Starting phenix.real_space_refine on Sun Sep 13 14:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tw2_56357/09_2026/9tw2_56357.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 14870 2.51 5 N 4056 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23420 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6583 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 773} Chain breaks: 1 Chain: "B" Number of atoms: 9481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1192, 9481 Classifications: {'peptide': 1192} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1134} Chain breaks: 6 Chain: "C" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2907 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 348} Chain: "D" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2641 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 982 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 103 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GDP': 1, 'MYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16378 SG CYS C 137 47.811 129.179 37.788 1.00 50.22 S ATOM 16402 SG CYS C 140 49.471 131.466 40.843 1.00 43.78 S ATOM 19036 SG CYS D 43 48.545 127.750 38.214 1.00 50.31 S ATOM 19057 SG CYS D 46 47.285 128.888 40.312 1.00 43.85 S ATOM 19133 SG CYS D 55 54.328 134.413 27.010 1.00 49.61 S ATOM 19153 SG CYS D 58 55.110 136.160 27.544 1.00 52.02 S ATOM 23301 SG CYS G 18 51.803 134.359 26.138 1.00 52.62 S ATOM 23327 SG CYS G 21 53.829 135.264 25.206 1.00 56.34 S Time building chain proxies: 4.86, per 1000 atoms: 0.21 Number of scatterers: 23420 At special positions: 0 Unit cell: (104.4, 181.975, 235.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 2 15.00 Mg 1 11.99 O 4361 8.00 N 4056 7.00 C 14870 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 600 " pdb="ZN ZN D 600 " - pdb=" SG CYS C 137 " pdb="ZN ZN D 600 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 600 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 600 " - pdb=" SG CYS C 140 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 601 " - pdb=" SG CYS G 18 " pdb="ZN ZN D 601 " - pdb=" SG CYS G 21 " Number of angles added : 12 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5522 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 22 sheets defined 50.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.023A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.538A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.860A pdb=" N GLU A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 207 No H-bonds generated for 'chain 'A' and resid 206 through 207' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.654A pdb=" N SER A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.867A pdb=" N HIS A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.696A pdb=" N PHE A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.551A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.527A pdb=" N SER A 368 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.948A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 412' Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.521A pdb=" N ALA A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.732A pdb=" N TRP A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.701A pdb=" N GLN A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 removed outlier: 4.003A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 560 Processing helix chain 'A' and resid 565 through 579 removed outlier: 3.820A pdb=" N LYS A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 660 removed outlier: 3.615A pdb=" N GLN A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 646 " --> pdb=" O ARG A 642 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.616A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.638A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 811 removed outlier: 3.838A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.701A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.694A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 851 through 868 removed outlier: 4.023A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.745A pdb=" N SER B 18 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 78 removed outlier: 4.059A pdb=" N TYR B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.603A pdb=" N ARG B 126 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.619A pdb=" N TYR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 238 through 254 removed outlier: 3.993A pdb=" N PHE B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.735A pdb=" N ASN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.680A pdb=" N ASN B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.615A pdb=" N LYS B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.578A pdb=" N THR B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.794A pdb=" N ALA B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.852A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.574A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.671A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.594A pdb=" N LEU B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.526A pdb=" N PHE B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.868A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.599A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.837A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.853A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.694A pdb=" N VAL B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 530 through 545 removed outlier: 3.609A pdb=" N GLU B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.783A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.615A pdb=" N VAL B 566 " --> pdb=" O THR B 562 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 569 " --> pdb=" O CYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.660A pdb=" N ASN B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.588A pdb=" N ILE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 removed outlier: 3.672A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 600 removed outlier: 3.801A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 599 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 4.049A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 Proline residue: B 618 - end of helix removed outlier: 3.767A pdb=" N GLN B 622 " --> pdb=" O PRO B 618 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.525A pdb=" N MET B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 657 removed outlier: 3.823A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 659 No H-bonds generated for 'chain 'B' and resid 658 through 659' Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.759A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.520A pdb=" N TYR B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 removed outlier: 3.765A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 712 through 718 removed outlier: 4.275A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 734 Processing helix chain 'B' and resid 737 through 753 removed outlier: 4.160A pdb=" N LEU B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 777 Processing helix chain 'B' and resid 781 through 790 removed outlier: 4.110A pdb=" N ASP B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 804 removed outlier: 3.657A pdb=" N LYS B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 801 " --> pdb=" O SER B 797 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 802 " --> pdb=" O ASN B 798 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 803 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 938 through 966 Processing helix chain 'B' and resid 1038 through 1042 removed outlier: 3.645A pdb=" N ILE B1041 " --> pdb=" O TYR B1038 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B1042 " --> pdb=" O SER B1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1038 through 1042' Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.503A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.741A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 127 removed outlier: 3.626A pdb=" N ARG C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 170 removed outlier: 4.126A pdb=" N LEU C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 163 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 267 removed outlier: 3.943A pdb=" N GLN C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP C 200 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 299 through 322 removed outlier: 3.820A pdb=" N ILE C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.934A pdb=" N ASP C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 removed outlier: 3.883A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.645A pdb=" N GLN D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 4.245A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 128 removed outlier: 3.507A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 153 removed outlier: 3.532A pdb=" N LEU D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'D' and resid 166 through 205 removed outlier: 3.638A pdb=" N ARG D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 287 removed outlier: 4.154A pdb=" N SER D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 301 through 322 removed outlier: 3.602A pdb=" N ALA D 306 " --> pdb=" O THR D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 362 removed outlier: 3.620A pdb=" N GLN D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 removed outlier: 3.647A pdb=" N ASN D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.897A pdb=" N GLN E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.901A pdb=" N ALA E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 78 removed outlier: 3.695A pdb=" N GLN E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU E 68 " --> pdb=" O HIS E 64 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 10 through 18 removed outlier: 3.905A pdb=" N ARG F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 90 through 98 Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 4.471A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 234 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 10 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 96 removed outlier: 9.079A pdb=" N TRP A 85 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU A 27 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE A 23 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU A 220 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 25 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 219 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.589A pdb=" N TYR A 58 " --> pdb=" O TRP A 111 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.636A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.636A pdb=" N LYS A 624 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 604 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE A 622 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.559A pdb=" N LEU A 750 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 758 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.304A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 102 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.437A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 984 through 989 removed outlier: 6.936A pdb=" N VAL B1356 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N HIS B 988 " --> pdb=" O VAL B1354 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B1354 " --> pdb=" O HIS B 988 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B1338 " --> pdb=" O PHE B1344 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B1348 " --> pdb=" O ASP B1334 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP B1334 " --> pdb=" O ALA B1348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 996 through 1001 removed outlier: 6.932A pdb=" N CYS B1011 " --> pdb=" O ASN B 997 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 999 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B1009 " --> pdb=" O ILE B 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1045 through 1049 removed outlier: 3.896A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B1086 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B1070 " --> pdb=" O PRO B1084 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1098 through 1104 removed outlier: 4.225A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE B1104 " --> pdb=" O VAL B1111 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B1111 " --> pdb=" O PHE B1104 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 3.921A pdb=" N SER B1146 " --> pdb=" O GLY B1159 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N CYS B1167 " --> pdb=" O SER B1177 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 4.557A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1209 " --> pdb=" O VAL B1204 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B1222 " --> pdb=" O MET B1212 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1242 through 1250 removed outlier: 3.531A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B1248 " --> pdb=" O ILE B1255 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B1250 " --> pdb=" O ASN B1253 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B1256 " --> pdb=" O TRP B1268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 97 through 99 removed outlier: 3.596A pdb=" N LEU F 50 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N LEU F 105 " --> pdb=" O ARG F 28 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 277 through 279 Processing sheet with id=AC2, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.675A pdb=" N TYR C 338 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AC4, first strand: chain 'D' and resid 210 through 211 992 hydrogen bonds defined for protein. 2826 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: 4.86 Time building geometry restraints manager: 2.28 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: 7658 1.34 - 1.46: 5167 1.46 - 1.58: 10868 1.58 - 1.71: 1 1.71 - 1.83: 202 Bond restraints: 23896 Sorted by residual: bond pdb=" C ASN D 298 " pdb=" N PRO D 299 " ideal model delta sigma weight residual 1.337 1.384 -0.047 1.24e-02 6.50e+03 1.46e+01 bond pdb=" N GLU F 19 " pdb=" CA GLU F 19 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" C5 GDP B1402 " pdb=" C4 GDP B1402 " ideal model delta sigma weight residual 1.490 1.433 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" N ARG F 40 " pdb=" CA ARG F 40 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.52e+00 bond pdb=" N MET D 294 " pdb=" CA MET D 294 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.94e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 31904 3.07 - 6.15: 326 6.15 - 9.22: 34 9.22 - 12.29: 4 12.29 - 15.37: 2 Bond angle restraints: 32270 Sorted by residual: angle pdb=" CA PHE F 60 " pdb=" CB PHE F 60 " pdb=" CG PHE F 60 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" C LYS F 66 " pdb=" N ARG F 67 " pdb=" CA ARG F 67 " ideal model delta sigma weight residual 120.63 128.10 -7.47 1.61e+00 3.86e-01 2.15e+01 angle pdb=" CA PHE B 167 " pdb=" C PHE B 167 " pdb=" O PHE B 167 " ideal model delta sigma weight residual 119.05 113.14 5.91 1.30e+00 5.92e-01 2.07e+01 angle pdb=" C ALA F 72 " pdb=" N GLU F 73 " pdb=" CA GLU F 73 " ideal model delta sigma weight residual 122.21 128.87 -6.66 1.48e+00 4.57e-01 2.02e+01 angle pdb=" C ILE D 165 " pdb=" N GLN D 166 " pdb=" CA GLN D 166 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 ... (remaining 32265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.71: 14129 27.71 - 55.41: 410 55.41 - 83.12: 47 83.12 - 110.82: 8 110.82 - 138.53: 1 Dihedral angle restraints: 14595 sinusoidal: 6089 harmonic: 8506 Sorted by residual: dihedral pdb=" O2B GDP B1402 " pdb=" O3A GDP B1402 " pdb=" PB GDP B1402 " pdb=" PA GDP B1402 " ideal model delta sinusoidal sigma weight residual -180.00 -41.47 -138.53 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" CA GLU A 267 " pdb=" C GLU A 267 " pdb=" N SER A 268 " pdb=" CA SER A 268 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O5' GDP B1402 " pdb=" O3A GDP B1402 " pdb=" PA GDP B1402 " pdb=" PB GDP B1402 " ideal model delta sinusoidal sigma weight residual -179.98 -74.94 -105.04 1 2.00e+01 2.50e-03 3.02e+01 ... (remaining 14592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2982 0.062 - 0.123: 488 0.123 - 0.185: 82 0.185 - 0.247: 6 0.247 - 0.308: 7 Chirality restraints: 3565 Sorted by residual: chirality pdb=" CA ASP F 45 " pdb=" N ASP F 45 " pdb=" C ASP F 45 " pdb=" CB ASP F 45 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA GLU F 19 " pdb=" N GLU F 19 " pdb=" C GLU F 19 " pdb=" CB GLU F 19 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA HIS F 69 " pdb=" N HIS F 69 " pdb=" C HIS F 69 " pdb=" CB HIS F 69 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3562 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 49 " 0.079 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 49 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 49 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR F 49 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 49 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR F 49 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 109 " 0.069 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR F 109 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 109 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 109 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR F 109 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 109 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR F 109 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 109 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 5 " 0.047 2.00e-02 2.50e+03 3.34e-02 2.24e+01 pdb=" CG TYR F 5 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR F 5 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 5 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 5 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR F 5 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR F 5 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR F 5 " 0.062 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7471 2.87 - 3.38: 20237 3.38 - 3.88: 34937 3.88 - 4.39: 39150 4.39 - 4.90: 69071 Nonbonded interactions: 170866 Sorted by model distance: nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1403 " model vdw 2.360 2.170 nonbonded pdb=" OD2 ASP B 166 " pdb="MG MG B1403 " model vdw 2.412 2.170 nonbonded pdb=" O2B GDP B1402 " pdb="MG MG B1403 " model vdw 2.429 2.170 nonbonded pdb=" CG ASP B 166 " pdb="MG MG B1403 " model vdw 2.440 2.400 nonbonded pdb=" OG1 THR B 189 " pdb=" O3B GDP B1402 " model vdw 2.451 3.040 ... (remaining 170861 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 group one per residue 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 23.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 23905 Z= 0.283 Angle : 1.190 67.123 32282 Z= 0.521 Chirality : 0.050 0.308 3565 Planarity : 0.006 0.078 4138 Dihedral : 13.597 138.526 9073 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.39 % Allowed : 5.14 % Favored : 94.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 2867 helix: -2.04 (0.12), residues: 1289 sheet: -0.34 (0.29), residues: 280 loop : -1.07 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 434 TYR 0.079 0.003 TYR F 49 PHE 0.052 0.002 PHE F 78 TRP 0.024 0.002 TRP B1268 HIS 0.008 0.001 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.28 (23896) covalent geometry : angle 0.84390 / 0.50 (32270) hydrogen bonds : bond 0.24248 / 15.96 ( 987) hydrogen bonds : angle 7.20225 / 4.88 ( 2826) metal coordination : bond 0.03090 / 1.81 ( 8) metal coordination : angle 43.52021 / 24.55 ( 12) Misc. bond : bond 0.08710 / 4.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 563 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 MET cc_start: 0.8193 (mtp) cc_final: 0.7910 (mtp) REVERT: B 155 MET cc_start: 0.8642 (mmm) cc_final: 0.8069 (mmt) REVERT: D 394 PRO cc_start: 0.8743 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: E 69 LEU cc_start: 0.8473 (tp) cc_final: 0.8197 (mp) REVERT: F 1 MET cc_start: 0.1728 (mmt) cc_final: -0.0761 (ttt) outliers start: 10 outliers final: 5 residues processed: 568 average time/residue: 0.1934 time to fit residues: 164.0933 Evaluate side-chains 312 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 307 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 546 GLN A 649 GLN A 860 GLN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 427 ASN B 559 ASN B 622 GLN B1328 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.175057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119159 restraints weight = 39736.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121561 restraints weight = 25877.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122068 restraints weight = 18190.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122182 restraints weight = 18566.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122465 restraints weight = 17630.414| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23905 Z= 0.137 Angle : 0.801 52.614 32282 Z= 0.325 Chirality : 0.042 0.340 3565 Planarity : 0.004 0.055 4138 Dihedral : 6.504 147.118 3181 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.09 % Allowed : 10.17 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2867 helix: -0.25 (0.14), residues: 1303 sheet: 0.11 (0.29), residues: 295 loop : -0.92 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 346 TYR 0.029 0.002 TYR D 301 PHE 0.024 0.002 PHE F 60 TRP 0.021 0.002 TRP C 300 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (23896) covalent geometry : angle 0.59928 / 0.31 (32270) hydrogen bonds : bond 0.04897 / 3.22 ( 987) hydrogen bonds : angle 4.62400 / 3.13 ( 2826) metal coordination : bond 0.01357 / 0.74 ( 8) metal coordination : angle 27.56826 / 16.60 ( 12) Misc. bond : bond 0.00644 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 ASN cc_start: 0.8473 (m-40) cc_final: 0.7788 (t0) REVERT: A 803 TYR cc_start: 0.7829 (p90) cc_final: 0.7357 (p90) REVERT: A 865 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7967 (mm-30) REVERT: B 155 MET cc_start: 0.8924 (mmm) cc_final: 0.8074 (mmt) REVERT: B 764 ASP cc_start: 0.5886 (t0) cc_final: 0.5238 (t70) REVERT: B 772 LYS cc_start: 0.9283 (tppt) cc_final: 0.9046 (pptt) REVERT: B 1013 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 1093 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8394 (tptm) REVERT: B 1213 TRP cc_start: 0.7960 (m100) cc_final: 0.7624 (m-10) REVERT: C 182 MET cc_start: 0.8233 (ppp) cc_final: 0.8026 (ppp) REVERT: C 329 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7620 (ptm160) REVERT: D 134 MET cc_start: 0.8486 (ttm) cc_final: 0.8090 (mmm) REVERT: D 263 ILE cc_start: 0.7876 (tt) cc_final: 0.6707 (pt) REVERT: D 301 TYR cc_start: 0.6329 (m-80) cc_final: 0.5729 (m-80) REVERT: D 315 ASN cc_start: 0.8285 (p0) cc_final: 0.8071 (m-40) REVERT: D 346 ARG cc_start: 0.9139 (mmm160) cc_final: 0.8521 (mmm160) REVERT: D 350 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8528 (mmmm) REVERT: D 380 TYR cc_start: 0.8552 (m-10) cc_final: 0.8298 (m-80) REVERT: E 69 LEU cc_start: 0.8287 (tp) cc_final: 0.7989 (mp) REVERT: F 1 MET cc_start: -0.0066 (mmt) cc_final: -0.1567 (ttt) REVERT: F 27 ASP cc_start: 0.7995 (t0) cc_final: 0.7640 (t0) outliers start: 54 outliers final: 28 residues processed: 374 average time/residue: 0.1764 time to fit residues: 101.4635 Evaluate side-chains 311 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1247 CYS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain C residue 333 TYR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 62 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 178 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 469 HIS B 954 GLN B1328 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS D 388 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.168270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111670 restraints weight = 39593.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112297 restraints weight = 26179.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112450 restraints weight = 19586.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112669 restraints weight = 20068.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.112957 restraints weight = 19064.203| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 23905 Z= 0.199 Angle : 0.700 40.110 32282 Z= 0.333 Chirality : 0.044 0.382 3565 Planarity : 0.005 0.051 4138 Dihedral : 6.090 142.599 3171 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.13 % Allowed : 10.79 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 2867 helix: 0.43 (0.15), residues: 1300 sheet: -0.03 (0.29), residues: 300 loop : -0.87 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1360 TYR 0.026 0.002 TYR A 803 PHE 0.019 0.002 PHE A 64 TRP 0.029 0.002 TRP C 300 HIS 0.009 0.001 HIS B 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (23896) covalent geometry : angle 0.63504 / 0.33 (32270) hydrogen bonds : bond 0.05096 / 3.32 ( 987) hydrogen bonds : angle 4.41604 / 2.98 ( 2826) metal coordination : bond 0.01463 / 0.85 ( 8) metal coordination : angle 15.26233 / 9.50 ( 12) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 TYR cc_start: 0.7822 (p90) cc_final: 0.7381 (p90) REVERT: A 865 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8020 (mm-30) REVERT: B 72 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: B 982 LYS cc_start: 0.8819 (tptp) cc_final: 0.8534 (tppt) REVERT: B 1025 MET cc_start: 0.8667 (mtp) cc_final: 0.8254 (mtt) REVERT: B 1179 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7283 (p-80) REVERT: B 1213 TRP cc_start: 0.8079 (m100) cc_final: 0.7743 (m-10) REVERT: C 321 MET cc_start: 0.8718 (mmm) cc_final: 0.8436 (mmm) REVERT: C 329 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7595 (ptm160) REVERT: D 327 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8505 (mmtp) REVERT: D 346 ARG cc_start: 0.9122 (mmm160) cc_final: 0.8442 (mmm160) REVERT: D 366 LEU cc_start: 0.7944 (tp) cc_final: 0.7532 (tp) REVERT: E 69 LEU cc_start: 0.8334 (tp) cc_final: 0.8106 (mp) REVERT: F 1 MET cc_start: 0.0096 (mmt) cc_final: -0.1444 (ttt) REVERT: F 27 ASP cc_start: 0.8138 (t0) cc_final: 0.7839 (t0) REVERT: F 104 PHE cc_start: 0.8080 (m-80) cc_final: 0.7873 (m-80) REVERT: G 23 GLN cc_start: 0.7848 (mp10) cc_final: 0.7110 (mp10) outliers start: 55 outliers final: 30 residues processed: 359 average time/residue: 0.1778 time to fit residues: 98.9663 Evaluate side-chains 312 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 280 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN A 745 HIS B 45 HIS B 140 HIS B1243 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN G 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.170468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115159 restraints weight = 39647.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115807 restraints weight = 25134.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115636 restraints weight = 18176.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116387 restraints weight = 19573.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116687 restraints weight = 17146.852| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23905 Z= 0.111 Angle : 0.599 34.060 32282 Z= 0.278 Chirality : 0.041 0.280 3565 Planarity : 0.003 0.048 4138 Dihedral : 5.842 143.805 3171 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.89 % Allowed : 12.30 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 2867 helix: 0.90 (0.15), residues: 1306 sheet: 0.26 (0.29), residues: 298 loop : -0.82 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 22 TYR 0.025 0.001 TYR C 333 PHE 0.020 0.001 PHE B1147 TRP 0.024 0.001 TRP C 300 HIS 0.004 0.001 HIS B 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (23896) covalent geometry : angle 0.53436 / 0.27 (32270) hydrogen bonds : bond 0.03871 / 2.49 ( 987) hydrogen bonds : angle 4.07609 / 2.75 ( 2826) metal coordination : bond 0.01242 / 0.66 ( 8) metal coordination : angle 13.99924 / 8.54 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 TYR cc_start: 0.7742 (p90) cc_final: 0.7334 (p90) REVERT: A 865 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7984 (mm-30) REVERT: B 72 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: B 1025 MET cc_start: 0.8670 (mtp) cc_final: 0.8222 (mtt) REVERT: B 1033 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7596 (ptm-80) REVERT: B 1179 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7419 (p-80) REVERT: B 1213 TRP cc_start: 0.8054 (m100) cc_final: 0.7781 (m-10) REVERT: B 1222 PHE cc_start: 0.8341 (t80) cc_final: 0.8125 (t80) REVERT: B 1275 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: C 321 MET cc_start: 0.8809 (mmm) cc_final: 0.8560 (mmm) REVERT: C 329 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7580 (ptm160) REVERT: D 134 MET cc_start: 0.8452 (ttm) cc_final: 0.8250 (mmm) REVERT: D 301 TYR cc_start: 0.6276 (m-80) cc_final: 0.5812 (m-80) REVERT: D 327 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8471 (mppt) REVERT: D 346 ARG cc_start: 0.9102 (mmm160) cc_final: 0.8399 (mmm160) REVERT: E 76 LYS cc_start: 0.8298 (mmmt) cc_final: 0.8079 (mtmt) REVERT: F 1 MET cc_start: 0.0193 (mmt) cc_final: -0.1375 (ttt) REVERT: F 27 ASP cc_start: 0.8167 (t0) cc_final: 0.7838 (t0) REVERT: G 16 PHE cc_start: 0.8273 (m-80) cc_final: 0.7964 (m-80) REVERT: G 23 GLN cc_start: 0.7981 (mp10) cc_final: 0.7275 (mp10) outliers start: 49 outliers final: 32 residues processed: 330 average time/residue: 0.1779 time to fit residues: 90.3113 Evaluate side-chains 301 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 4 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 279 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN B 140 HIS B 744 HIS B1208 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107162 restraints weight = 39238.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107937 restraints weight = 26379.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108217 restraints weight = 20404.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108671 restraints weight = 21399.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108823 restraints weight = 19312.721| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23905 Z= 0.220 Angle : 0.668 32.920 32282 Z= 0.321 Chirality : 0.045 0.188 3565 Planarity : 0.004 0.045 4138 Dihedral : 5.920 141.271 3171 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.59 % Allowed : 12.14 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2867 helix: 0.84 (0.15), residues: 1304 sheet: 0.12 (0.30), residues: 289 loop : -0.93 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 114 TYR 0.025 0.002 TYR A 803 PHE 0.027 0.002 PHE B1147 TRP 0.023 0.002 TRP C 300 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.22 (23896) covalent geometry : angle 0.62561 / 0.32 (32270) hydrogen bonds : bond 0.04801 / 3.14 ( 987) hydrogen bonds : angle 4.27131 / 2.88 ( 2826) metal coordination : bond 0.01181 / 0.64 ( 8) metal coordination : angle 12.17727 / 7.59 ( 12) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 TYR cc_start: 0.7808 (p90) cc_final: 0.7416 (p90) REVERT: A 865 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8018 (mm-30) REVERT: B 764 ASP cc_start: 0.5917 (t0) cc_final: 0.5257 (t70) REVERT: B 982 LYS cc_start: 0.8891 (tptp) cc_final: 0.8659 (tppt) REVERT: B 1025 MET cc_start: 0.8725 (mtp) cc_final: 0.8387 (mtp) REVERT: B 1179 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7264 (p-80) REVERT: B 1213 TRP cc_start: 0.8151 (m100) cc_final: 0.7830 (m-10) REVERT: C 321 MET cc_start: 0.8871 (mmm) cc_final: 0.8634 (mmm) REVERT: C 329 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7685 (ptm160) REVERT: D 71 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: D 301 TYR cc_start: 0.6351 (m-80) cc_final: 0.5910 (m-80) REVERT: D 346 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8374 (mmm160) REVERT: F 1 MET cc_start: 0.0047 (mmt) cc_final: -0.1730 (ttt) REVERT: F 27 ASP cc_start: 0.8217 (t0) cc_final: 0.7905 (t0) outliers start: 67 outliers final: 50 residues processed: 337 average time/residue: 0.1765 time to fit residues: 92.4397 Evaluate side-chains 320 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 268 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 164 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.166781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111439 restraints weight = 39370.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110180 restraints weight = 25643.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111720 restraints weight = 21875.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112337 restraints weight = 20123.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112272 restraints weight = 18748.461| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23905 Z= 0.123 Angle : 0.596 32.174 32282 Z= 0.282 Chirality : 0.041 0.174 3565 Planarity : 0.004 0.050 4138 Dihedral : 5.719 141.727 3171 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.82 % Allowed : 14.00 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2867 helix: 1.06 (0.15), residues: 1314 sheet: 0.12 (0.30), residues: 298 loop : -0.87 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1275 TYR 0.025 0.001 TYR D 279 PHE 0.023 0.001 PHE D 344 TRP 0.020 0.001 TRP C 300 HIS 0.003 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (23896) covalent geometry : angle 0.55010 / 0.28 (32270) hydrogen bonds : bond 0.04006 / 2.58 ( 987) hydrogen bonds : angle 4.06655 / 2.74 ( 2826) metal coordination : bond 0.01293 / 0.72 ( 8) metal coordination : angle 11.88887 / 7.41 ( 12) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TRP cc_start: 0.8843 (p90) cc_final: 0.8348 (p90) REVERT: A 803 TYR cc_start: 0.7764 (p90) cc_final: 0.7528 (p90) REVERT: A 865 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8023 (mm-30) REVERT: B 72 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 764 ASP cc_start: 0.5796 (t0) cc_final: 0.5147 (t70) REVERT: B 772 LYS cc_start: 0.9219 (tppt) cc_final: 0.8969 (pptt) REVERT: B 1020 TRP cc_start: 0.8355 (m100) cc_final: 0.8026 (m-10) REVERT: B 1025 MET cc_start: 0.8784 (mtp) cc_final: 0.8494 (mtp) REVERT: B 1033 ARG cc_start: 0.7872 (ptm-80) cc_final: 0.7620 (ptm-80) REVERT: B 1179 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7381 (p-80) REVERT: B 1213 TRP cc_start: 0.8116 (m100) cc_final: 0.7778 (m-10) REVERT: C 328 TYR cc_start: 0.7703 (m-80) cc_final: 0.7299 (m-80) REVERT: C 329 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7651 (ptm160) REVERT: D 301 TYR cc_start: 0.6493 (m-80) cc_final: 0.5943 (m-80) REVERT: E -2 MET cc_start: 0.4214 (ppp) cc_final: 0.3946 (ppp) REVERT: E 77 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7676 (ttp-170) REVERT: F 1 MET cc_start: -0.0164 (mmt) cc_final: -0.1855 (ttt) REVERT: F 27 ASP cc_start: 0.8285 (t0) cc_final: 0.7955 (t0) outliers start: 47 outliers final: 40 residues processed: 309 average time/residue: 0.1765 time to fit residues: 84.8130 Evaluate side-chains 308 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1050 PHE Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 221 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B1152 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110955 restraints weight = 39152.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110871 restraints weight = 26255.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112497 restraints weight = 21853.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113317 restraints weight = 17790.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113403 restraints weight = 16948.715| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23905 Z= 0.112 Angle : 0.575 28.626 32282 Z= 0.273 Chirality : 0.040 0.172 3565 Planarity : 0.003 0.038 4138 Dihedral : 5.523 139.906 3171 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.93 % Allowed : 14.08 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2867 helix: 1.26 (0.15), residues: 1313 sheet: 0.11 (0.30), residues: 303 loop : -0.80 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1275 TYR 0.024 0.001 TYR A 803 PHE 0.025 0.001 PHE D 344 TRP 0.019 0.001 TRP C 438 HIS 0.004 0.001 HIS C 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (23896) covalent geometry : angle 0.53615 / 0.27 (32270) hydrogen bonds : bond 0.03652 / 2.35 ( 987) hydrogen bonds : angle 3.91055 / 2.64 ( 2826) metal coordination : bond 0.01028 / 0.54 ( 8) metal coordination : angle 10.73246 / 6.64 ( 12) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TRP cc_start: 0.8730 (p90) cc_final: 0.8305 (p90) REVERT: A 803 TYR cc_start: 0.7733 (p90) cc_final: 0.7271 (p90) REVERT: A 865 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8011 (mm-30) REVERT: B 72 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: B 764 ASP cc_start: 0.5787 (t0) cc_final: 0.5188 (t70) REVERT: B 772 LYS cc_start: 0.9171 (tppt) cc_final: 0.8962 (mttt) REVERT: B 1025 MET cc_start: 0.8699 (mtp) cc_final: 0.8379 (mtp) REVERT: B 1033 ARG cc_start: 0.7829 (ptm-80) cc_final: 0.7526 (ptm-80) REVERT: B 1179 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7358 (p-80) REVERT: B 1213 TRP cc_start: 0.8072 (m100) cc_final: 0.7734 (m-10) REVERT: B 1275 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.7050 (mtm-85) REVERT: C 328 TYR cc_start: 0.7658 (m-80) cc_final: 0.7252 (m-80) REVERT: C 329 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7958 (ptm160) REVERT: C 413 TYR cc_start: 0.7554 (m-10) cc_final: 0.7312 (m-10) REVERT: D 134 MET cc_start: 0.8306 (mmm) cc_final: 0.8063 (mmm) REVERT: D 301 TYR cc_start: 0.6293 (m-80) cc_final: 0.5981 (m-80) REVERT: D 346 ARG cc_start: 0.9068 (mmm160) cc_final: 0.8383 (mmm160) REVERT: D 350 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8750 (mmmm) REVERT: D 380 TYR cc_start: 0.8616 (m-80) cc_final: 0.8382 (m-80) REVERT: E -1 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: F 1 MET cc_start: -0.0237 (mmt) cc_final: -0.2087 (ttt) REVERT: F 27 ASP cc_start: 0.8164 (t0) cc_final: 0.7849 (t0) outliers start: 50 outliers final: 36 residues processed: 312 average time/residue: 0.1736 time to fit residues: 84.8148 Evaluate side-chains 311 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 350 LYS Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain E residue -1 GLU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 110 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 245 optimal weight: 0.3980 chunk 221 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN G 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.165981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109679 restraints weight = 39151.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110758 restraints weight = 25650.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110067 restraints weight = 21016.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110719 restraints weight = 21471.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110715 restraints weight = 20495.969| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23905 Z= 0.156 Angle : 0.583 13.382 32282 Z= 0.287 Chirality : 0.042 0.162 3565 Planarity : 0.004 0.041 4138 Dihedral : 5.555 139.155 3171 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.13 % Allowed : 14.08 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2867 helix: 1.29 (0.15), residues: 1302 sheet: 0.22 (0.31), residues: 287 loop : -0.83 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 46 TYR 0.024 0.001 TYR A 803 PHE 0.026 0.001 PHE B1147 TRP 0.023 0.001 TRP C 438 HIS 0.004 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23896) covalent geometry : angle 0.56786 / 0.29 (32270) hydrogen bonds : bond 0.04009 / 2.61 ( 987) hydrogen bonds : angle 3.97540 / 2.69 ( 2826) metal coordination : bond 0.01069 / 0.63 ( 8) metal coordination : angle 6.78594 / 3.79 ( 12) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TRP cc_start: 0.8850 (p90) cc_final: 0.8424 (p90) REVERT: A 572 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7013 (tpt170) REVERT: A 803 TYR cc_start: 0.7758 (p90) cc_final: 0.7544 (p90) REVERT: A 865 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8058 (mm-30) REVERT: B 4 GLN cc_start: 0.6762 (pp30) cc_final: 0.6100 (pm20) REVERT: B 72 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: B 737 ASP cc_start: 0.8520 (p0) cc_final: 0.8157 (p0) REVERT: B 764 ASP cc_start: 0.5748 (t0) cc_final: 0.5107 (t70) REVERT: B 1020 TRP cc_start: 0.8386 (m100) cc_final: 0.8127 (m-10) REVERT: B 1025 MET cc_start: 0.8812 (mtp) cc_final: 0.8513 (mtp) REVERT: B 1033 ARG cc_start: 0.7900 (ptm-80) cc_final: 0.7618 (ptm-80) REVERT: B 1039 SER cc_start: 0.8573 (p) cc_final: 0.8212 (t) REVERT: B 1179 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7432 (p-80) REVERT: B 1213 TRP cc_start: 0.8123 (m100) cc_final: 0.7780 (m-10) REVERT: C 183 GLU cc_start: 0.8471 (tp30) cc_final: 0.8266 (tp30) REVERT: C 328 TYR cc_start: 0.7715 (m-80) cc_final: 0.7339 (m-80) REVERT: C 329 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7982 (ptm160) REVERT: C 413 TYR cc_start: 0.7600 (m-10) cc_final: 0.7373 (m-10) REVERT: D 134 MET cc_start: 0.8380 (mmm) cc_final: 0.8114 (mmm) REVERT: D 301 TYR cc_start: 0.6339 (m-80) cc_final: 0.5979 (m-80) REVERT: D 346 ARG cc_start: 0.9097 (mmm160) cc_final: 0.8428 (mmm160) REVERT: D 380 TYR cc_start: 0.8692 (m-10) cc_final: 0.8463 (m-80) REVERT: F 1 MET cc_start: -0.0178 (mmt) cc_final: -0.2074 (ttt) REVERT: F 27 ASP cc_start: 0.8191 (t0) cc_final: 0.7874 (t0) outliers start: 55 outliers final: 44 residues processed: 312 average time/residue: 0.1708 time to fit residues: 83.7530 Evaluate side-chains 316 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1016 THR Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1242 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 278 optimal weight: 0.1980 chunk 199 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 251 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108639 restraints weight = 39117.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111225 restraints weight = 26296.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111595 restraints weight = 19327.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111669 restraints weight = 18671.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111970 restraints weight = 17961.163| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23905 Z= 0.107 Angle : 0.556 12.658 32282 Z= 0.272 Chirality : 0.040 0.212 3565 Planarity : 0.003 0.056 4138 Dihedral : 5.419 139.078 3171 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 14.81 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2867 helix: 1.44 (0.15), residues: 1310 sheet: 0.12 (0.30), residues: 303 loop : -0.74 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 77 TYR 0.024 0.001 TYR A 803 PHE 0.028 0.001 PHE D 344 TRP 0.024 0.001 TRP C 438 HIS 0.003 0.000 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23896) covalent geometry : angle 0.54188 / 0.27 (32270) hydrogen bonds : bond 0.03508 / 2.27 ( 987) hydrogen bonds : angle 3.83205 / 2.59 ( 2826) metal coordination : bond 0.00885 / 0.50 ( 8) metal coordination : angle 6.44147 / 3.58 ( 12) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TRP cc_start: 0.8791 (p90) cc_final: 0.8400 (p90) REVERT: A 803 TYR cc_start: 0.7717 (p90) cc_final: 0.7262 (p90) REVERT: A 865 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8047 (mm-30) REVERT: B 72 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 731 TYR cc_start: 0.7828 (t80) cc_final: 0.7282 (t80) REVERT: B 764 ASP cc_start: 0.5700 (t0) cc_final: 0.5086 (t70) REVERT: B 772 LYS cc_start: 0.9182 (tppt) cc_final: 0.8917 (pptt) REVERT: B 1025 MET cc_start: 0.8752 (mtp) cc_final: 0.8431 (mtp) REVERT: B 1033 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7516 (ptm-80) REVERT: B 1039 SER cc_start: 0.8551 (p) cc_final: 0.8180 (t) REVERT: B 1179 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7327 (p-80) REVERT: B 1192 MET cc_start: 0.8768 (mmm) cc_final: 0.8545 (mpp) REVERT: B 1213 TRP cc_start: 0.8067 (m100) cc_final: 0.7763 (m-10) REVERT: B 1330 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: C 328 TYR cc_start: 0.7633 (m-80) cc_final: 0.7281 (m-80) REVERT: C 329 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7951 (ptm160) REVERT: C 413 TYR cc_start: 0.7565 (m-10) cc_final: 0.7351 (m-10) REVERT: D 134 MET cc_start: 0.8369 (mmm) cc_final: 0.8124 (mmm) REVERT: D 301 TYR cc_start: 0.6221 (m-80) cc_final: 0.5834 (m-80) REVERT: D 344 PHE cc_start: 0.8083 (m-10) cc_final: 0.7875 (m-10) REVERT: D 346 ARG cc_start: 0.9065 (mmm160) cc_final: 0.8388 (mmm160) REVERT: F 1 MET cc_start: -0.0406 (mmt) cc_final: -0.2211 (ttt) REVERT: F 27 ASP cc_start: 0.8128 (t0) cc_final: 0.7827 (t0) outliers start: 37 outliers final: 28 residues processed: 301 average time/residue: 0.1755 time to fit residues: 82.7389 Evaluate side-chains 304 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 31 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 chunk 69 optimal weight: 0.0570 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.166908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109684 restraints weight = 39240.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112049 restraints weight = 26093.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111195 restraints weight = 18331.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111877 restraints weight = 19912.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111997 restraints weight = 18498.859| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23905 Z= 0.112 Angle : 0.559 14.471 32282 Z= 0.273 Chirality : 0.041 0.159 3565 Planarity : 0.003 0.045 4138 Dihedral : 5.368 138.131 3171 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.59 % Allowed : 14.77 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2867 helix: 1.45 (0.15), residues: 1309 sheet: 0.15 (0.30), residues: 303 loop : -0.72 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 46 TYR 0.024 0.001 TYR A 803 PHE 0.023 0.001 PHE B1147 TRP 0.028 0.001 TRP C 438 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (23896) covalent geometry : angle 0.54706 / 0.27 (32270) hydrogen bonds : bond 0.03482 / 2.25 ( 987) hydrogen bonds : angle 3.81485 / 2.58 ( 2826) metal coordination : bond 0.00823 / 0.49 ( 8) metal coordination : angle 5.92661 / 3.27 ( 12) Misc. bond : bond 0.00008 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5734 Ramachandran restraints generated. 2867 Oldfield, 0 Emsley, 2867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 TRP cc_start: 0.8819 (p90) cc_final: 0.8441 (p90) REVERT: A 572 ARG cc_start: 0.7675 (tpp80) cc_final: 0.6796 (tpp80) REVERT: A 617 MET cc_start: 0.8355 (mtm) cc_final: 0.8089 (mtp) REVERT: A 803 TYR cc_start: 0.7704 (p90) cc_final: 0.7274 (p90) REVERT: A 865 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8058 (mm-30) REVERT: B 4 GLN cc_start: 0.6729 (pp30) cc_final: 0.6089 (pm20) REVERT: B 72 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: B 731 TYR cc_start: 0.7851 (t80) cc_final: 0.6492 (t80) REVERT: B 764 ASP cc_start: 0.5699 (t0) cc_final: 0.5096 (t70) REVERT: B 772 LYS cc_start: 0.9217 (tppt) cc_final: 0.8948 (mmtt) REVERT: B 773 LYS cc_start: 0.9230 (tppt) cc_final: 0.8962 (tptm) REVERT: B 1025 MET cc_start: 0.8780 (mtp) cc_final: 0.8455 (mtp) REVERT: B 1033 ARG cc_start: 0.7841 (ptm-80) cc_final: 0.7509 (ptm-80) REVERT: B 1039 SER cc_start: 0.8570 (p) cc_final: 0.8200 (t) REVERT: B 1179 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7397 (p-80) REVERT: B 1213 TRP cc_start: 0.8049 (m100) cc_final: 0.7693 (m-10) REVERT: B 1330 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: C 182 MET cc_start: 0.8290 (ppp) cc_final: 0.8066 (ppp) REVERT: C 328 TYR cc_start: 0.7697 (m-80) cc_final: 0.7347 (m-80) REVERT: C 329 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7953 (ptm160) REVERT: C 413 TYR cc_start: 0.7621 (m-10) cc_final: 0.7412 (m-10) REVERT: D 63 ASP cc_start: 0.7363 (t0) cc_final: 0.7112 (t70) REVERT: D 134 MET cc_start: 0.8429 (mmm) cc_final: 0.8181 (mmm) REVERT: D 296 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6201 (tp40) REVERT: D 301 TYR cc_start: 0.6281 (m-80) cc_final: 0.5824 (m-80) REVERT: D 344 PHE cc_start: 0.8166 (m-10) cc_final: 0.7945 (m-80) REVERT: D 346 ARG cc_start: 0.9093 (mmm160) cc_final: 0.8399 (mmm160) REVERT: F 1 MET cc_start: -0.0441 (mmt) cc_final: -0.2210 (ttt) REVERT: F 27 ASP cc_start: 0.8151 (t0) cc_final: 0.7835 (t0) outliers start: 41 outliers final: 29 residues processed: 304 average time/residue: 0.1718 time to fit residues: 82.0493 Evaluate side-chains 301 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 940 CYS Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1098 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1208 ASN Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 177 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 155 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B1208 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN F 59 GLN G 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106279 restraints weight = 39105.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106593 restraints weight = 26137.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106624 restraints weight = 19964.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106899 restraints weight = 21164.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107139 restraints weight = 19702.943| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23905 Z= 0.215 Angle : 0.640 14.559 32282 Z= 0.317 Chirality : 0.044 0.158 3565 Planarity : 0.004 0.048 4138 Dihedral : 5.626 139.914 3171 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.82 % Allowed : 14.66 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2867 helix: 1.22 (0.15), residues: 1299 sheet: 0.23 (0.31), residues: 287 loop : -0.87 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 46 TYR 0.024 0.001 TYR A 803 PHE 0.026 0.002 PHE B1147 TRP 0.028 0.002 TRP C 438 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.21 (23896) covalent geometry : angle 0.62766 / 0.32 (32270) hydrogen bonds : bond 0.04513 / 2.96 ( 987) hydrogen bonds : angle 4.10297 / 2.78 ( 2826) metal coordination : bond 0.01126 / 0.70 ( 8) metal coordination : angle 6.41707 / 3.59 ( 12) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.69 seconds wall clock time: 88 minutes 32.35 seconds (5312.35 seconds total)