_final: 0.7002 (mm) REVERT: D 631 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7138 (ttm-80) REVERT: D 649 GLU cc_start: 0.7722 (mp0) cc_final: 0.6937 (mt-10) REVERT: D 661 MET cc_start: 0.6308 (mmm) cc_final: 0.5090 (mtp) REVERT: E 11 ARG cc_start: 0.8107 (tpm170) cc_final: 0.7571 (tpp-160) REVERT: E 50 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.6678 (t80) REVERT: E 82 TYR cc_start: 0.7795 (t80) cc_final: 0.6351 (t80) REVERT: E 148 ASP cc_start: 0.5114 (OUTLIER) cc_final: 0.4089 (t0) REVERT: E 342 MET cc_start: 0.4510 (tpt) cc_final: 0.4159 (mmm) REVERT: E 359 GLU cc_start: 0.7144 (mp0) cc_final: 0.6369 (tt0) REVERT: E 412 ARG cc_start: 0.5769 (ptp90) cc_final: 0.5337 (mmm160) REVERT: E 436 LYS cc_start: 0.8057 (pttt) cc_final: 0.7449 (ptmt) REVERT: E 510 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7297 (mmp-170) outliers start: 75 outliers final: 51 residues processed: 288 average time/residue: 0.4494 time to fit residues: 194.3966 Evaluate side-chains 281 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 39 ASP 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 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 B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 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 135 GLU Chi-restraints excluded: chain C residue 147 SER 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 429 ASN Chi-restraints excluded: chain C residue 527 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 267 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 331 THR 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 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 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 447 THR Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER 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 134 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 429 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120677 restraints weight = 25271.953| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.67 r_work: 0.3247 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 17570 Z= 0.130 Angle : 0.557 10.056 23791 Z= 0.283 Chirality : 0.043 0.236 2605 Planarity : 0.004 0.039 3068 Dihedral : 4.565 30.841 2343 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.75 % Allowed : 18.26 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2118 helix: 0.07 (0.19), residues: 789 sheet: -0.27 (0.43), residues: 144 loop : -2.03 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 320 HIS 0.004 0.001 HIS C 458 PHE 0.019 0.001 PHE C 240 TYR 0.020 0.001 TYR E 63 ARG 0.007 0.000 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 535) hydrogen bonds : angle 4.29625 ( 1500) metal coordination : bond 0.00986 ( 4) metal coordination : angle 5.40301 ( 6) covalent geometry : bond 0.00331 (17566) covalent geometry : angle 0.55006 (23785) *********************** 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 303 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5674 (OUTLIER) cc_final: 0.5107 (m-70) REVERT: A 224 LYS cc_start: 0.7262 (pttm) cc_final: 0.6579 (tptm) REVERT: A 256 MET cc_start: 0.6695 (mpp) cc_final: 0.5562 (tpt) REVERT: A 419 ASP cc_start: 0.7552 (t0) cc_final: 0.7303 (t0) REVERT: B 308 GLN cc_start: 0.5953 (mp10) cc_final: 0.4251 (tp-100) REVERT: C 388 THR cc_start: 0.8941 (m) cc_final: 0.8718 (m) REVERT: C 551 TYR cc_start: 0.8772 (p90) cc_final: 0.8416 (p90) REVERT: C 678 ARG cc_start: 0.7000 (ttt180) cc_final: 0.6768 (mtp180) REVERT: D 96 LYS cc_start: 0.8828 (tttm) cc_final: 0.8396 (ttmm) REVERT: D 205 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7706 (mmtp) REVERT: D 267 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: D 574 LYS cc_start: 0.7779 (tttm) cc_final: 0.7039 (ttmm) REVERT: D 631 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7151 (ttm-80) REVERT: D 649 GLU cc_start: 0.7781 (mp0) cc_final: 0.6995 (mt-10) REVERT: D 661 MET cc_start: 0.6314 (mmm) cc_final: 0.5049 (mtp) REVERT: E 11 ARG cc_start: 0.8179 (tpm170) cc_final: 0.7504 (tpp-160) REVERT: E 50 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6679 (t80) REVERT: E 82 TYR cc_start: 0.7839 (t80) cc_final: 0.6408 (t80) REVERT: E 148 ASP cc_start: 0.5299 (OUTLIER) cc_final: 0.4229 (t0) REVERT: E 342 MET cc_start: 0.4457 (tpt) cc_final: 0.4138 (mmm) REVERT: E 359 GLU cc_start: 0.7166 (mp0) cc_final: 0.6407 (tt0) REVERT: E 412 ARG cc_start: 0.5775 (ptp90) cc_final: 0.5347 (mmm160) REVERT: E 436 LYS cc_start: 0.8095 (pttt) cc_final: 0.7485 (ptmt) REVERT: E 510 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7267 (mmp-170) outliers start: 70 outliers final: 57 residues processed: 291 average time/residue: 0.3114 time to fit residues: 133.7559 Evaluate side-chains 285 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 223 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 179 ILE 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 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 B residue 512 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 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 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 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 429 ASN Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 535 LYS 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 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 585 THR 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 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 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 484 SER 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 86 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 429 ASN C 501 HIS D 66 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121981 restraints weight = 25028.029| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.66 r_work: 0.3269 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 17570 Z= 0.108 Angle : 0.535 9.487 23791 Z= 0.272 Chirality : 0.042 0.205 2605 Planarity : 0.003 0.035 3068 Dihedral : 4.417 30.765 2343 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.59 % Allowed : 19.07 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2118 helix: 0.28 (0.19), residues: 789 sheet: -0.09 (0.45), residues: 138 loop : -1.95 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 PHE 0.015 0.001 PHE C 240 TYR 0.019 0.001 TYR E 63 ARG 0.007 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 535) hydrogen bonds : angle 4.20270 ( 1500) metal coordination : bond 0.00902 ( 4) metal coordination : angle 5.16986 ( 6) covalent geometry : bond 0.00266 (17566) covalent geometry : angle 0.52889 (23785) *********************** 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 305 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5172 (m-70) REVERT: A 224 LYS cc_start: 0.7224 (pttm) cc_final: 0.6568 (tptm) REVERT: A 256 MET cc_start: 0.6587 (mpp) cc_final: 0.5500 (tpt) REVERT: A 419 ASP cc_start: 0.7466 (t0) cc_final: 0.7182 (t0) REVERT: B 308 GLN cc_start: 0.6001 (mp10) cc_final: 0.4330 (tp-100) REVERT: C 388 THR cc_start: 0.8912 (m) cc_final: 0.8690 (m) REVERT: C 551 TYR cc_start: 0.8760 (p90) cc_final: 0.8464 (p90) REVERT: C 621 GLU cc_start: 0.8366 (mp0) cc_final: 0.7990 (mp0) REVERT: C 678 ARG cc_start: 0.6923 (ttt180) cc_final: 0.6702 (mtp180) REVERT: D 96 LYS cc_start: 0.8824 (tttm) cc_final: 0.8390 (ttmm) REVERT: D 205 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7673 (mmtp) REVERT: D 267 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: D 574 LYS cc_start: 0.7699 (tttm) cc_final: 0.6982 (ttmm) REVERT: D 631 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7159 (ttm-80) REVERT: D 649 GLU cc_start: 0.7736 (mp0) cc_final: 0.6941 (mt-10) REVERT: D 661 MET cc_start: 0.6252 (mmm) cc_final: 0.5009 (mtm) REVERT: E 11 ARG cc_start: 0.8050 (tpm170) cc_final: 0.7438 (tpp-160) REVERT: E 50 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6708 (t80) REVERT: E 82 TYR cc_start: 0.7859 (t80) cc_final: 0.6357 (t80) REVERT: E 148 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.4305 (t0) REVERT: E 342 MET cc_start: 0.4457 (tpt) cc_final: 0.4126 (mmm) REVERT: E 359 GLU cc_start: 0.7131 (mp0) cc_final: 0.6427 (tt0) REVERT: E 412 ARG cc_start: 0.5741 (ptp90) cc_final: 0.5316 (mmm160) REVERT: E 436 LYS cc_start: 0.8111 (pttt) cc_final: 0.7513 (ptmt) REVERT: E 510 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7258 (mmp-170) outliers start: 67 outliers final: 48 residues processed: 292 average time/residue: 0.3524 time to fit residues: 154.3100 Evaluate side-chains 284 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 179 ILE 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 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 394 SER 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 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 135 GLU 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 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 527 VAL 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 D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 585 THR 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 466 GLN 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 119 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 6 optimal weight: 0.0770 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN D 163 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120306 restraints weight = 24999.175| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.67 r_work: 0.3248 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 17570 Z= 0.138 Angle : 0.560 9.945 23791 Z= 0.285 Chirality : 0.043 0.217 2605 Planarity : 0.004 0.036 3068 Dihedral : 4.518 31.631 2343 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.64 % Allowed : 18.91 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2118 helix: 0.36 (0.19), residues: 786 sheet: -0.16 (0.44), residues: 144 loop : -1.94 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 103 HIS 0.005 0.001 HIS C 501 PHE 0.020 0.001 PHE C 240 TYR 0.019 0.001 TYR E 63 ARG 0.008 0.000 ARG D 282 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 535) hydrogen bonds : angle 4.26125 ( 1500) metal coordination : bond 0.01010 ( 4) metal coordination : angle 5.44644 ( 6) covalent geometry : bond 0.00348 (17566) covalent geometry : angle 0.55315 (23785) *********************** 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 301 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5558 (OUTLIER) cc_final: 0.5022 (m-70) REVERT: A 224 LYS cc_start: 0.7263 (pttm) cc_final: 0.6586 (tptm) REVERT: A 256 MET cc_start: 0.6601 (mpp) cc_final: 0.5525 (tpt) REVERT: A 419 ASP cc_start: 0.7510 (t0) cc_final: 0.7232 (t0) REVERT: B 308 GLN cc_start: 0.6128 (mp10) cc_final: 0.4354 (tp-100) REVERT: C 482 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8301 (mt-10) REVERT: C 551 TYR cc_start: 0.8776 (p90) cc_final: 0.8430 (p90) REVERT: C 678 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6716 (mtp180) REVERT: D 96 LYS cc_start: 0.8814 (tttm) cc_final: 0.8386 (ttmm) REVERT: D 205 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7718 (mmtp) REVERT: D 267 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: D 574 LYS cc_start: 0.7709 (tttm) cc_final: 0.6982 (ttmm) REVERT: D 595 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (tt) REVERT: D 631 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7108 (ttm-80) REVERT: D 649 GLU cc_start: 0.7749 (mp0) cc_final: 0.6969 (mt-10) REVERT: D 661 MET cc_start: 0.6360 (mmm) cc_final: 0.5097 (mtp) REVERT: E 11 ARG cc_start: 0.8138 (tpm170) cc_final: 0.7479 (tpp-160) REVERT: E 50 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6806 (t80) REVERT: E 148 ASP cc_start: 0.5382 (OUTLIER) cc_final: 0.4267 (t0) REVERT: E 342 MET cc_start: 0.4477 (tpt) cc_final: 0.4169 (mmm) REVERT: E 359 GLU cc_start: 0.7160 (mp0) cc_final: 0.6424 (tt0) REVERT: E 412 ARG cc_start: 0.5736 (ptp90) cc_final: 0.5335 (mmm160) REVERT: E 436 LYS cc_start: 0.8113 (pttt) cc_final: 0.7504 (ptmt) REVERT: E 510 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7297 (mmp-170) outliers start: 68 outliers final: 59 residues processed: 285 average time/residue: 0.3243 time to fit residues: 135.3134 Evaluate side-chains 291 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 2.049 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 179 ILE 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 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 13 LEU Chi-restraints excluded: chain C residue 27 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 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 429 ASN Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 535 LYS 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 267 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE 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 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 448 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 484 SER 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 6 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 164 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 245 HIS C 429 ASN D 653 ASN E 450 ASN E 466 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.145777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123485 restraints weight = 25103.703| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.66 r_work: 0.3288 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.159 17570 Z= 0.096 Angle : 0.522 9.227 23791 Z= 0.265 Chirality : 0.042 0.227 2605 Planarity : 0.003 0.034 3068 Dihedral : 4.271 29.816 2343 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.89 % Allowed : 20.25 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2118 helix: 0.58 (0.19), residues: 782 sheet: -0.15 (0.44), residues: 147 loop : -1.82 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 320 HIS 0.004 0.001 HIS C 501 PHE 0.013 0.001 PHE D 269 TYR 0.020 0.001 TYR E 63 ARG 0.008 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 535) hydrogen bonds : angle 4.09793 ( 1500) metal coordination : bond 0.00811 ( 4) metal coordination : angle 5.00271 ( 6) covalent geometry : bond 0.00243 (17566) covalent geometry : angle 0.51565 (23785) *********************** 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 295 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5647 (OUTLIER) cc_final: 0.5040 (m-70) REVERT: A 152 LEU cc_start: 0.4333 (OUTLIER) cc_final: 0.4129 (mt) REVERT: A 256 MET cc_start: 0.6525 (mpp) cc_final: 0.5456 (tpt) REVERT: A 419 ASP cc_start: 0.7460 (t0) cc_final: 0.7182 (t0) REVERT: B 308 GLN cc_start: 0.5988 (mp10) cc_final: 0.4345 (tp-100) REVERT: C 216 MET cc_start: 0.7642 (mpp) cc_final: 0.7147 (mtt) REVERT: C 388 THR cc_start: 0.8799 (m) cc_final: 0.8509 (m) REVERT: C 551 TYR cc_start: 0.8732 (p90) cc_final: 0.8428 (p90) REVERT: C 621 GLU cc_start: 0.8356 (mp0) cc_final: 0.7950 (mp0) REVERT: C 678 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6671 (mtp180) REVERT: D 96 LYS cc_start: 0.8777 (tttm) cc_final: 0.8353 (ttmm) REVERT: D 205 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7691 (mmtp) REVERT: D 267 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: D 351 MET cc_start: 0.8804 (tpp) cc_final: 0.8570 (mmt) REVERT: D 574 LYS cc_start: 0.7646 (tttm) cc_final: 0.6936 (ttmm) REVERT: D 595 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8330 (tt) REVERT: D 631 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7180 (ttm-80) REVERT: D 649 GLU cc_start: 0.7750 (mp0) cc_final: 0.7209 (mp0) REVERT: D 661 MET cc_start: 0.6242 (mmm) cc_final: 0.4996 (mtm) REVERT: E 11 ARG cc_start: 0.8077 (tpm170) cc_final: 0.7465 (tpp-160) REVERT: E 50 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6726 (t80) REVERT: E 83 ASN cc_start: 0.7720 (t0) cc_final: 0.7472 (t0) REVERT: E 342 MET cc_start: 0.4495 (tpt) cc_final: 0.4174 (mmm) REVERT: E 359 GLU cc_start: 0.7120 (mp0) cc_final: 0.6432 (tt0) REVERT: E 412 ARG cc_start: 0.5603 (ptp90) cc_final: 0.5301 (mmm160) REVERT: E 436 LYS cc_start: 0.8129 (pttt) cc_final: 0.7512 (ptmt) REVERT: E 510 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7265 (mmt180) outliers start: 54 outliers final: 42 residues processed: 285 average time/residue: 0.3124 time to fit residues: 131.1908 Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 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 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR 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 13 LEU Chi-restraints excluded: chain C residue 91 ILE 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 152 ILE Chi-restraints excluded: chain C residue 163 THR 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 429 ASN 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 36 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE 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 448 MET 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 81 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 2 optimal weight: 0.0000 chunk 51 optimal weight: 9.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN C 495 HIS D 163 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121995 restraints weight = 25005.142| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.65 r_work: 0.3272 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 17570 Z= 0.115 Angle : 0.536 9.876 23791 Z= 0.272 Chirality : 0.042 0.200 2605 Planarity : 0.003 0.036 3068 Dihedral : 4.315 30.392 2343 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.37 % Allowed : 19.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2118 helix: 0.63 (0.19), residues: 783 sheet: -0.32 (0.43), residues: 152 loop : -1.81 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 320 HIS 0.005 0.001 HIS C 245 PHE 0.016 0.001 PHE C 240 TYR 0.021 0.001 TYR A 477 ARG 0.008 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 535) hydrogen bonds : angle 4.11654 ( 1500) metal coordination : bond 0.00924 ( 4) metal coordination : angle 5.18662 ( 6) covalent geometry : bond 0.00288 (17566) covalent geometry : angle 0.52992 (23785) ********************** 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 292 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.5699 (OUTLIER) cc_final: 0.5074 (m-70) REVERT: A 152 LEU cc_start: 0.4434 (OUTLIER) cc_final: 0.4224 (mt) REVERT: A 224 LYS cc_start: 0.7204 (pttm) cc_final: 0.6559 (tptm) REVERT: A 256 MET cc_start: 0.6535 (mpp) cc_final: 0.5437 (tpt) REVERT: A 419 ASP cc_start: 0.7366 (t0) cc_final: 0.7114 (t0) REVERT: B 308 GLN cc_start: 0.6067 (mp10) cc_final: 0.4326 (tp-100) REVERT: C 216 MET cc_start: 0.7625 (mpp) cc_final: 0.7144 (mtt) REVERT: C 551 TYR cc_start: 0.8732 (p90) cc_final: 0.8378 (p90) REVERT: C 621 GLU cc_start: 0.8384 (mp0) cc_final: 0.7997 (mp0) REVERT: C 678 ARG cc_start: 0.6885 (ttt180) cc_final: 0.6666 (mtp180) REVERT: D 96 LYS cc_start: 0.8808 (tttm) cc_final: 0.8377 (ttmm) REVERT: D 205 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7715 (mmtp) REVERT: D 267 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: D 574 LYS cc_start: 0.7651 (tttm) cc_final: 0.6923 (ttmm) REVERT: D 595 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8323 (tt) REVERT: D 631 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7165 (ttm-80) REVERT: D 649 GLU cc_start: 0.7793 (mp0) cc_final: 0.6983 (mt-10) REVERT: D 661 MET cc_start: 0.6268 (mmm) cc_final: 0.5022 (mtm) REVERT: D 676 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5980 (mt) REVERT: E 11 ARG cc_start: 0.8109 (tpm170) cc_final: 0.7496 (tpp-160) REVERT: E 50 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6787 (t80) REVERT: E 83 ASN cc_start: 0.7779 (t0) cc_final: 0.7498 (t0) REVERT: E 148 ASP cc_start: 0.5273 (OUTLIER) cc_final: 0.4179 (t0) REVERT: E 342 MET cc_start: 0.4463 (tpt) cc_final: 0.4163 (mmm) REVERT: E 359 GLU cc_start: 0.7139 (mp0) cc_final: 0.6418 (tt0) REVERT: E 412 ARG cc_start: 0.5663 (ptp90) cc_final: 0.5301 (mmm160) REVERT: E 436 LYS cc_start: 0.8098 (pttt) cc_final: 0.7499 (ptmt) REVERT: E 510 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7251 (mmp-170) outliers start: 63 outliers final: 51 residues processed: 278 average time/residue: 0.3070 time to fit residues: 125.5719 Evaluate side-chains 286 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 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 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR 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 B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 91 ILE 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 429 ASN 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 36 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 676 LEU 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 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 448 MET Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 466 GLN 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 65 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 205 optimal weight: 0.0570 overall best weight: 1.1502 ------------------------------------------------------------------------------- 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 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS E 466 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122764 restraints weight = 24946.648| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.66 r_work: 0.3280 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 17570 Z= 0.101 Angle : 0.526 9.506 23791 Z= 0.267 Chirality : 0.042 0.193 2605 Planarity : 0.003 0.037 3068 Dihedral : 4.256 30.177 2343 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.32 % Allowed : 19.93 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2118 helix: 0.63 (0.19), residues: 790 sheet: -0.24 (0.44), residues: 143 loop : -1.76 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 320 HIS 0.005 0.001 HIS C 501 PHE 0.014 0.001 PHE C 240 TYR 0.019 0.001 TYR E 63 ARG 0.008 0.000 ARG C 615 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 535) hydrogen bonds : angle 4.09051 ( 1500) metal coordination : bond 0.00803 ( 4) metal coordination : angle 4.85370 ( 6) covalent geometry : bond 0.00243 (17566) covalent geometry : angle 0.52055 (23785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9732.84 seconds wall clock time: 171 minutes 57.46 seconds (10317.46 seconds total)