Starting phenix.real_space_refine on Tue Aug 26 17:28:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivx_60936/08_2025/9ivx_60936.cif" } resolution = 3.23 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= 0.022 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: 4 Type Number sf(0) Gaussians S 222 5.16 5 C 25032 2.51 5 N 6780 2.21 5 O 7287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39321 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6255 Classifications: {'peptide': 786} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 732} Chain breaks: 6 Chain: "G" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3074 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "F" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3778 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 27, 'TRANS': 441} Chain breaks: 4 Restraints were copied for chains: B, C, H, I, D, E Time building chain proxies: 10.57, per 1000 atoms: 0.27 Number of scatterers: 39321 At special positions: 0 Unit cell: (166.25, 175, 183.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 222 16.00 O 7287 8.00 N 6780 7.00 C 25032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 515 " - pdb=" SG CYS F 516 " distance=2.03 Simple disulfide: pdb=" SG CYS G 516 " - pdb=" SG CYS F 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 515 " - pdb=" SG CYS D 516 " distance=2.03 Simple disulfide: pdb=" SG CYS I 515 " - pdb=" SG CYS E 516 " distance=2.03 Simple disulfide: pdb=" SG CYS H 516 " - pdb=" SG CYS D 515 " distance=2.03 Simple disulfide: pdb=" SG CYS I 516 " - pdb=" SG CYS E 515 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9294 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 49 sheets defined 39.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.520A pdb=" N VAL A 327 " --> pdb=" O ASP A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.539A pdb=" N ARG A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.523A pdb=" N ARG A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.541A pdb=" N ASP A 522 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'G' and resid 189 through 195 removed outlier: 3.652A pdb=" N GLN G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 Processing helix chain 'G' and resid 273 through 285 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.212A pdb=" N GLY G 305 " --> pdb=" O GLN G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 319 Processing helix chain 'G' and resid 322 through 352 removed outlier: 5.263A pdb=" N VAL G 341 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 352 " --> pdb=" O ARG G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 368 Processing helix chain 'G' and resid 370 through 380 Processing helix chain 'G' and resid 382 through 386 removed outlier: 4.244A pdb=" N ASN G 385 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 407 removed outlier: 3.631A pdb=" N SER G 405 " --> pdb=" O VAL G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 438 Processing helix chain 'G' and resid 440 through 460 removed outlier: 5.479A pdb=" N LYS G 456 " --> pdb=" O LYS G 452 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP G 457 " --> pdb=" O GLN G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 476 Processing helix chain 'G' and resid 477 through 486 Processing helix chain 'G' and resid 493 through 509 Processing helix chain 'G' and resid 518 through 523 removed outlier: 3.658A pdb=" N ASP G 521 " --> pdb=" O LEU G 518 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL G 523 " --> pdb=" O SER G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 533 No H-bonds generated for 'chain 'G' and resid 531 through 533' Processing helix chain 'G' and resid 534 through 551 Processing helix chain 'F' and resid 183 through 188 removed outlier: 4.987A pdb=" N SER F 188 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 195 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.940A pdb=" N LEU F 256 " --> pdb=" O ARG F 252 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.552A pdb=" N VAL F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.905A pdb=" N LEU F 326 " --> pdb=" O GLU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 352 through 368 Processing helix chain 'F' and resid 370 through 380 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 408 through 438 removed outlier: 3.746A pdb=" N ARG F 413 " --> pdb=" O GLY F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 459 removed outlier: 3.546A pdb=" N LYS F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS F 456 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP F 457 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 476 Processing helix chain 'F' and resid 477 through 486 Processing helix chain 'F' and resid 493 through 508 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 526 through 530 Processing helix chain 'F' and resid 531 through 533 No H-bonds generated for 'chain 'F' and resid 531 through 533' Processing helix chain 'F' and resid 534 through 551 Processing helix chain 'F' and resid 581 through 590 removed outlier: 3.649A pdb=" N ILE F 590 " --> pdb=" O SER F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 624 removed outlier: 3.566A pdb=" N TRP F 617 " --> pdb=" O THR F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 678 removed outlier: 3.761A pdb=" N LEU F 660 " --> pdb=" O GLN F 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.520A pdb=" N VAL B 327 " --> pdb=" O ASP B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 358 through 370 Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.539A pdb=" N ARG B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.523A pdb=" N ARG B 499 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.541A pdb=" N ASP B 522 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 543 Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 615 through 626 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 755 through 765 Processing helix chain 'B' and resid 810 through 814 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.519A pdb=" N VAL C 327 " --> pdb=" O ASP C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.539A pdb=" N ARG C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 492 through 499 removed outlier: 3.523A pdb=" N ARG C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.541A pdb=" N ASP C 522 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN C 523 " --> pdb=" O PRO C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 Processing helix chain 'C' and resid 557 through 563 Processing helix chain 'C' and resid 580 through 584 Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 615 through 626 Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 755 through 765 Processing helix chain 'C' and resid 810 through 814 Processing helix chain 'H' and resid 189 through 195 removed outlier: 3.652A pdb=" N GLN H 193 " --> pdb=" O ARG H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 260 Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.212A pdb=" N GLY H 305 " --> pdb=" O GLN H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 319 Processing helix chain 'H' and resid 322 through 352 removed outlier: 5.263A pdb=" N VAL H 341 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU H 342 " --> pdb=" O LEU H 338 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP H 352 " --> pdb=" O ARG H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 368 Processing helix chain 'H' and resid 370 through 380 Processing helix chain 'H' and resid 382 through 386 removed outlier: 4.244A pdb=" N ASN H 385 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 407 removed outlier: 3.631A pdb=" N SER H 405 " --> pdb=" O VAL H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 438 Processing helix chain 'H' and resid 440 through 460 removed outlier: 5.478A pdb=" N LYS H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP H 457 " --> pdb=" O GLN H 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 476 Processing helix chain 'H' and resid 477 through 486 Processing helix chain 'H' and resid 493 through 509 Processing helix chain 'H' and resid 518 through 523 removed outlier: 3.658A pdb=" N ASP H 521 " --> pdb=" O LEU H 518 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL H 523 " --> pdb=" O SER H 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 533 No H-bonds generated for 'chain 'H' and resid 531 through 533' Processing helix chain 'H' and resid 534 through 551 Processing helix chain 'D' and resid 183 through 188 removed outlier: 4.987A pdb=" N SER D 188 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 195 Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.941A pdb=" N LEU D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.552A pdb=" N VAL D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.905A pdb=" N LEU D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 352 through 368 Processing helix chain 'D' and resid 370 through 380 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 408 through 438 removed outlier: 3.746A pdb=" N ARG D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 459 removed outlier: 3.546A pdb=" N LYS D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 476 Processing helix chain 'D' and resid 477 through 486 Processing helix chain 'D' and resid 493 through 508 Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 526 through 530 Processing helix chain 'D' and resid 531 through 533 No H-bonds generated for 'chain 'D' and resid 531 through 533' Processing helix chain 'D' and resid 534 through 551 Processing helix chain 'D' and resid 581 through 590 removed outlier: 3.649A pdb=" N ILE D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.566A pdb=" N TRP D 617 " --> pdb=" O THR D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 678 removed outlier: 3.761A pdb=" N LEU D 660 " --> pdb=" O GLN D 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 195 removed outlier: 3.652A pdb=" N GLN I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 260 Processing helix chain 'I' and resid 273 through 285 Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.211A pdb=" N GLY I 305 " --> pdb=" O GLN I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 319 Processing helix chain 'I' and resid 322 through 352 removed outlier: 5.263A pdb=" N VAL I 341 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU I 342 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP I 352 " --> pdb=" O ARG I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 368 Processing helix chain 'I' and resid 370 through 380 Processing helix chain 'I' and resid 382 through 386 removed outlier: 4.244A pdb=" N ASN I 385 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 407 removed outlier: 3.631A pdb=" N SER I 405 " --> pdb=" O VAL I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 438 Processing helix chain 'I' and resid 440 through 460 removed outlier: 5.479A pdb=" N LYS I 456 " --> pdb=" O LYS I 452 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP I 457 " --> pdb=" O GLN I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 476 Processing helix chain 'I' and resid 477 through 486 Processing helix chain 'I' and resid 493 through 509 Processing helix chain 'I' and resid 518 through 523 removed outlier: 3.658A pdb=" N ASP I 521 " --> pdb=" O LEU I 518 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL I 523 " --> pdb=" O SER I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 533 No H-bonds generated for 'chain 'I' and resid 531 through 533' Processing helix chain 'I' and resid 534 through 551 Processing helix chain 'E' and resid 183 through 188 removed outlier: 4.987A pdb=" N SER E 188 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 195 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.941A pdb=" N LEU E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG E 258 " --> pdb=" O ALA E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.552A pdb=" N VAL E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 Processing helix chain 'E' and resid 322 through 339 removed outlier: 3.905A pdb=" N LEU E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'E' and resid 352 through 368 Processing helix chain 'E' and resid 370 through 380 Processing helix chain 'E' and resid 403 through 407 Processing helix chain 'E' and resid 408 through 438 removed outlier: 3.747A pdb=" N ARG E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 459 removed outlier: 3.546A pdb=" N LYS E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP E 457 " --> pdb=" O GLN E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 476 Processing helix chain 'E' and resid 477 through 486 Processing helix chain 'E' and resid 493 through 508 Processing helix chain 'E' and resid 518 through 522 Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 531 through 533 No H-bonds generated for 'chain 'E' and resid 531 through 533' Processing helix chain 'E' and resid 534 through 551 Processing helix chain 'E' and resid 581 through 590 removed outlier: 3.650A pdb=" N ILE E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 613 through 624 removed outlier: 3.566A pdb=" N TRP E 617 " --> pdb=" O THR E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 678 removed outlier: 3.761A pdb=" N LEU E 660 " --> pdb=" O GLN E 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 removed outlier: 3.747A pdb=" N LEU A 64 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR A 610 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER A 98 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N PHE A 612 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N MET A 96 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 565 through 566 removed outlier: 4.085A pdb=" N HIS A 551 " --> pdb=" O LEU F 683 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.639A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.842A pdb=" N GLU B 443 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 153 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS B 417 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.158A pdb=" N LYS A 209 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 12.004A pdb=" N MET A 261 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 424 " --> pdb=" O MET A 261 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 263 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 423 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 433 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA9, first strand: chain 'A' and resid 292 through 296 removed outlier: 6.287A pdb=" N GLN A 311 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 322 Processing sheet with id=AB2, first strand: chain 'A' and resid 406 through 409 Processing sheet with id=AB3, first strand: chain 'A' and resid 417 through 419 removed outlier: 4.158A pdb=" N HIS A 417 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 443 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 432 through 434 removed outlier: 3.830A pdb=" N GLU A 433 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 423 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 263 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 424 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N MET C 261 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 642 through 648 removed outlier: 3.622A pdb=" N TRP A 670 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 659 removed outlier: 3.950A pdb=" N LEU A 893 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 712 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 790 through 798 Processing sheet with id=AB8, first strand: chain 'G' and resid 176 through 177 removed outlier: 3.554A pdb=" N CYS G 177 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 174 through 176 Processing sheet with id=AC1, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AC2, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.747A pdb=" N LEU B 64 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR B 610 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER B 98 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N PHE B 612 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N MET B 96 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 565 through 566 removed outlier: 4.085A pdb=" N HIS B 551 " --> pdb=" O LEU D 683 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.639A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.842A pdb=" N GLU C 443 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 153 " --> pdb=" O GLU C 443 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS C 417 " --> pdb=" O ILE C 444 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 157 through 159 removed outlier: 4.158A pdb=" N LYS B 209 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 168 through 170 Processing sheet with id=AC8, first strand: chain 'B' and resid 213 through 215 removed outlier: 12.003A pdb=" N MET B 261 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 424 " --> pdb=" O MET B 261 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 263 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 423 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU C 433 " --> pdb=" O LYS C 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AD1, first strand: chain 'B' and resid 292 through 296 removed outlier: 6.287A pdb=" N GLN B 311 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 320 through 322 Processing sheet with id=AD3, first strand: chain 'B' and resid 642 through 648 removed outlier: 3.622A pdb=" N TRP B 670 " --> pdb=" O ILE B 865 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 659 removed outlier: 3.951A pdb=" N LEU B 893 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 712 " --> pdb=" O GLU B 898 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 790 through 798 Processing sheet with id=AD6, first strand: chain 'C' and resid 64 through 68 removed outlier: 3.747A pdb=" N LEU C 64 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N THR C 610 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER C 98 " --> pdb=" O THR C 610 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N PHE C 612 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 9.993A pdb=" N MET C 96 " --> pdb=" O PHE C 612 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 565 through 566 removed outlier: 4.085A pdb=" N HIS C 551 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.639A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.158A pdb=" N LYS C 209 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 168 through 170 Processing sheet with id=AE2, first strand: chain 'C' and resid 241 through 242 Processing sheet with id=AE3, first strand: chain 'C' and resid 292 through 296 removed outlier: 6.287A pdb=" N GLN C 311 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 320 through 322 Processing sheet with id=AE5, first strand: chain 'C' and resid 642 through 648 removed outlier: 3.622A pdb=" N TRP C 670 " --> pdb=" O ILE C 865 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 659 removed outlier: 3.951A pdb=" N LEU C 893 " --> pdb=" O ILE C 659 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 712 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 790 through 798 Processing sheet with id=AE8, first strand: chain 'H' and resid 176 through 177 removed outlier: 3.554A pdb=" N CYS H 177 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 174 through 176 Processing sheet with id=AF1, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AF2, first strand: chain 'I' and resid 176 through 177 removed outlier: 3.554A pdb=" N CYS I 177 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 174 through 176 Processing sheet with id=AF4, first strand: chain 'E' and resid 386 through 387 1506 hydrogen bonds defined for protein. 4185 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: 7.87 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 6516 1.28 - 1.41: 10197 1.41 - 1.55: 23166 1.55 - 1.69: 18 1.69 - 1.82: 351 Bond restraints: 40248 Sorted by residual: bond pdb=" C ASP G 521 " pdb=" N PHE G 522 " ideal model delta sigma weight residual 1.328 1.446 -0.119 1.13e-02 7.83e+03 1.10e+02 bond pdb=" C ASP I 521 " pdb=" N PHE I 522 " ideal model delta sigma weight residual 1.328 1.446 -0.118 1.13e-02 7.83e+03 1.10e+02 bond pdb=" C ASP H 521 " pdb=" N PHE H 522 " ideal model delta sigma weight residual 1.328 1.446 -0.118 1.13e-02 7.83e+03 1.10e+02 bond pdb=" C HIS D 470 " pdb=" O HIS D 470 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.22e-02 6.72e+03 6.32e+01 bond pdb=" C HIS F 470 " pdb=" O HIS F 470 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.22e-02 6.72e+03 6.24e+01 ... (remaining 40243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 52900 2.44 - 4.88: 1519 4.88 - 7.31: 190 7.31 - 9.75: 36 9.75 - 12.19: 6 Bond angle restraints: 54651 Sorted by residual: angle pdb=" N CYS I 345 " pdb=" CA CYS I 345 " pdb=" C CYS I 345 " ideal model delta sigma weight residual 111.28 103.84 7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N CYS G 345 " pdb=" CA CYS G 345 " pdb=" C CYS G 345 " ideal model delta sigma weight residual 111.28 103.84 7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N CYS H 345 " pdb=" CA CYS H 345 " pdb=" C CYS H 345 " ideal model delta sigma weight residual 111.28 103.85 7.43 1.09e+00 8.42e-01 4.65e+01 angle pdb=" CA VAL H 262 " pdb=" C VAL H 262 " pdb=" O VAL H 262 " ideal model delta sigma weight residual 121.97 115.74 6.23 9.80e-01 1.04e+00 4.05e+01 angle pdb=" CA VAL I 262 " pdb=" C VAL I 262 " pdb=" O VAL I 262 " ideal model delta sigma weight residual 121.97 115.78 6.19 9.80e-01 1.04e+00 3.99e+01 ... (remaining 54646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 20575 17.96 - 35.91: 2739 35.91 - 53.87: 784 53.87 - 71.82: 136 71.82 - 89.78: 75 Dihedral angle restraints: 24309 sinusoidal: 9936 harmonic: 14373 Sorted by residual: dihedral pdb=" CB CYS G 515 " pdb=" SG CYS G 515 " pdb=" SG CYS F 516 " pdb=" CB CYS F 516 " ideal model delta sinusoidal sigma weight residual -86.00 -137.18 51.18 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS H 515 " pdb=" SG CYS H 515 " pdb=" SG CYS D 516 " pdb=" CB CYS D 516 " ideal model delta sinusoidal sigma weight residual -86.00 -137.15 51.15 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS I 515 " pdb=" SG CYS I 515 " pdb=" SG CYS E 516 " pdb=" CB CYS E 516 " ideal model delta sinusoidal sigma weight residual -86.00 -137.13 51.13 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 24306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5017 0.058 - 0.117: 783 0.117 - 0.175: 159 0.175 - 0.234: 29 0.234 - 0.292: 15 Chirality restraints: 6003 Sorted by residual: chirality pdb=" CA ASP G 457 " pdb=" N ASP G 457 " pdb=" C ASP G 457 " pdb=" CB ASP G 457 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA SER G 508 " pdb=" N SER G 508 " pdb=" C SER G 508 " pdb=" CB SER G 508 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA SER H 508 " pdb=" N SER H 508 " pdb=" C SER H 508 " pdb=" CB SER H 508 " 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 6000 not shown) Planarity restraints: 7119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 259 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C SER D 259 " 0.083 2.00e-02 2.50e+03 pdb=" O SER D 259 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE D 260 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 259 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C SER F 259 " -0.083 2.00e-02 2.50e+03 pdb=" O SER F 259 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE F 260 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 259 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C SER E 259 " 0.083 2.00e-02 2.50e+03 pdb=" O SER E 259 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE E 260 " -0.029 2.00e-02 2.50e+03 ... (remaining 7116 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 867 2.67 - 3.23: 39750 3.23 - 3.78: 60467 3.78 - 4.34: 80316 4.34 - 4.90: 129995 Nonbonded interactions: 311395 Sorted by model distance: nonbonded pdb=" O THR C 57 " pdb=" OG1 THR C 58 " model vdw 2.108 3.040 nonbonded pdb=" O THR A 57 " pdb=" OG1 THR A 58 " model vdw 2.109 3.040 nonbonded pdb=" O THR B 57 " pdb=" OG1 THR B 58 " model vdw 2.109 3.040 nonbonded pdb=" N GLU B 433 " pdb=" OE1 GLU B 433 " model vdw 2.120 3.120 nonbonded pdb=" N GLU C 433 " pdb=" OE1 GLU C 433 " model vdw 2.120 3.120 ... (remaining 311390 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.580 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 40254 Z= 0.385 Angle : 0.893 12.190 54663 Z= 0.578 Chirality : 0.050 0.292 6003 Planarity : 0.005 0.067 7119 Dihedral : 18.039 89.779 14997 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.37 % Allowed : 26.73 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.12), residues: 4821 helix: 0.71 (0.13), residues: 1605 sheet: -1.70 (0.23), residues: 477 loop : -1.38 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 92 TYR 0.016 0.001 TYR G 546 PHE 0.021 0.001 PHE H 503 TRP 0.027 0.002 TRP G 459 HIS 0.005 0.001 HIS D 658 Details of bonding type rmsd covalent geometry : bond 0.00568 (40248) covalent geometry : angle 0.89287 (54651) SS BOND : bond 0.00125 ( 6) SS BOND : angle 0.72883 ( 12) hydrogen bonds : bond 0.19956 ( 1506) hydrogen bonds : angle 7.51349 ( 4185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1150 time to evaluate : 1.301 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: 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: 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 277 GLU cc_start: 0.7842 (tp30) cc_final: 0.7613 (tp30) REVERT: A 562 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8047 (mmmm) REVERT: A 591 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7980 (p0) REVERT: G 187 ARG cc_start: 0.7232 (mmm-85) cc_final: 0.6968 (mmm-85) REVERT: G 287 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7145 (tpp80) REVERT: G 333 MET cc_start: 0.7457 (ptm) cc_final: 0.7181 (ptt) REVERT: G 344 GLU cc_start: 0.8243 (tp30) cc_final: 0.7461 (tp30) REVERT: G 360 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5553 (mp0) REVERT: G 408 LYS cc_start: 0.7882 (tppt) cc_final: 0.7366 (tppt) REVERT: G 419 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7555 (m) REVERT: G 464 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: G 495 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8191 (p) REVERT: G 496 MET cc_start: 0.7943 (tpp) cc_final: 0.7697 (tpp) REVERT: G 498 GLN cc_start: 0.8808 (tp40) cc_final: 0.8540 (tp40) REVERT: G 499 ASN cc_start: 0.8923 (m-40) cc_final: 0.8705 (m-40) REVERT: G 502 ASN cc_start: 0.8486 (t0) cc_final: 0.8192 (t0) REVERT: G 528 ARG cc_start: 0.7199 (ptp-170) cc_final: 0.6908 (ptt180) REVERT: G 546 TYR cc_start: 0.7640 (t80) cc_final: 0.7329 (t80) REVERT: F 170 TYR cc_start: 0.7232 (m-80) cc_final: 0.6409 (t80) REVERT: F 180 PRO cc_start: 0.8405 (Cg_exo) cc_final: 0.8189 (Cg_endo) REVERT: F 277 MET cc_start: 0.7844 (mmt) cc_final: 0.7374 (mmt) REVERT: F 313 GLN cc_start: 0.6604 (mm-40) cc_final: 0.5479 (tt0) REVERT: F 342 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7738 (mm-30) REVERT: F 347 GLN cc_start: 0.8825 (tp40) cc_final: 0.8549 (tp-100) REVERT: F 441 GLU cc_start: 0.6851 (pm20) cc_final: 0.6636 (tt0) REVERT: F 465 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6296 (mtm180) REVERT: F 498 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 501 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8273 (ttm-80) REVERT: F 528 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7050 (ptt90) REVERT: F 538 CYS cc_start: 0.8339 (m) cc_final: 0.7549 (t) REVERT: F 595 GLU cc_start: 0.4351 (pm20) cc_final: 0.3552 (pm20) REVERT: F 621 TYR cc_start: 0.8327 (t80) cc_final: 0.7851 (t80) REVERT: F 660 LEU cc_start: 0.8513 (tt) cc_final: 0.8301 (mt) REVERT: F 672 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7279 (tm-30) REVERT: F 676 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: B 49 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7117 (p) REVERT: B 150 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8277 (m110) REVERT: B 190 GLN cc_start: 0.7470 (mt0) cc_final: 0.7232 (mt0) REVERT: B 213 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7811 (ptm160) REVERT: B 256 GLU cc_start: 0.7530 (tp30) cc_final: 0.7317 (tp30) REVERT: B 264 PHE cc_start: 0.8247 (m-80) cc_final: 0.8013 (m-80) REVERT: B 277 GLU cc_start: 0.7803 (tp30) cc_final: 0.7553 (tp30) REVERT: B 311 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8144 (mt0) REVERT: B 330 MET cc_start: 0.8367 (mmm) cc_final: 0.8008 (mmm) REVERT: B 360 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8037 (mp0) REVERT: B 413 ILE cc_start: 0.8086 (mt) cc_final: 0.7856 (mt) REVERT: B 417 HIS cc_start: 0.8050 (m-70) cc_final: 0.7776 (m170) REVERT: B 420 GLN cc_start: 0.7742 (pt0) cc_final: 0.7500 (pt0) REVERT: B 445 THR cc_start: 0.8534 (t) cc_final: 0.8250 (p) REVERT: B 453 GLU cc_start: 0.7974 (pt0) cc_final: 0.7622 (pt0) REVERT: B 562 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8299 (mmmm) REVERT: B 565 LEU cc_start: 0.7289 (mt) cc_final: 0.7077 (mt) REVERT: B 712 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7818 (ttpp) REVERT: B 715 ILE cc_start: 0.8713 (mt) cc_final: 0.8399 (mm) REVERT: B 738 LYS cc_start: 0.8407 (ptmm) cc_final: 0.7594 (tppt) REVERT: B 758 PHE cc_start: 0.8631 (t80) cc_final: 0.8412 (t80) REVERT: B 762 MET cc_start: 0.8576 (mmp) cc_final: 0.8290 (mmm) REVERT: B 805 ASP cc_start: 0.7359 (t0) cc_final: 0.7039 (t0) REVERT: B 832 GLU cc_start: 0.8144 (pt0) cc_final: 0.7899 (pt0) REVERT: B 895 MET cc_start: 0.8079 (mtt) cc_final: 0.7858 (mtp) REVERT: B 900 ASP cc_start: 0.8377 (m-30) cc_final: 0.8158 (m-30) REVERT: B 912 PHE cc_start: 0.6864 (m-80) cc_final: 0.6650 (m-80) REVERT: C 65 MET cc_start: 0.8434 (ppp) cc_final: 0.8228 (ppp) REVERT: C 91 ASN cc_start: 0.7590 (t0) cc_final: 0.7023 (t0) REVERT: C 96 MET cc_start: 0.8032 (tpt) cc_final: 0.7654 (tpt) REVERT: C 137 VAL cc_start: 0.8067 (t) cc_final: 0.7863 (m) REVERT: C 154 ILE cc_start: 0.8462 (mt) cc_final: 0.8259 (mp) REVERT: C 167 LEU cc_start: 0.8067 (tp) cc_final: 0.7609 (tt) REVERT: C 187 LYS cc_start: 0.8267 (ptpp) cc_final: 0.7965 (ptpp) REVERT: C 193 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7192 (Cg_endo) REVERT: C 213 ARG cc_start: 0.8029 (ptp-170) cc_final: 0.7482 (ptm160) REVERT: C 255 GLU cc_start: 0.7673 (mp0) cc_final: 0.7424 (mp0) REVERT: C 257 PRO cc_start: 0.8649 (Cg_exo) cc_final: 0.8067 (Cg_endo) REVERT: C 277 GLU cc_start: 0.7779 (tp30) cc_final: 0.7567 (tp30) REVERT: C 330 MET cc_start: 0.8326 (mmm) cc_final: 0.7959 (mmm) REVERT: C 420 GLN cc_start: 0.7171 (pt0) cc_final: 0.6922 (pt0) REVERT: C 445 THR cc_start: 0.8460 (t) cc_final: 0.8053 (p) REVERT: C 494 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8314 (mt-10) REVERT: C 562 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8221 (mmmm) REVERT: C 671 SER cc_start: 0.8812 (m) cc_final: 0.8586 (p) REVERT: C 680 THR cc_start: 0.8822 (m) cc_final: 0.8446 (p) REVERT: C 712 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7794 (ttmm) REVERT: C 784 TYR cc_start: 0.8203 (m-80) cc_final: 0.7952 (m-10) REVERT: C 801 VAL cc_start: 0.8632 (m) cc_final: 0.8251 (p) REVERT: C 812 PRO cc_start: 0.8883 (Cg_exo) cc_final: 0.8682 (Cg_endo) REVERT: C 838 TYR cc_start: 0.8095 (t80) cc_final: 0.7860 (t80) REVERT: C 854 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8382 (mtmm) REVERT: C 893 LEU cc_start: 0.8698 (tt) cc_final: 0.8485 (tp) REVERT: C 900 ASP cc_start: 0.8528 (m-30) cc_final: 0.8288 (m-30) REVERT: H 257 LYS cc_start: 0.7873 (mttm) cc_final: 0.7642 (mttm) REVERT: H 344 GLU cc_start: 0.8416 (tp30) cc_final: 0.7637 (tp30) REVERT: H 347 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8180 (tm130) REVERT: H 356 GLN cc_start: 0.6547 (tm-30) cc_final: 0.6022 (tm-30) REVERT: H 419 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7649 (m) REVERT: H 455 LEU cc_start: 0.8697 (tp) cc_final: 0.8445 (mt) REVERT: H 464 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: H 471 LEU cc_start: 0.8483 (mt) cc_final: 0.8269 (mm) REVERT: H 495 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8274 (p) REVERT: H 496 MET cc_start: 0.8023 (tpp) cc_final: 0.7784 (tpp) REVERT: H 502 ASN cc_start: 0.8562 (t0) cc_final: 0.7033 (t0) REVERT: H 506 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7182 (mm-30) REVERT: H 535 TRP cc_start: 0.7923 (m-10) cc_final: 0.7498 (m-10) REVERT: D 181 LEU cc_start: 0.8085 (tp) cc_final: 0.7556 (tp) REVERT: D 186 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6789 (t0) REVERT: D 202 ILE cc_start: 0.9050 (tt) cc_final: 0.8748 (mm) REVERT: D 253 LEU cc_start: 0.8570 (mm) cc_final: 0.8148 (pp) REVERT: D 267 TYR cc_start: 0.7565 (m-80) cc_final: 0.7358 (m-10) REVERT: D 277 MET cc_start: 0.7775 (mmt) cc_final: 0.7075 (mmt) REVERT: D 313 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6052 (tt0) REVERT: D 342 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7908 (mm-30) REVERT: D 357 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7804 (ttt180) REVERT: D 367 PHE cc_start: 0.8422 (m-10) cc_final: 0.8049 (m-10) REVERT: D 373 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7907 (ttt180) REVERT: D 374 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8117 (mm-40) REVERT: D 412 ARG cc_start: 0.8457 (ttt180) cc_final: 0.7314 (mtp-110) REVERT: D 415 TYR cc_start: 0.7821 (t80) cc_final: 0.7606 (t80) REVERT: D 418 ASP cc_start: 0.7554 (t70) cc_final: 0.7040 (t70) REVERT: D 441 GLU cc_start: 0.6953 (pm20) cc_final: 0.6596 (mt-10) REVERT: D 452 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7739 (mtmt) REVERT: D 453 GLN cc_start: 0.8466 (tt0) cc_final: 0.8221 (tm-30) REVERT: D 498 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7289 (tm-30) REVERT: D 499 ASN cc_start: 0.8087 (t0) cc_final: 0.7713 (m-40) REVERT: D 501 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8120 (ttm110) REVERT: D 596 LEU cc_start: 0.7164 (mp) cc_final: 0.6705 (pp) REVERT: D 621 TYR cc_start: 0.8298 (t80) cc_final: 0.7949 (t80) REVERT: D 660 LEU cc_start: 0.8399 (tt) cc_final: 0.8059 (tp) REVERT: D 664 GLN cc_start: 0.8208 (mm110) cc_final: 0.7827 (mm110) REVERT: D 668 LYS cc_start: 0.8170 (tptt) cc_final: 0.7942 (tptt) REVERT: I 287 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7029 (tpp80) REVERT: I 344 GLU cc_start: 0.8352 (tp30) cc_final: 0.7600 (tp30) REVERT: I 361 GLU cc_start: 0.7289 (tt0) cc_final: 0.7004 (tp30) REVERT: I 419 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7497 (m) REVERT: I 436 GLN cc_start: 0.8108 (tp40) cc_final: 0.7795 (tp-100) REVERT: I 464 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: I 495 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8303 (p) REVERT: I 502 ASN cc_start: 0.8517 (t0) cc_final: 0.7512 (t0) REVERT: I 503 PHE cc_start: 0.8340 (t80) cc_final: 0.8090 (t80) REVERT: I 506 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7244 (mm-30) REVERT: I 538 CYS cc_start: 0.8098 (m) cc_final: 0.7639 (m) REVERT: I 546 TYR cc_start: 0.7282 (t80) cc_final: 0.7058 (t80) REVERT: E 170 TYR cc_start: 0.7196 (m-80) cc_final: 0.6245 (t80) REVERT: E 186 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6640 (t0) REVERT: E 253 LEU cc_start: 0.8424 (mm) cc_final: 0.7875 (pp) REVERT: E 277 MET cc_start: 0.7951 (mmt) cc_final: 0.7551 (mmt) REVERT: E 342 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7561 (mm-30) REVERT: E 347 GLN cc_start: 0.8929 (tp40) cc_final: 0.8670 (tp40) REVERT: E 367 PHE cc_start: 0.8545 (m-10) cc_final: 0.8108 (m-10) REVERT: E 385 ASN cc_start: 0.8075 (p0) cc_final: 0.7851 (t0) REVERT: E 412 ARG cc_start: 0.8339 (ttt180) cc_final: 0.7189 (mtp-110) REVERT: E 418 ASP cc_start: 0.7595 (t70) cc_final: 0.7366 (t70) REVERT: E 441 GLU cc_start: 0.6889 (pm20) cc_final: 0.6571 (tt0) REVERT: E 452 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7367 (mttt) REVERT: E 465 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6285 (ttm-80) REVERT: E 485 GLN cc_start: 0.7737 (mt0) cc_final: 0.7392 (mt0) REVERT: E 624 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7670 (tttm) REVERT: E 664 GLN cc_start: 0.8255 (mm110) cc_final: 0.8022 (mm110) REVERT: E 666 ILE cc_start: 0.8776 (tt) cc_final: 0.8572 (pt) REVERT: E 672 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6962 (tm-30) outliers start: 102 outliers final: 40 residues processed: 1203 average time/residue: 0.2649 time to fit residues: 499.2919 Evaluate side-chains 1119 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1059 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 419 CYS Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain F residue 252 ARG Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 357 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 465 ARG Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 478 GLU Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 526 LYS Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain C residue 789 ASN Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 456 LYS Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 475 ILE Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 495 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 357 ARG Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 475 ILE Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 465 ARG Chi-restraints excluded: chain E residue 507 ARG Chi-restraints excluded: chain E residue 526 LYS Chi-restraints excluded: chain E residue 624 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 344 GLN G 347 GLN G 429 GLN F 347 GLN F 374 GLN F 454 ASN F 545 ASN ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 344 GLN B 553 GLN B 815 HIS C 190 GLN C 344 GLN C 448 ASN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN C 817 ASN H 429 GLN H 454 ASN D 485 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 HIS ** I 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 429 GLN ** I 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 GLN E 429 GLN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 GLN ** E 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.179063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134853 restraints weight = 65470.090| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.89 r_work: 0.3457 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40254 Z= 0.177 Angle : 0.687 10.549 54663 Z= 0.348 Chirality : 0.046 0.310 6003 Planarity : 0.005 0.055 7119 Dihedral : 6.717 93.458 5537 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.07 % Allowed : 23.29 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.12), residues: 4821 helix: 1.06 (0.12), residues: 1641 sheet: -1.30 (0.21), residues: 561 loop : -1.18 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 417 TYR 0.020 0.001 TYR C 806 PHE 0.018 0.001 PHE F 173 TRP 0.014 0.002 TRP I 459 HIS 0.006 0.001 HIS C 530 Details of bonding type rmsd covalent geometry : bond 0.00402 (40248) covalent geometry : angle 0.68687 (54651) SS BOND : bond 0.00199 ( 6) SS BOND : angle 1.38846 ( 12) hydrogen bonds : bond 0.04716 ( 1506) hydrogen bonds : angle 5.47608 ( 4185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1094 time to evaluate : 1.165 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: 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: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.8492 (m-80) cc_final: 0.8188 (m-10) REVERT: A 213 ARG cc_start: 0.8163 (ptp-170) cc_final: 0.7717 (ptm160) REVERT: A 254 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7829 (t) REVERT: A 257 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8358 (Cg_endo) REVERT: A 281 TYR cc_start: 0.8572 (m-10) cc_final: 0.8306 (m-10) REVERT: A 433 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 521 MET cc_start: 0.8698 (mmp) cc_final: 0.8479 (mmm) REVERT: A 541 LEU cc_start: 0.8733 (tp) cc_final: 0.8468 (tt) REVERT: A 562 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8255 (mmmm) REVERT: A 591 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.8119 (p0) REVERT: A 614 MET cc_start: 0.6848 (tpp) cc_final: 0.6375 (tpp) REVERT: A 805 ASP cc_start: 0.7738 (t0) cc_final: 0.7441 (t0) REVERT: G 187 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.7138 (mmm-85) REVERT: G 287 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7264 (tpp80) REVERT: G 333 MET cc_start: 0.7701 (ptm) cc_final: 0.7454 (ptm) REVERT: G 348 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7623 (mmt90) REVERT: G 349 PHE cc_start: 0.8721 (t80) cc_final: 0.8318 (t80) REVERT: G 355 MET cc_start: 0.7749 (tpp) cc_final: 0.7425 (tpp) REVERT: G 368 ARG cc_start: 0.7062 (ttt-90) cc_final: 0.6432 (mmm160) REVERT: G 413 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7276 (mtm-85) REVERT: G 418 ASP cc_start: 0.7909 (t0) cc_final: 0.7557 (t0) REVERT: G 437 GLN cc_start: 0.8459 (tp40) cc_final: 0.7973 (tm-30) REVERT: G 448 GLN cc_start: 0.8316 (mt0) cc_final: 0.7879 (mm-40) REVERT: G 464 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: G 470 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.8240 (m-70) REVERT: G 485 GLN cc_start: 0.8264 (mt0) cc_final: 0.7777 (mm110) REVERT: G 488 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7133 (tm) REVERT: G 498 GLN cc_start: 0.8941 (tp40) cc_final: 0.8710 (tp40) REVERT: G 502 ASN cc_start: 0.8529 (t0) cc_final: 0.7816 (t0) REVERT: G 506 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7498 (mm-30) REVERT: G 528 ARG cc_start: 0.7415 (ptp-170) cc_final: 0.6972 (ptt180) REVERT: G 546 TYR cc_start: 0.7631 (t80) cc_final: 0.7186 (t80) REVERT: F 167 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6399 (mt) REVERT: F 170 TYR cc_start: 0.7669 (m-80) cc_final: 0.6825 (t80) REVERT: F 173 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: F 277 MET cc_start: 0.7148 (mmt) cc_final: 0.6480 (mmt) REVERT: F 313 GLN cc_start: 0.6919 (mm-40) cc_final: 0.5862 (tt0) REVERT: F 330 ARG cc_start: 0.6397 (tpp-160) cc_final: 0.6192 (tpp-160) REVERT: F 346 MET cc_start: 0.8339 (mmt) cc_final: 0.7894 (mmt) REVERT: F 347 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8362 (tp-100) REVERT: F 389 TYR cc_start: 0.7384 (t80) cc_final: 0.7159 (t80) REVERT: F 414 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7196 (t0) REVERT: F 428 TRP cc_start: 0.7097 (t-100) cc_final: 0.6441 (t-100) REVERT: F 441 GLU cc_start: 0.7080 (pm20) cc_final: 0.6557 (tt0) REVERT: F 498 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7826 (tm-30) REVERT: F 501 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8316 (ttm-80) REVERT: F 528 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7035 (ptm-80) REVERT: F 538 CYS cc_start: 0.8482 (m) cc_final: 0.7853 (t) REVERT: F 621 TYR cc_start: 0.8411 (t80) cc_final: 0.7799 (t80) REVERT: F 662 GLN cc_start: 0.7637 (mt0) cc_final: 0.7400 (pt0) REVERT: F 670 ARG cc_start: 0.7463 (tpp-160) cc_final: 0.5708 (mmt90) REVERT: F 671 GLN cc_start: 0.8519 (tt0) cc_final: 0.8254 (tp40) REVERT: F 672 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7387 (tm-30) REVERT: F 676 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.7971 (ttm-80) REVERT: F 684 ASP cc_start: 0.8072 (t70) cc_final: 0.7710 (t0) REVERT: B 49 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.7138 (p) REVERT: B 157 MET cc_start: 0.7705 (tpp) cc_final: 0.7501 (tpp) REVERT: B 190 GLN cc_start: 0.7623 (mt0) cc_final: 0.7363 (mt0) REVERT: B 213 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7902 (ptm160) REVERT: B 299 GLU cc_start: 0.7386 (tp30) cc_final: 0.7106 (tp30) REVERT: B 330 MET cc_start: 0.8431 (mmm) cc_final: 0.8073 (mmm) REVERT: B 379 MET cc_start: 0.8057 (mpp) cc_final: 0.7691 (mpp) REVERT: B 453 GLU cc_start: 0.7573 (pt0) cc_final: 0.7220 (pt0) REVERT: B 541 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8543 (tt) REVERT: B 562 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8282 (mmmm) REVERT: B 738 LYS cc_start: 0.8379 (ptmm) cc_final: 0.7599 (tppt) REVERT: B 758 PHE cc_start: 0.8589 (t80) cc_final: 0.8364 (t80) REVERT: B 762 MET cc_start: 0.8661 (mmp) cc_final: 0.8408 (mmm) REVERT: B 805 ASP cc_start: 0.7666 (t0) cc_final: 0.7150 (t0) REVERT: B 810 THR cc_start: 0.8659 (m) cc_final: 0.8329 (t) REVERT: B 832 GLU cc_start: 0.8270 (pt0) cc_final: 0.8047 (pt0) REVERT: C 66 LEU cc_start: 0.8750 (mt) cc_final: 0.8474 (mp) REVERT: C 91 ASN cc_start: 0.7657 (t0) cc_final: 0.7010 (t0) REVERT: C 96 MET cc_start: 0.8178 (tpt) cc_final: 0.7782 (tpt) REVERT: C 167 LEU cc_start: 0.8022 (tp) cc_final: 0.7653 (tt) REVERT: C 168 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 187 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8186 (ptpp) REVERT: C 193 PRO cc_start: 0.7731 (Cg_exo) cc_final: 0.7466 (Cg_endo) REVERT: C 210 PHE cc_start: 0.8488 (m-80) cc_final: 0.8253 (m-10) REVERT: C 213 ARG cc_start: 0.8125 (ptp-170) cc_final: 0.7530 (ptm160) REVERT: C 216 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8063 (mtmt) REVERT: C 254 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7744 (p) REVERT: C 255 GLU cc_start: 0.8109 (mp0) cc_final: 0.7866 (mp0) REVERT: C 277 GLU cc_start: 0.7847 (tp30) cc_final: 0.7587 (tp30) REVERT: C 288 GLU cc_start: 0.8023 (pt0) cc_final: 0.7820 (pt0) REVERT: C 330 MET cc_start: 0.8314 (mmm) cc_final: 0.8054 (mmm) REVERT: C 483 ASN cc_start: 0.8702 (m-40) cc_final: 0.8478 (m-40) REVERT: C 488 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8647 (t) REVERT: C 541 LEU cc_start: 0.8872 (tp) cc_final: 0.8664 (tp) REVERT: C 562 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8295 (mmmm) REVERT: C 574 GLU cc_start: 0.7866 (pm20) cc_final: 0.7610 (pm20) REVERT: C 611 PHE cc_start: 0.7718 (m-80) cc_final: 0.7125 (m-80) REVERT: C 655 ILE cc_start: 0.8611 (mm) cc_final: 0.8283 (mm) REVERT: C 671 SER cc_start: 0.8891 (m) cc_final: 0.8674 (p) REVERT: C 680 THR cc_start: 0.8793 (m) cc_final: 0.8436 (p) REVERT: C 712 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7989 (ttmm) REVERT: C 762 MET cc_start: 0.8280 (mmm) cc_final: 0.8058 (mmm) REVERT: C 784 TYR cc_start: 0.8116 (m-80) cc_final: 0.7839 (m-10) REVERT: C 805 ASP cc_start: 0.7749 (t0) cc_final: 0.7383 (t0) REVERT: C 806 TYR cc_start: 0.8513 (t80) cc_final: 0.8306 (t80) REVERT: C 815 HIS cc_start: 0.7972 (p-80) cc_final: 0.7485 (p-80) REVERT: C 854 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8451 (mtmm) REVERT: C 898 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7162 (mm-30) REVERT: C 903 ASP cc_start: 0.8098 (t0) cc_final: 0.7663 (t70) REVERT: H 175 GLN cc_start: 0.8470 (tt0) cc_final: 0.8209 (tt0) REVERT: H 250 ASN cc_start: 0.7221 (t0) cc_final: 0.6919 (t0) REVERT: H 284 LEU cc_start: 0.8256 (tp) cc_final: 0.7886 (tp) REVERT: H 344 GLU cc_start: 0.8186 (tp30) cc_final: 0.7266 (tp30) REVERT: H 346 MET cc_start: 0.8505 (mtt) cc_final: 0.8270 (mtt) REVERT: H 347 GLN cc_start: 0.8530 (tm130) cc_final: 0.8313 (tm-30) REVERT: H 349 PHE cc_start: 0.8573 (t80) cc_final: 0.8346 (t80) REVERT: H 352 ASP cc_start: 0.7048 (t0) cc_final: 0.6800 (t0) REVERT: H 356 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6214 (tm-30) REVERT: H 419 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7628 (m) REVERT: H 432 MET cc_start: 0.8152 (mmm) cc_final: 0.7897 (mmm) REVERT: H 444 LEU cc_start: 0.8445 (mm) cc_final: 0.7836 (mt) REVERT: H 445 LYS cc_start: 0.8276 (mptp) cc_final: 0.7892 (mptp) REVERT: H 455 LEU cc_start: 0.8652 (tp) cc_final: 0.8433 (mt) REVERT: H 464 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: H 465 ARG cc_start: 0.7420 (mmt90) cc_final: 0.7153 (tpt90) REVERT: H 471 LEU cc_start: 0.8486 (mt) cc_final: 0.8190 (mm) REVERT: H 488 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7240 (tm) REVERT: H 495 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8526 (p) REVERT: H 496 MET cc_start: 0.8051 (tpp) cc_final: 0.7684 (tpp) REVERT: H 500 PHE cc_start: 0.8622 (t80) cc_final: 0.8205 (t80) REVERT: H 502 ASN cc_start: 0.8509 (t0) cc_final: 0.7355 (t0) REVERT: H 506 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7341 (mm-30) REVERT: H 528 ARG cc_start: 0.7485 (ptp-170) cc_final: 0.7154 (mtm180) REVERT: H 535 TRP cc_start: 0.8040 (m-10) cc_final: 0.7594 (m-10) REVERT: H 540 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (mm) REVERT: H 547 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7961 (mt) REVERT: D 167 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6437 (tt) REVERT: D 181 LEU cc_start: 0.8182 (tp) cc_final: 0.7764 (tp) REVERT: D 186 ASN cc_start: 0.7047 (OUTLIER) cc_final: 0.6798 (t0) REVERT: D 253 LEU cc_start: 0.8677 (mm) cc_final: 0.8415 (mm) REVERT: D 277 MET cc_start: 0.7161 (mmt) cc_final: 0.5920 (mmt) REVERT: D 281 MET cc_start: 0.6998 (mmp) cc_final: 0.6539 (mmp) REVERT: D 313 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6073 (tt0) REVERT: D 342 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 355 MET cc_start: 0.8158 (tpp) cc_final: 0.7773 (tpp) REVERT: D 367 PHE cc_start: 0.8536 (m-10) cc_final: 0.8302 (m-10) REVERT: D 369 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6743 (tm-30) REVERT: D 373 ARG cc_start: 0.8449 (ttt180) cc_final: 0.7974 (ttt180) REVERT: D 395 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5896 (pp20) REVERT: D 413 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7708 (ttm-80) REVERT: D 414 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7434 (t0) REVERT: D 415 TYR cc_start: 0.7996 (t80) cc_final: 0.7697 (t80) REVERT: D 425 CYS cc_start: 0.8711 (m) cc_final: 0.8425 (t) REVERT: D 428 TRP cc_start: 0.7181 (t-100) cc_final: 0.6679 (t-100) REVERT: D 439 LEU cc_start: 0.4622 (OUTLIER) cc_final: 0.4159 (tp) REVERT: D 441 GLU cc_start: 0.7323 (pm20) cc_final: 0.6803 (mt-10) REVERT: D 452 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7734 (mtmt) REVERT: D 453 GLN cc_start: 0.8389 (tt0) cc_final: 0.8010 (tm-30) REVERT: D 485 GLN cc_start: 0.7779 (mt0) cc_final: 0.7567 (mt0) REVERT: D 498 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 499 ASN cc_start: 0.8037 (t0) cc_final: 0.7699 (m-40) REVERT: D 526 LYS cc_start: 0.7229 (mttp) cc_final: 0.7027 (mttp) REVERT: D 617 TRP cc_start: 0.8257 (t60) cc_final: 0.7731 (t60) REVERT: D 623 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7187 (ttm110) REVERT: D 660 LEU cc_start: 0.8531 (tt) cc_final: 0.8291 (tt) REVERT: D 664 GLN cc_start: 0.8374 (mm110) cc_final: 0.8126 (mm-40) REVERT: D 672 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 682 TYR cc_start: 0.8484 (m-80) cc_final: 0.8120 (m-80) REVERT: I 257 LYS cc_start: 0.7710 (mttm) cc_final: 0.7451 (mttm) REVERT: I 263 THR cc_start: 0.7970 (p) cc_final: 0.7642 (p) REVERT: I 267 TYR cc_start: 0.8027 (m-80) cc_final: 0.7633 (m-80) REVERT: I 287 ARG cc_start: 0.7313 (ttm110) cc_final: 0.7000 (tpp80) REVERT: I 344 GLU cc_start: 0.8276 (tp30) cc_final: 0.7257 (tp30) REVERT: I 347 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: I 361 GLU cc_start: 0.7337 (tt0) cc_final: 0.7132 (tp30) REVERT: I 419 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7670 (m) REVERT: I 463 ASN cc_start: 0.8055 (p0) cc_final: 0.7778 (p0) REVERT: I 464 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: I 488 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6731 (tm) REVERT: I 495 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8522 (p) REVERT: I 502 ASN cc_start: 0.8432 (t0) cc_final: 0.7386 (t0) REVERT: I 506 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7302 (mm-30) REVERT: I 540 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7690 (mm) REVERT: I 549 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6897 (t80) REVERT: E 167 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6431 (mp) REVERT: E 186 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6591 (t0) REVERT: E 242 VAL cc_start: 0.8244 (t) cc_final: 0.8008 (p) REVERT: E 253 LEU cc_start: 0.8539 (mm) cc_final: 0.8181 (mp) REVERT: E 275 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6304 (mmmt) REVERT: E 277 MET cc_start: 0.7232 (mmt) cc_final: 0.6973 (mmt) REVERT: E 313 GLN cc_start: 0.7042 (mm-40) cc_final: 0.5951 (tt0) REVERT: E 342 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7402 (mm-30) REVERT: E 347 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8441 (tp40) REVERT: E 367 PHE cc_start: 0.8640 (m-10) cc_final: 0.8299 (m-10) REVERT: E 385 ASN cc_start: 0.8015 (p0) cc_final: 0.7523 (t0) REVERT: E 412 ARG cc_start: 0.8276 (ttt180) cc_final: 0.7725 (ttt90) REVERT: E 413 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: E 428 TRP cc_start: 0.7337 (t-100) cc_final: 0.7042 (t-100) REVERT: E 429 GLN cc_start: 0.8227 (mt0) cc_final: 0.7982 (mt0) REVERT: E 441 GLU cc_start: 0.6820 (pm20) cc_final: 0.6327 (tt0) REVERT: E 452 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7444 (mttt) REVERT: E 453 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8140 (tm-30) REVERT: E 498 GLN cc_start: 0.8246 (tp40) cc_final: 0.8012 (tm-30) REVERT: E 503 PHE cc_start: 0.7969 (t80) cc_final: 0.7718 (t80) REVERT: E 506 GLU cc_start: 0.7617 (pt0) cc_final: 0.7203 (pt0) REVERT: E 526 LYS cc_start: 0.7166 (mttp) cc_final: 0.6899 (mttp) REVERT: E 595 GLU cc_start: 0.4100 (pm20) cc_final: 0.3579 (pm20) REVERT: E 672 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7215 (tm-30) REVERT: E 686 GLN cc_start: 0.8358 (tp40) cc_final: 0.8129 (mp10) outliers start: 175 outliers final: 81 residues processed: 1190 average time/residue: 0.2645 time to fit residues: 497.3084 Evaluate side-chains 1150 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1034 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 482 LYS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 173 PHE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 528 ARG Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain H residue 179 ILE Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 482 LYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 495 SER Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 482 LYS Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 495 SER Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 346 MET Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 528 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 407 optimal weight: 3.9990 chunk 422 optimal weight: 9.9990 chunk 283 optimal weight: 0.0870 chunk 169 optimal weight: 0.6980 chunk 398 optimal weight: 20.0000 chunk 377 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 461 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 399 optimal weight: 1.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN G 499 ASN F 186 ASN ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 GLN B 420 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN B 815 HIS C 190 GLN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN H 486 GLN H 498 GLN D 374 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN I 264 HIS ** I 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 542 GLN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.178548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134775 restraints weight = 65675.442| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.83 r_work: 0.3447 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 40254 Z= 0.178 Angle : 0.630 11.202 54663 Z= 0.319 Chirality : 0.045 0.302 6003 Planarity : 0.005 0.047 7119 Dihedral : 5.500 53.329 5443 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.44 % Allowed : 23.83 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.12), residues: 4821 helix: 1.24 (0.13), residues: 1647 sheet: -1.14 (0.21), residues: 564 loop : -1.14 (0.13), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 507 TYR 0.021 0.001 TYR F 421 PHE 0.014 0.001 PHE B 687 TRP 0.015 0.002 TRP A 380 HIS 0.013 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00406 (40248) covalent geometry : angle 0.62936 (54651) SS BOND : bond 0.00180 ( 6) SS BOND : angle 1.12588 ( 12) hydrogen bonds : bond 0.04245 ( 1506) hydrogen bonds : angle 5.10695 ( 4185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1082 time to evaluate : 1.499 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: 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 133 SER cc_start: 0.8605 (p) cc_final: 0.8179 (m) REVERT: A 210 PHE cc_start: 0.8481 (m-80) cc_final: 0.8115 (m-10) REVERT: A 213 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7992 (ptm160) REVERT: A 230 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8532 (ttp-110) REVERT: A 257 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.8401 (Cg_endo) REVERT: A 281 TYR cc_start: 0.8556 (m-10) cc_final: 0.8172 (m-80) REVERT: A 283 GLU cc_start: 0.7718 (pm20) cc_final: 0.7485 (pm20) REVERT: A 299 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 379 MET cc_start: 0.8023 (mpp) cc_final: 0.7822 (mpp) REVERT: A 445 THR cc_start: 0.8352 (t) cc_final: 0.8114 (p) REVERT: A 643 ASN cc_start: 0.8143 (m-40) cc_final: 0.7839 (m-40) REVERT: A 805 ASP cc_start: 0.7909 (t0) cc_final: 0.7396 (t0) REVERT: A 860 ARG cc_start: 0.8586 (ptm160) cc_final: 0.8095 (mtm180) REVERT: A 904 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: G 187 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.7047 (mmm-85) REVERT: G 293 GLU cc_start: 0.6423 (tm-30) cc_final: 0.6062 (tm-30) REVERT: G 314 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7704 (tt) REVERT: G 333 MET cc_start: 0.7637 (ptm) cc_final: 0.7294 (ptm) REVERT: G 334 MET cc_start: 0.7293 (tmm) cc_final: 0.7069 (tmm) REVERT: G 344 GLU cc_start: 0.8205 (tp30) cc_final: 0.7140 (tp30) REVERT: G 349 PHE cc_start: 0.8712 (t80) cc_final: 0.8502 (t80) REVERT: G 352 ASP cc_start: 0.7521 (t0) cc_final: 0.7279 (t0) REVERT: G 354 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7172 (tm-30) REVERT: G 355 MET cc_start: 0.8035 (tpp) cc_final: 0.7767 (tpp) REVERT: G 368 ARG cc_start: 0.6863 (ttt-90) cc_final: 0.6336 (tpt170) REVERT: G 418 ASP cc_start: 0.7869 (t0) cc_final: 0.7488 (t0) REVERT: G 437 GLN cc_start: 0.8420 (tp40) cc_final: 0.7987 (tm-30) REVERT: G 454 ASN cc_start: 0.8287 (m-40) cc_final: 0.8085 (m-40) REVERT: G 458 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7424 (mm) REVERT: G 464 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: G 470 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.8238 (m-70) REVERT: G 488 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7175 (tm) REVERT: G 506 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7476 (mm-30) REVERT: G 528 ARG cc_start: 0.7349 (ptp-170) cc_final: 0.6888 (ptt90) REVERT: G 546 TYR cc_start: 0.7629 (t80) cc_final: 0.7243 (t80) REVERT: F 170 TYR cc_start: 0.7639 (m-80) cc_final: 0.6889 (t80) REVERT: F 173 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: F 277 MET cc_start: 0.7169 (mmt) cc_final: 0.6418 (mmt) REVERT: F 313 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6018 (tt0) REVERT: F 346 MET cc_start: 0.8435 (mmt) cc_final: 0.7557 (mmt) REVERT: F 347 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8312 (tp-100) REVERT: F 371 TYR cc_start: 0.8113 (p90) cc_final: 0.7534 (p90) REVERT: F 389 TYR cc_start: 0.7457 (t80) cc_final: 0.7120 (t80) REVERT: F 428 TRP cc_start: 0.7178 (t-100) cc_final: 0.6499 (t-100) REVERT: F 455 LEU cc_start: 0.7050 (pp) cc_final: 0.6786 (tt) REVERT: F 464 GLU cc_start: 0.5536 (tm-30) cc_final: 0.5062 (tm-30) REVERT: F 501 ARG cc_start: 0.8686 (ttp-110) cc_final: 0.8418 (ttm-80) REVERT: F 506 GLU cc_start: 0.7574 (pt0) cc_final: 0.6817 (pt0) REVERT: F 538 CYS cc_start: 0.8403 (m) cc_final: 0.8100 (m) REVERT: F 623 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: F 671 GLN cc_start: 0.8543 (tt0) cc_final: 0.8323 (tp40) REVERT: F 672 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7395 (tm-30) REVERT: F 676 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8077 (ttm-80) REVERT: F 679 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7852 (mtm-85) REVERT: F 684 ASP cc_start: 0.8080 (t70) cc_final: 0.7710 (t70) REVERT: B 49 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.7069 (p) REVERT: B 148 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7246 (p) REVERT: B 157 MET cc_start: 0.7783 (tpp) cc_final: 0.7524 (tpp) REVERT: B 158 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7812 (tptm) REVERT: B 190 GLN cc_start: 0.7759 (mt0) cc_final: 0.7474 (mt0) REVERT: B 210 PHE cc_start: 0.8611 (m-80) cc_final: 0.8363 (m-10) REVERT: B 213 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7936 (ptm160) REVERT: B 299 GLU cc_start: 0.7521 (tp30) cc_final: 0.7207 (tp30) REVERT: B 330 MET cc_start: 0.8458 (mmm) cc_final: 0.8080 (mmm) REVERT: B 358 ASN cc_start: 0.8404 (t0) cc_final: 0.8057 (t0) REVERT: B 379 MET cc_start: 0.7993 (mpp) cc_final: 0.7616 (mpp) REVERT: B 453 GLU cc_start: 0.7676 (pt0) cc_final: 0.7350 (pt0) REVERT: B 541 LEU cc_start: 0.8739 (tp) cc_final: 0.8528 (tt) REVERT: B 562 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8240 (mmmm) REVERT: B 570 SER cc_start: 0.8576 (t) cc_final: 0.8301 (p) REVERT: B 713 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 735 PHE cc_start: 0.8199 (m-80) cc_final: 0.7710 (m-80) REVERT: B 738 LYS cc_start: 0.8354 (ptmm) cc_final: 0.8134 (ptmt) REVERT: B 758 PHE cc_start: 0.8555 (t80) cc_final: 0.8337 (t80) REVERT: B 805 ASP cc_start: 0.7802 (t0) cc_final: 0.7196 (t0) REVERT: B 832 GLU cc_start: 0.8278 (pt0) cc_final: 0.8040 (pt0) REVERT: C 66 LEU cc_start: 0.8773 (mt) cc_final: 0.8440 (mp) REVERT: C 96 MET cc_start: 0.8121 (tpt) cc_final: 0.7794 (tpp) REVERT: C 148 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7095 (p) REVERT: C 158 LYS cc_start: 0.8074 (tptp) cc_final: 0.7827 (tptp) REVERT: C 167 LEU cc_start: 0.8042 (tp) cc_final: 0.7709 (tt) REVERT: C 168 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7716 (tm-30) REVERT: C 187 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8132 (ptpp) REVERT: C 193 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7667 (Cg_endo) REVERT: C 210 PHE cc_start: 0.8524 (m-80) cc_final: 0.8140 (m-10) REVERT: C 213 ARG cc_start: 0.8147 (ptp-170) cc_final: 0.7629 (ptm160) REVERT: C 254 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7788 (p) REVERT: C 255 GLU cc_start: 0.8110 (mp0) cc_final: 0.7884 (mp0) REVERT: C 330 MET cc_start: 0.8274 (mmm) cc_final: 0.7860 (mmm) REVERT: C 483 ASN cc_start: 0.8715 (m-40) cc_final: 0.8511 (m-40) REVERT: C 488 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8686 (t) REVERT: C 541 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8643 (tp) REVERT: C 556 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: C 562 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8305 (mmmm) REVERT: C 565 LEU cc_start: 0.7033 (mt) cc_final: 0.6827 (mp) REVERT: C 574 GLU cc_start: 0.7900 (pm20) cc_final: 0.7468 (pm20) REVERT: C 611 PHE cc_start: 0.7689 (m-80) cc_final: 0.6984 (m-80) REVERT: C 614 MET cc_start: 0.6708 (tpp) cc_final: 0.6401 (tpp) REVERT: C 671 SER cc_start: 0.8874 (m) cc_final: 0.8662 (p) REVERT: C 712 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7934 (ttmm) REVERT: C 734 GLU cc_start: 0.8019 (pm20) cc_final: 0.7697 (mp0) REVERT: C 762 MET cc_start: 0.8325 (mmm) cc_final: 0.8069 (mmm) REVERT: C 784 TYR cc_start: 0.8130 (m-80) cc_final: 0.7851 (m-10) REVERT: C 805 ASP cc_start: 0.7767 (t0) cc_final: 0.7286 (t0) REVERT: C 806 TYR cc_start: 0.8575 (t80) cc_final: 0.8119 (t80) REVERT: C 815 HIS cc_start: 0.7918 (p-80) cc_final: 0.7380 (p-80) REVERT: C 898 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7041 (mm-30) REVERT: H 175 GLN cc_start: 0.8580 (tt0) cc_final: 0.8320 (tt0) REVERT: H 250 ASN cc_start: 0.7596 (t0) cc_final: 0.7305 (t0) REVERT: H 257 LYS cc_start: 0.7685 (mttm) cc_final: 0.7335 (mmmt) REVERT: H 272 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7470 (mt) REVERT: H 284 LEU cc_start: 0.8271 (tp) cc_final: 0.7864 (tp) REVERT: H 314 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7060 (tt) REVERT: H 344 GLU cc_start: 0.8151 (tp30) cc_final: 0.7197 (tp30) REVERT: H 346 MET cc_start: 0.8451 (mtt) cc_final: 0.8180 (mtt) REVERT: H 356 GLN cc_start: 0.6953 (tm-30) cc_final: 0.5882 (tm-30) REVERT: H 360 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6140 (mp0) REVERT: H 413 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6707 (ttm-80) REVERT: H 419 CYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7598 (m) REVERT: H 444 LEU cc_start: 0.8424 (mm) cc_final: 0.7880 (mt) REVERT: H 464 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: H 471 LEU cc_start: 0.8489 (mt) cc_final: 0.8181 (mm) REVERT: H 488 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7306 (tm) REVERT: H 496 MET cc_start: 0.7964 (tpp) cc_final: 0.7709 (tpp) REVERT: H 500 PHE cc_start: 0.8675 (t80) cc_final: 0.8222 (t80) REVERT: H 502 ASN cc_start: 0.8595 (t0) cc_final: 0.7558 (t0) REVERT: H 506 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7269 (mm-30) REVERT: H 528 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7251 (mtm180) REVERT: H 547 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7863 (mt) REVERT: D 167 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6373 (mp) REVERT: D 181 LEU cc_start: 0.8238 (tp) cc_final: 0.7916 (tp) REVERT: D 186 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6791 (t0) REVERT: D 253 LEU cc_start: 0.8649 (mm) cc_final: 0.8285 (mm) REVERT: D 271 ASN cc_start: 0.7358 (p0) cc_final: 0.6760 (p0) REVERT: D 277 MET cc_start: 0.7104 (mmt) cc_final: 0.5936 (mmt) REVERT: D 281 MET cc_start: 0.7000 (mmp) cc_final: 0.6553 (mmp) REVERT: D 313 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6392 (tt0) REVERT: D 355 MET cc_start: 0.8123 (tpp) cc_final: 0.7819 (tpp) REVERT: D 367 PHE cc_start: 0.8563 (m-10) cc_final: 0.8246 (m-10) REVERT: D 369 GLN cc_start: 0.7003 (tm-30) cc_final: 0.6544 (tm-30) REVERT: D 373 ARG cc_start: 0.8434 (ttt180) cc_final: 0.7963 (ttt180) REVERT: D 416 VAL cc_start: 0.8523 (p) cc_final: 0.8211 (m) REVERT: D 428 TRP cc_start: 0.7106 (t-100) cc_final: 0.6635 (t-100) REVERT: D 439 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4111 (tp) REVERT: D 441 GLU cc_start: 0.7289 (pm20) cc_final: 0.6831 (mt-10) REVERT: D 452 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7896 (ttmt) REVERT: D 485 GLN cc_start: 0.7891 (mt0) cc_final: 0.7542 (mt0) REVERT: D 496 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7722 (ptp) REVERT: D 498 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 499 ASN cc_start: 0.8019 (t0) cc_final: 0.7722 (m-40) REVERT: D 501 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8293 (ttp-170) REVERT: D 502 ASN cc_start: 0.8369 (t0) cc_final: 0.8061 (t0) REVERT: D 503 PHE cc_start: 0.8201 (t80) cc_final: 0.7816 (t80) REVERT: D 526 LYS cc_start: 0.7283 (mttp) cc_final: 0.7058 (mttp) REVERT: D 539 TYR cc_start: 0.7793 (t80) cc_final: 0.7517 (t80) REVERT: D 543 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8949 (tp) REVERT: D 617 TRP cc_start: 0.8311 (t60) cc_final: 0.7734 (t60) REVERT: D 623 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7110 (ttm110) REVERT: D 634 GLU cc_start: 0.6653 (pt0) cc_final: 0.6237 (pt0) REVERT: D 659 ILE cc_start: 0.8072 (tt) cc_final: 0.7771 (mt) REVERT: D 660 LEU cc_start: 0.8603 (tt) cc_final: 0.8294 (tt) REVERT: D 672 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7301 (tm-30) REVERT: I 257 LYS cc_start: 0.7791 (mttm) cc_final: 0.7568 (mmmm) REVERT: I 287 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7050 (tpp80) REVERT: I 344 GLU cc_start: 0.8262 (tp30) cc_final: 0.6224 (tp30) REVERT: I 347 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: I 348 ARG cc_start: 0.8061 (mtt180) cc_final: 0.6553 (mtt90) REVERT: I 361 GLU cc_start: 0.7320 (tt0) cc_final: 0.7070 (tp30) REVERT: I 419 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7611 (m) REVERT: I 456 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7298 (tmtm) REVERT: I 464 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: I 470 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7702 (t-90) REVERT: I 488 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6823 (tm) REVERT: I 500 PHE cc_start: 0.8526 (t80) cc_final: 0.8270 (t80) REVERT: I 502 ASN cc_start: 0.8442 (t0) cc_final: 0.7496 (t0) REVERT: I 506 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7278 (mm-30) REVERT: I 549 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6953 (t80) REVERT: E 186 ASN cc_start: 0.6922 (OUTLIER) cc_final: 0.6640 (t0) REVERT: E 242 VAL cc_start: 0.8298 (t) cc_final: 0.8094 (p) REVERT: E 253 LEU cc_start: 0.8519 (mm) cc_final: 0.8140 (mp) REVERT: E 277 MET cc_start: 0.7064 (mmt) cc_final: 0.6668 (mmt) REVERT: E 281 MET cc_start: 0.6951 (ptt) cc_final: 0.6675 (ptt) REVERT: E 313 GLN cc_start: 0.6930 (mm-40) cc_final: 0.5994 (tt0) REVERT: E 342 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6998 (mm-30) REVERT: E 346 MET cc_start: 0.8556 (mmt) cc_final: 0.7244 (mmm) REVERT: E 347 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8499 (tp-100) REVERT: E 361 GLU cc_start: 0.7206 (pp20) cc_final: 0.6882 (pp20) REVERT: E 367 PHE cc_start: 0.8716 (m-10) cc_final: 0.8342 (m-10) REVERT: E 385 ASN cc_start: 0.7982 (p0) cc_final: 0.7439 (t0) REVERT: E 412 ARG cc_start: 0.8275 (ttt180) cc_final: 0.7781 (ttt90) REVERT: E 413 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7553 (ttm-80) REVERT: E 428 TRP cc_start: 0.7294 (t-100) cc_final: 0.7041 (t-100) REVERT: E 429 GLN cc_start: 0.8213 (mt0) cc_final: 0.7999 (mt0) REVERT: E 452 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7436 (mttt) REVERT: E 485 GLN cc_start: 0.7859 (mt0) cc_final: 0.7493 (mt0) REVERT: E 503 PHE cc_start: 0.8031 (t80) cc_final: 0.7708 (t80) REVERT: E 506 GLU cc_start: 0.7689 (pt0) cc_final: 0.7258 (pt0) REVERT: E 507 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8071 (tpm170) REVERT: E 526 LYS cc_start: 0.7221 (mttp) cc_final: 0.6921 (mmtp) REVERT: E 617 TRP cc_start: 0.8123 (t60) cc_final: 0.7656 (t60) REVERT: E 624 LYS cc_start: 0.8037 (tttm) cc_final: 0.7553 (ttmt) REVERT: E 662 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: E 671 GLN cc_start: 0.8493 (tt0) cc_final: 0.8154 (tp40) REVERT: E 672 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 191 outliers final: 88 residues processed: 1191 average time/residue: 0.2701 time to fit residues: 510.9890 Evaluate side-chains 1180 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1055 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 173 PHE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 432 MET Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 450 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 482 LYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 538 CYS Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 507 ARG Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 662 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 395 optimal weight: 5.9990 chunk 348 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 391 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 440 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 381 ASN G 499 ASN F 186 ASN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN F 454 ASN F 545 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS C 190 GLN C 397 HIS C 591 ASN ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 GLN H 498 GLN D 347 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN I 264 HIS ** I 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 356 GLN E 542 GLN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.178430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134797 restraints weight = 65243.321| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.83 r_work: 0.3444 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 40254 Z= 0.179 Angle : 0.626 10.430 54663 Z= 0.314 Chirality : 0.045 0.301 6003 Planarity : 0.005 0.047 7119 Dihedral : 5.224 53.899 5426 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.42 % Allowed : 24.13 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.12), residues: 4821 helix: 1.31 (0.13), residues: 1650 sheet: -0.99 (0.21), residues: 567 loop : -1.13 (0.13), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 357 TYR 0.026 0.001 TYR D 621 PHE 0.025 0.001 PHE C 687 TRP 0.013 0.001 TRP D 428 HIS 0.009 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00408 (40248) covalent geometry : angle 0.62602 (54651) SS BOND : bond 0.00180 ( 6) SS BOND : angle 1.05995 ( 12) hydrogen bonds : bond 0.03953 ( 1506) hydrogen bonds : angle 4.95592 ( 4185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1079 time to evaluate : 1.552 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: 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 133 SER cc_start: 0.8485 (p) cc_final: 0.8134 (m) REVERT: A 210 PHE cc_start: 0.8481 (m-80) cc_final: 0.8080 (m-10) REVERT: A 234 ILE cc_start: 0.8970 (tp) cc_final: 0.8732 (tp) REVERT: A 257 PRO cc_start: 0.8663 (Cg_exo) cc_final: 0.8383 (Cg_endo) REVERT: A 281 TYR cc_start: 0.8531 (m-10) cc_final: 0.8266 (m-80) REVERT: A 283 GLU cc_start: 0.7659 (pm20) cc_final: 0.7448 (pm20) REVERT: A 379 MET cc_start: 0.7940 (mpp) cc_final: 0.7728 (mpp) REVERT: A 614 MET cc_start: 0.6794 (tpp) cc_final: 0.6362 (tpp) REVERT: A 643 ASN cc_start: 0.8135 (m-40) cc_final: 0.7903 (m-40) REVERT: A 805 ASP cc_start: 0.7998 (t0) cc_final: 0.7355 (t0) REVERT: A 860 ARG cc_start: 0.8565 (ptm160) cc_final: 0.8139 (mtm180) REVERT: A 904 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: G 187 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7007 (mmm-85) REVERT: G 272 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7321 (mp) REVERT: G 293 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6120 (tm-30) REVERT: G 333 MET cc_start: 0.7645 (ptm) cc_final: 0.7317 (ptm) REVERT: G 334 MET cc_start: 0.7386 (tmm) cc_final: 0.7143 (tmm) REVERT: G 344 GLU cc_start: 0.8174 (tp30) cc_final: 0.6127 (tp30) REVERT: G 347 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8471 (tm-30) REVERT: G 348 ARG cc_start: 0.8102 (mtt180) cc_final: 0.6741 (mpt-90) REVERT: G 355 MET cc_start: 0.8066 (tpp) cc_final: 0.7714 (tpp) REVERT: G 356 GLN cc_start: 0.6962 (pp30) cc_final: 0.6446 (pp30) REVERT: G 360 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: G 368 ARG cc_start: 0.6888 (ttt-90) cc_final: 0.6350 (tpt170) REVERT: G 413 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.6929 (mtm-85) REVERT: G 418 ASP cc_start: 0.7887 (t0) cc_final: 0.7627 (t0) REVERT: G 437 GLN cc_start: 0.8426 (tp40) cc_final: 0.7901 (tm-30) REVERT: G 458 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7422 (mm) REVERT: G 464 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: G 465 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7175 (mmt-90) REVERT: G 470 HIS cc_start: 0.8618 (OUTLIER) cc_final: 0.8260 (m-70) REVERT: G 471 LEU cc_start: 0.8621 (mt) cc_final: 0.8336 (mm) REVERT: G 479 ARG cc_start: 0.8154 (tmt170) cc_final: 0.7864 (ptm160) REVERT: G 488 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7222 (tm) REVERT: G 498 GLN cc_start: 0.8903 (tp40) cc_final: 0.8664 (tp40) REVERT: G 502 ASN cc_start: 0.8517 (t0) cc_final: 0.7416 (t0) REVERT: G 506 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 528 ARG cc_start: 0.7370 (ptp-170) cc_final: 0.6896 (ptt180) REVERT: G 546 TYR cc_start: 0.7699 (t80) cc_final: 0.7220 (t80) REVERT: F 167 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6729 (mt) REVERT: F 170 TYR cc_start: 0.7607 (m-80) cc_final: 0.6849 (t80) REVERT: F 173 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: F 186 ASN cc_start: 0.6760 (t0) cc_final: 0.6480 (t0) REVERT: F 277 MET cc_start: 0.7112 (mmt) cc_final: 0.6382 (mmt) REVERT: F 313 GLN cc_start: 0.6977 (mm-40) cc_final: 0.6051 (tt0) REVERT: F 346 MET cc_start: 0.8350 (mmt) cc_final: 0.7721 (mmt) REVERT: F 347 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8319 (tp-100) REVERT: F 371 TYR cc_start: 0.8118 (p90) cc_final: 0.7627 (p90) REVERT: F 385 ASN cc_start: 0.7886 (p0) cc_final: 0.7425 (t0) REVERT: F 389 TYR cc_start: 0.7490 (t80) cc_final: 0.7132 (t80) REVERT: F 428 TRP cc_start: 0.7158 (t-100) cc_final: 0.6520 (t-100) REVERT: F 455 LEU cc_start: 0.7066 (pp) cc_final: 0.6837 (tt) REVERT: F 464 GLU cc_start: 0.5690 (tm-30) cc_final: 0.5211 (tm-30) REVERT: F 498 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7536 (tm-30) REVERT: F 506 GLU cc_start: 0.7523 (pt0) cc_final: 0.6753 (pt0) REVERT: F 530 CYS cc_start: 0.7865 (t) cc_final: 0.7404 (t) REVERT: F 538 CYS cc_start: 0.8330 (m) cc_final: 0.7623 (t) REVERT: F 617 TRP cc_start: 0.8203 (t60) cc_final: 0.7609 (t60) REVERT: F 662 GLN cc_start: 0.7645 (mt0) cc_final: 0.7402 (pt0) REVERT: F 668 LYS cc_start: 0.8321 (tptt) cc_final: 0.8055 (tptt) REVERT: F 670 ARG cc_start: 0.7589 (tpp-160) cc_final: 0.6895 (tpp80) REVERT: F 671 GLN cc_start: 0.8547 (tt0) cc_final: 0.8328 (tp40) REVERT: F 672 GLU cc_start: 0.7979 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 676 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: F 684 ASP cc_start: 0.8068 (t70) cc_final: 0.7674 (t0) REVERT: F 686 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: F 687 SER cc_start: 0.8663 (t) cc_final: 0.8282 (t) REVERT: B 157 MET cc_start: 0.7770 (tpp) cc_final: 0.7485 (tpp) REVERT: B 158 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7799 (tptm) REVERT: B 168 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 190 GLN cc_start: 0.7769 (mt0) cc_final: 0.7561 (mt0) REVERT: B 277 GLU cc_start: 0.7794 (tp30) cc_final: 0.7571 (tp30) REVERT: B 283 GLU cc_start: 0.7532 (pm20) cc_final: 0.7162 (pm20) REVERT: B 299 GLU cc_start: 0.7585 (tp30) cc_final: 0.7307 (tp30) REVERT: B 330 MET cc_start: 0.8472 (mmm) cc_final: 0.8145 (mmm) REVERT: B 358 ASN cc_start: 0.8415 (t0) cc_final: 0.8068 (t0) REVERT: B 379 MET cc_start: 0.8010 (mpp) cc_final: 0.7616 (mpp) REVERT: B 453 GLU cc_start: 0.7778 (pt0) cc_final: 0.7436 (pt0) REVERT: B 541 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 562 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8201 (mmmm) REVERT: B 570 SER cc_start: 0.8493 (t) cc_final: 0.8186 (p) REVERT: B 713 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 735 PHE cc_start: 0.8254 (m-80) cc_final: 0.7826 (m-80) REVERT: B 738 LYS cc_start: 0.8384 (ptmm) cc_final: 0.8177 (ptmt) REVERT: B 762 MET cc_start: 0.8642 (mmm) cc_final: 0.8404 (mmm) REVERT: B 805 ASP cc_start: 0.7816 (t0) cc_final: 0.7207 (t0) REVERT: B 810 THR cc_start: 0.8678 (m) cc_final: 0.8414 (t) REVERT: B 828 MET cc_start: 0.7327 (ptt) cc_final: 0.7045 (ptt) REVERT: B 832 GLU cc_start: 0.8238 (pt0) cc_final: 0.7969 (pt0) REVERT: C 66 LEU cc_start: 0.8737 (mt) cc_final: 0.8366 (mp) REVERT: C 81 LYS cc_start: 0.8216 (tttt) cc_final: 0.7680 (tttt) REVERT: C 96 MET cc_start: 0.8111 (tpt) cc_final: 0.7804 (tpt) REVERT: C 148 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7142 (p) REVERT: C 158 LYS cc_start: 0.8096 (tptp) cc_final: 0.7850 (tptp) REVERT: C 167 LEU cc_start: 0.8003 (tp) cc_final: 0.7682 (tt) REVERT: C 168 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 187 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8164 (ptpp) REVERT: C 193 PRO cc_start: 0.7956 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: C 210 PHE cc_start: 0.8541 (m-80) cc_final: 0.8179 (m-10) REVERT: C 213 ARG cc_start: 0.8077 (ptp-170) cc_final: 0.7557 (ptm160) REVERT: C 216 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8033 (mtmt) REVERT: C 254 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 277 GLU cc_start: 0.7834 (tp30) cc_final: 0.7578 (tp30) REVERT: C 330 MET cc_start: 0.8312 (mmm) cc_final: 0.7777 (mtp) REVERT: C 331 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7527 (t80) REVERT: C 355 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4297 (mt0) REVERT: C 379 MET cc_start: 0.7872 (mpp) cc_final: 0.7440 (mpp) REVERT: C 483 ASN cc_start: 0.8712 (m-40) cc_final: 0.8497 (m-40) REVERT: C 488 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8723 (t) REVERT: C 541 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8622 (tp) REVERT: C 556 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: C 562 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8316 (mmmm) REVERT: C 574 GLU cc_start: 0.7950 (pm20) cc_final: 0.7508 (pm20) REVERT: C 611 PHE cc_start: 0.7672 (m-80) cc_final: 0.6923 (m-80) REVERT: C 614 MET cc_start: 0.6878 (tpp) cc_final: 0.6639 (tpp) REVERT: C 655 ILE cc_start: 0.8620 (mm) cc_final: 0.8299 (mm) REVERT: C 712 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7933 (ttmm) REVERT: C 762 MET cc_start: 0.8351 (mmm) cc_final: 0.8123 (mmm) REVERT: C 801 VAL cc_start: 0.8737 (m) cc_final: 0.8291 (p) REVERT: C 805 ASP cc_start: 0.7774 (t0) cc_final: 0.7232 (t0) REVERT: C 806 TYR cc_start: 0.8599 (t80) cc_final: 0.8227 (t80) REVERT: C 815 HIS cc_start: 0.7903 (p-80) cc_final: 0.7024 (p-80) REVERT: C 898 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7066 (mm-30) REVERT: H 175 GLN cc_start: 0.8576 (tt0) cc_final: 0.8291 (tt0) REVERT: H 257 LYS cc_start: 0.7635 (mttm) cc_final: 0.7242 (mmmt) REVERT: H 284 LEU cc_start: 0.8230 (tp) cc_final: 0.7782 (tp) REVERT: H 314 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7099 (tt) REVERT: H 344 GLU cc_start: 0.8255 (tp30) cc_final: 0.6534 (tp30) REVERT: H 348 ARG cc_start: 0.8092 (mtt180) cc_final: 0.6955 (mtt90) REVERT: H 356 GLN cc_start: 0.6975 (tm-30) cc_final: 0.6154 (tm-30) REVERT: H 413 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6851 (ttm110) REVERT: H 419 CYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7544 (m) REVERT: H 444 LEU cc_start: 0.8432 (mm) cc_final: 0.7864 (mt) REVERT: H 464 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: H 471 LEU cc_start: 0.8494 (mt) cc_final: 0.8096 (tp) REVERT: H 488 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7233 (tm) REVERT: H 496 MET cc_start: 0.7951 (tpp) cc_final: 0.7713 (tpp) REVERT: H 500 PHE cc_start: 0.8675 (t80) cc_final: 0.8176 (t80) REVERT: H 502 ASN cc_start: 0.8615 (t0) cc_final: 0.7796 (t0) REVERT: H 506 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7322 (mm-30) REVERT: H 528 ARG cc_start: 0.7544 (ptp-170) cc_final: 0.7188 (mtm180) REVERT: H 547 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7838 (mt) REVERT: D 167 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6591 (tt) REVERT: D 253 LEU cc_start: 0.8657 (mm) cc_final: 0.8247 (mm) REVERT: D 277 MET cc_start: 0.7141 (mmt) cc_final: 0.6019 (mmt) REVERT: D 281 MET cc_start: 0.6934 (mmp) cc_final: 0.6485 (mmp) REVERT: D 313 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6429 (tt0) REVERT: D 355 MET cc_start: 0.8168 (tpp) cc_final: 0.7903 (tpp) REVERT: D 367 PHE cc_start: 0.8597 (m-10) cc_final: 0.8262 (m-10) REVERT: D 369 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 416 VAL cc_start: 0.8473 (p) cc_final: 0.8163 (m) REVERT: D 428 TRP cc_start: 0.7110 (t-100) cc_final: 0.6648 (t-100) REVERT: D 439 LEU cc_start: 0.4508 (OUTLIER) cc_final: 0.4062 (tp) REVERT: D 441 GLU cc_start: 0.7266 (pm20) cc_final: 0.6896 (mt-10) REVERT: D 485 GLN cc_start: 0.7915 (mt0) cc_final: 0.7487 (mt0) REVERT: D 496 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8008 (ptm) REVERT: D 498 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 499 ASN cc_start: 0.8004 (t0) cc_final: 0.7734 (m-40) REVERT: D 502 ASN cc_start: 0.8388 (t0) cc_final: 0.8167 (t0) REVERT: D 507 ARG cc_start: 0.8311 (tpt90) cc_final: 0.7841 (tpm170) REVERT: D 526 LYS cc_start: 0.7338 (mttp) cc_final: 0.7099 (mttp) REVERT: D 539 TYR cc_start: 0.7735 (t80) cc_final: 0.7473 (t80) REVERT: D 543 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8961 (tp) REVERT: D 623 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7135 (ttm110) REVERT: D 624 LYS cc_start: 0.7571 (ttpp) cc_final: 0.7309 (ttpt) REVERT: D 634 GLU cc_start: 0.6636 (pt0) cc_final: 0.6160 (pt0) REVERT: D 671 GLN cc_start: 0.8544 (tt0) cc_final: 0.8290 (tp40) REVERT: D 672 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 676 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8101 (ttm-80) REVERT: D 682 TYR cc_start: 0.8458 (m-80) cc_final: 0.8212 (m-80) REVERT: I 257 LYS cc_start: 0.7805 (mttm) cc_final: 0.7540 (mttm) REVERT: I 314 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7699 (tt) REVERT: I 332 LEU cc_start: 0.7935 (tt) cc_final: 0.7402 (pp) REVERT: I 344 GLU cc_start: 0.8209 (tp30) cc_final: 0.7175 (tp30) REVERT: I 347 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: I 361 GLU cc_start: 0.7313 (tt0) cc_final: 0.7051 (tp30) REVERT: I 419 CYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7640 (m) REVERT: I 437 GLN cc_start: 0.8388 (tp40) cc_final: 0.7832 (tm-30) REVERT: I 456 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7386 (tmtm) REVERT: I 464 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: I 470 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7744 (t-90) REVERT: I 488 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6938 (tm) REVERT: I 500 PHE cc_start: 0.8472 (t80) cc_final: 0.8209 (t80) REVERT: I 501 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7326 (ttm110) REVERT: I 502 ASN cc_start: 0.8526 (t0) cc_final: 0.7566 (t0) REVERT: I 506 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7323 (mm-30) REVERT: E 167 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6523 (mp) REVERT: E 242 VAL cc_start: 0.8334 (t) cc_final: 0.8116 (p) REVERT: E 253 LEU cc_start: 0.8477 (mm) cc_final: 0.8112 (mp) REVERT: E 277 MET cc_start: 0.7046 (mmt) cc_final: 0.6578 (mmt) REVERT: E 281 MET cc_start: 0.6915 (ptt) cc_final: 0.6584 (ptt) REVERT: E 313 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6125 (tt0) REVERT: E 342 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7186 (mm-30) REVERT: E 346 MET cc_start: 0.8609 (mmt) cc_final: 0.7332 (mmm) REVERT: E 354 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6920 (tm-30) REVERT: E 355 MET cc_start: 0.8204 (tpp) cc_final: 0.7034 (tpp) REVERT: E 358 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7769 (pttt) REVERT: E 359 LEU cc_start: 0.8364 (mm) cc_final: 0.8102 (mm) REVERT: E 361 GLU cc_start: 0.7230 (pp20) cc_final: 0.6840 (pp20) REVERT: E 367 PHE cc_start: 0.8708 (m-10) cc_final: 0.8418 (m-10) REVERT: E 385 ASN cc_start: 0.7907 (p0) cc_final: 0.7433 (t0) REVERT: E 412 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7809 (ttt90) REVERT: E 413 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: E 452 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7484 (mttt) REVERT: E 454 ASN cc_start: 0.7747 (m-40) cc_final: 0.7258 (t0) REVERT: E 485 GLN cc_start: 0.7890 (mt0) cc_final: 0.7540 (mt0) REVERT: E 506 GLU cc_start: 0.7652 (pt0) cc_final: 0.7060 (pt0) REVERT: E 507 ARG cc_start: 0.8449 (tpm170) cc_final: 0.7999 (tpm170) REVERT: E 518 LEU cc_start: 0.7158 (mp) cc_final: 0.6731 (pt) REVERT: E 526 LYS cc_start: 0.7322 (mttp) cc_final: 0.7047 (mmtp) REVERT: E 534 LEU cc_start: 0.8016 (mt) cc_final: 0.7799 (mm) REVERT: E 542 GLN cc_start: 0.8571 (mp-120) cc_final: 0.8255 (mm-40) REVERT: E 624 LYS cc_start: 0.7966 (tttm) cc_final: 0.7423 (ttmt) REVERT: E 662 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: E 671 GLN cc_start: 0.8465 (tt0) cc_final: 0.8174 (tp40) REVERT: E 672 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7230 (tm-30) REVERT: E 689 GLU cc_start: 0.6909 (mp0) cc_final: 0.6674 (mp0) outliers start: 190 outliers final: 109 residues processed: 1181 average time/residue: 0.2560 time to fit residues: 481.5401 Evaluate side-chains 1208 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1062 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 540 LEU Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 173 PHE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 482 LYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 338 LEU Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 343 LEU Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 456 LYS Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 662 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 433 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 450 optimal weight: 2.9990 chunk 385 optimal weight: 0.5980 chunk 246 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 344 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN G 429 GLN ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN G 499 ASN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 448 ASN B 815 HIS C 190 GLN C 591 ASN ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN H 429 GLN H 486 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.178721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135083 restraints weight = 65116.817| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.95 r_work: 0.3443 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40254 Z= 0.149 Angle : 0.613 10.716 54663 Z= 0.306 Chirality : 0.044 0.389 6003 Planarity : 0.005 0.052 7119 Dihedral : 5.092 54.918 5421 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.58 % Allowed : 24.52 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 4821 helix: 1.39 (0.13), residues: 1650 sheet: -0.90 (0.21), residues: 588 loop : -1.10 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 357 TYR 0.023 0.001 TYR D 621 PHE 0.020 0.001 PHE C 687 TRP 0.031 0.001 TRP E 428 HIS 0.009 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00341 (40248) covalent geometry : angle 0.61307 (54651) SS BOND : bond 0.00192 ( 6) SS BOND : angle 1.02396 ( 12) hydrogen bonds : bond 0.03716 ( 1506) hydrogen bonds : angle 4.85481 ( 4185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1084 time to evaluate : 1.604 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: 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 78 TYR cc_start: 0.8560 (m-80) cc_final: 0.8068 (m-80) REVERT: A 133 SER cc_start: 0.8466 (p) cc_final: 0.8169 (m) REVERT: A 210 PHE cc_start: 0.8475 (m-80) cc_final: 0.8145 (m-10) REVERT: A 213 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7645 (ptp-110) REVERT: A 283 GLU cc_start: 0.7516 (pm20) cc_final: 0.7305 (pm20) REVERT: A 379 MET cc_start: 0.8005 (mpp) cc_final: 0.7777 (mpp) REVERT: A 521 MET cc_start: 0.8792 (mmp) cc_final: 0.8442 (mmm) REVERT: A 614 MET cc_start: 0.6807 (tpp) cc_final: 0.6588 (tpp) REVERT: A 805 ASP cc_start: 0.8002 (t0) cc_final: 0.7344 (t0) REVERT: A 860 ARG cc_start: 0.8560 (ptm160) cc_final: 0.8156 (mtm180) REVERT: G 187 ARG cc_start: 0.7437 (mmm-85) cc_final: 0.7022 (mmm-85) REVERT: G 252 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7766 (ttp-110) REVERT: G 290 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7701 (mtp85) REVERT: G 293 GLU cc_start: 0.6450 (tm-30) cc_final: 0.6149 (tm-30) REVERT: G 332 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7656 (pp) REVERT: G 333 MET cc_start: 0.7629 (ptm) cc_final: 0.7271 (ptm) REVERT: G 334 MET cc_start: 0.7401 (tmm) cc_final: 0.7115 (tmm) REVERT: G 344 GLU cc_start: 0.8181 (tp30) cc_final: 0.7053 (tp30) REVERT: G 347 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8525 (tm-30) REVERT: G 352 ASP cc_start: 0.7564 (t0) cc_final: 0.6841 (t0) REVERT: G 354 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6941 (tm-30) REVERT: G 355 MET cc_start: 0.8024 (tpp) cc_final: 0.7708 (tpp) REVERT: G 356 GLN cc_start: 0.7050 (pp30) cc_final: 0.6594 (pp30) REVERT: G 360 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: G 418 ASP cc_start: 0.7901 (t0) cc_final: 0.7600 (t0) REVERT: G 429 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: G 436 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7970 (tp-100) REVERT: G 448 GLN cc_start: 0.8341 (mt0) cc_final: 0.7971 (mm110) REVERT: G 454 ASN cc_start: 0.7957 (m110) cc_final: 0.7742 (m110) REVERT: G 458 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7385 (mm) REVERT: G 464 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: G 470 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8307 (m-70) REVERT: G 471 LEU cc_start: 0.8655 (mt) cc_final: 0.8378 (mm) REVERT: G 479 ARG cc_start: 0.8263 (tmt170) cc_final: 0.7985 (ptm160) REVERT: G 488 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7186 (tm) REVERT: G 498 GLN cc_start: 0.8911 (tp40) cc_final: 0.8624 (tp40) REVERT: G 502 ASN cc_start: 0.8537 (t0) cc_final: 0.7762 (t0) REVERT: G 506 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7550 (mm-30) REVERT: G 528 ARG cc_start: 0.7389 (ptp-170) cc_final: 0.6872 (ptt180) REVERT: G 546 TYR cc_start: 0.7661 (t80) cc_final: 0.7194 (t80) REVERT: F 167 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6728 (mt) REVERT: F 170 TYR cc_start: 0.7563 (m-80) cc_final: 0.6782 (t80) REVERT: F 173 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8095 (m-10) REVERT: F 186 ASN cc_start: 0.6774 (t0) cc_final: 0.6513 (t0) REVERT: F 261 GLU cc_start: 0.1646 (mp0) cc_final: 0.0994 (pt0) REVERT: F 277 MET cc_start: 0.7255 (mmt) cc_final: 0.6315 (mmt) REVERT: F 313 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6056 (tt0) REVERT: F 330 ARG cc_start: 0.6515 (ttm-80) cc_final: 0.6049 (mtt-85) REVERT: F 346 MET cc_start: 0.8383 (mmt) cc_final: 0.7723 (mmt) REVERT: F 347 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8178 (tp-100) REVERT: F 371 TYR cc_start: 0.8113 (p90) cc_final: 0.7704 (p90) REVERT: F 385 ASN cc_start: 0.7977 (p0) cc_final: 0.7434 (t0) REVERT: F 389 TYR cc_start: 0.7444 (t80) cc_final: 0.7102 (t80) REVERT: F 397 ARG cc_start: 0.3765 (OUTLIER) cc_final: 0.3058 (ttt180) REVERT: F 418 ASP cc_start: 0.7628 (t70) cc_final: 0.7026 (t70) REVERT: F 428 TRP cc_start: 0.7295 (t-100) cc_final: 0.6558 (t-100) REVERT: F 452 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7933 (ttpt) REVERT: F 455 LEU cc_start: 0.7097 (pp) cc_final: 0.6856 (tt) REVERT: F 464 GLU cc_start: 0.5751 (tm-30) cc_final: 0.5268 (tm-30) REVERT: F 498 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7842 (tm-30) REVERT: F 501 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8141 (ttm110) REVERT: F 506 GLU cc_start: 0.7596 (pt0) cc_final: 0.6806 (pt0) REVERT: F 530 CYS cc_start: 0.7830 (t) cc_final: 0.6728 (t) REVERT: F 595 GLU cc_start: 0.3823 (pm20) cc_final: 0.3134 (pm20) REVERT: F 617 TRP cc_start: 0.8189 (t60) cc_final: 0.7625 (t60) REVERT: F 623 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7567 (mtm-85) REVERT: F 662 GLN cc_start: 0.7700 (mt0) cc_final: 0.7445 (pt0) REVERT: F 668 LYS cc_start: 0.8369 (tptt) cc_final: 0.8106 (tptt) REVERT: F 672 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7412 (tm-30) REVERT: F 676 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: F 684 ASP cc_start: 0.8087 (t70) cc_final: 0.7663 (t0) REVERT: F 686 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: F 687 SER cc_start: 0.8576 (t) cc_final: 0.8093 (t) REVERT: B 148 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7319 (p) REVERT: B 157 MET cc_start: 0.7702 (tpp) cc_final: 0.7364 (tpp) REVERT: B 158 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7558 (mmmm) REVERT: B 168 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7077 (tm-30) REVERT: B 277 GLU cc_start: 0.7771 (tp30) cc_final: 0.7547 (tp30) REVERT: B 299 GLU cc_start: 0.7680 (tp30) cc_final: 0.7340 (tp30) REVERT: B 330 MET cc_start: 0.8467 (mmm) cc_final: 0.8145 (mmm) REVERT: B 358 ASN cc_start: 0.8422 (t0) cc_final: 0.8010 (t0) REVERT: B 379 MET cc_start: 0.8050 (mpp) cc_final: 0.7667 (mpp) REVERT: B 453 GLU cc_start: 0.7795 (pt0) cc_final: 0.7449 (pt0) REVERT: B 541 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8503 (tt) REVERT: B 562 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8164 (mmmm) REVERT: B 565 LEU cc_start: 0.6797 (mt) cc_final: 0.6492 (mt) REVERT: B 570 SER cc_start: 0.8486 (t) cc_final: 0.8165 (p) REVERT: B 735 PHE cc_start: 0.8262 (m-80) cc_final: 0.7868 (m-80) REVERT: B 738 LYS cc_start: 0.8365 (ptmm) cc_final: 0.8117 (ptmt) REVERT: B 783 MET cc_start: 0.8384 (ttm) cc_final: 0.8125 (ttm) REVERT: B 805 ASP cc_start: 0.7840 (t0) cc_final: 0.7191 (t0) REVERT: B 832 GLU cc_start: 0.8251 (pt0) cc_final: 0.7971 (pt0) REVERT: C 66 LEU cc_start: 0.8784 (mt) cc_final: 0.8391 (mp) REVERT: C 81 LYS cc_start: 0.8209 (tttt) cc_final: 0.7736 (tttt) REVERT: C 96 MET cc_start: 0.8081 (tpt) cc_final: 0.7806 (tpt) REVERT: C 107 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8540 (tp) REVERT: C 167 LEU cc_start: 0.8062 (tp) cc_final: 0.7744 (tt) REVERT: C 168 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 187 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8171 (ptpp) REVERT: C 193 PRO cc_start: 0.7962 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: C 210 PHE cc_start: 0.8493 (m-80) cc_final: 0.8254 (m-10) REVERT: C 213 ARG cc_start: 0.8085 (ptp-170) cc_final: 0.7567 (ptm160) REVERT: C 216 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8029 (mtmt) REVERT: C 254 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7814 (p) REVERT: C 277 GLU cc_start: 0.7846 (tp30) cc_final: 0.7572 (tp30) REVERT: C 330 MET cc_start: 0.8332 (mmm) cc_final: 0.7761 (mtp) REVERT: C 355 GLN cc_start: 0.4685 (OUTLIER) cc_final: 0.4392 (mt0) REVERT: C 379 MET cc_start: 0.7879 (mpp) cc_final: 0.7436 (mpp) REVERT: C 395 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7907 (mm-30) REVERT: C 433 GLU cc_start: 0.8218 (pm20) cc_final: 0.7986 (pm20) REVERT: C 483 ASN cc_start: 0.8706 (m-40) cc_final: 0.8496 (m-40) REVERT: C 488 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8716 (t) REVERT: C 541 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 556 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: C 562 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8291 (mmmm) REVERT: C 611 PHE cc_start: 0.7655 (m-80) cc_final: 0.6883 (m-80) REVERT: C 655 ILE cc_start: 0.8626 (mm) cc_final: 0.8312 (mm) REVERT: C 712 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7913 (ttmm) REVERT: C 762 MET cc_start: 0.8378 (mmm) cc_final: 0.8169 (mmm) REVERT: C 805 ASP cc_start: 0.7852 (t0) cc_final: 0.7383 (t0) REVERT: C 806 TYR cc_start: 0.8592 (t80) cc_final: 0.7635 (t80) REVERT: C 898 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7218 (mm-30) REVERT: H 175 GLN cc_start: 0.8559 (tt0) cc_final: 0.8265 (tt0) REVERT: H 187 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6900 (mmm-85) REVERT: H 250 ASN cc_start: 0.7498 (t0) cc_final: 0.7293 (t0) REVERT: H 257 LYS cc_start: 0.7635 (mttm) cc_final: 0.7229 (mmmt) REVERT: H 272 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7434 (mp) REVERT: H 284 LEU cc_start: 0.8187 (tp) cc_final: 0.7835 (tp) REVERT: H 313 GLN cc_start: 0.6956 (tp40) cc_final: 0.6320 (tm-30) REVERT: H 314 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7116 (tt) REVERT: H 329 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7501 (tpt-90) REVERT: H 344 GLU cc_start: 0.8233 (tp30) cc_final: 0.7264 (tp30) REVERT: H 347 GLN cc_start: 0.8813 (tm130) cc_final: 0.8403 (tm130) REVERT: H 356 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6396 (tm-30) REVERT: H 413 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6845 (ttm110) REVERT: H 432 MET cc_start: 0.8097 (mmm) cc_final: 0.7767 (mmm) REVERT: H 444 LEU cc_start: 0.8399 (mm) cc_final: 0.7864 (mt) REVERT: H 464 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: H 470 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.8012 (t-90) REVERT: H 471 LEU cc_start: 0.8474 (mt) cc_final: 0.8143 (mm) REVERT: H 488 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7218 (tm) REVERT: H 500 PHE cc_start: 0.8674 (t80) cc_final: 0.8112 (t80) REVERT: H 502 ASN cc_start: 0.8596 (t0) cc_final: 0.7848 (t0) REVERT: H 506 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7395 (mm-30) REVERT: H 528 ARG cc_start: 0.7510 (ptp-170) cc_final: 0.7095 (mtm180) REVERT: D 167 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6558 (mt) REVERT: D 186 ASN cc_start: 0.6854 (t0) cc_final: 0.6649 (t0) REVERT: D 253 LEU cc_start: 0.8621 (mm) cc_final: 0.8218 (mm) REVERT: D 277 MET cc_start: 0.7211 (mmt) cc_final: 0.6045 (mmt) REVERT: D 281 MET cc_start: 0.6913 (mmp) cc_final: 0.6427 (mmp) REVERT: D 283 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6328 (tm-30) REVERT: D 313 GLN cc_start: 0.7480 (mm-40) cc_final: 0.6543 (tt0) REVERT: D 355 MET cc_start: 0.8153 (tpp) cc_final: 0.7908 (tpp) REVERT: D 367 PHE cc_start: 0.8603 (m-10) cc_final: 0.8234 (m-10) REVERT: D 369 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6469 (tm-30) REVERT: D 412 ARG cc_start: 0.8399 (ttt90) cc_final: 0.8061 (ttt90) REVERT: D 416 VAL cc_start: 0.8381 (p) cc_final: 0.8090 (m) REVERT: D 428 TRP cc_start: 0.7134 (t-100) cc_final: 0.6679 (t-100) REVERT: D 439 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4149 (tp) REVERT: D 441 GLU cc_start: 0.7344 (pm20) cc_final: 0.7033 (mt-10) REVERT: D 485 GLN cc_start: 0.7937 (mt0) cc_final: 0.7367 (mt0) REVERT: D 496 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8086 (ptm) REVERT: D 498 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 499 ASN cc_start: 0.8018 (t0) cc_final: 0.7762 (m-40) REVERT: D 501 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8405 (ttp-110) REVERT: D 503 PHE cc_start: 0.8335 (t80) cc_final: 0.7962 (t80) REVERT: D 507 ARG cc_start: 0.8345 (tpt90) cc_final: 0.7826 (tpm170) REVERT: D 526 LYS cc_start: 0.7347 (mttp) cc_final: 0.7061 (mttp) REVERT: D 539 TYR cc_start: 0.7715 (t80) cc_final: 0.7473 (t80) REVERT: D 554 MET cc_start: 0.8499 (ptp) cc_final: 0.8281 (ptp) REVERT: D 593 THR cc_start: 0.7718 (p) cc_final: 0.7385 (p) REVERT: D 594 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6202 (t80) REVERT: D 623 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.7154 (mtm110) REVERT: D 624 LYS cc_start: 0.7572 (ttpp) cc_final: 0.7251 (ttpt) REVERT: D 634 GLU cc_start: 0.6847 (pt0) cc_final: 0.6196 (pt0) REVERT: D 671 GLN cc_start: 0.8581 (tt0) cc_final: 0.8340 (tp40) REVERT: D 672 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7262 (tm-30) REVERT: D 676 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8109 (ttm-80) REVERT: D 682 TYR cc_start: 0.8453 (m-80) cc_final: 0.8122 (m-80) REVERT: I 283 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7710 (mm-30) REVERT: I 314 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7803 (tt) REVERT: I 332 LEU cc_start: 0.7845 (tt) cc_final: 0.7396 (pp) REVERT: I 344 GLU cc_start: 0.8174 (tp30) cc_final: 0.7161 (tp30) REVERT: I 347 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8151 (tm-30) REVERT: I 361 GLU cc_start: 0.7308 (tt0) cc_final: 0.7056 (tp30) REVERT: I 419 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7641 (m) REVERT: I 437 GLN cc_start: 0.8381 (tp40) cc_final: 0.7831 (tm-30) REVERT: I 464 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: I 470 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7829 (t-90) REVERT: I 488 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6942 (tm) REVERT: I 500 PHE cc_start: 0.8523 (t80) cc_final: 0.8247 (t80) REVERT: I 501 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7234 (ttm110) REVERT: I 502 ASN cc_start: 0.8494 (t0) cc_final: 0.7655 (t0) REVERT: I 506 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7328 (mm-30) REVERT: I 526 LYS cc_start: 0.7609 (ptmt) cc_final: 0.6170 (ptmt) REVERT: I 528 ARG cc_start: 0.6824 (ptp-170) cc_final: 0.6224 (ptt-90) REVERT: I 549 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.7093 (t80) REVERT: E 167 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6771 (mp) REVERT: E 186 ASN cc_start: 0.6807 (t0) cc_final: 0.6588 (t0) REVERT: E 253 LEU cc_start: 0.8367 (mm) cc_final: 0.7805 (mp) REVERT: E 256 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7904 (tp) REVERT: E 277 MET cc_start: 0.7072 (mmt) cc_final: 0.6568 (mmt) REVERT: E 281 MET cc_start: 0.6924 (ptt) cc_final: 0.6565 (ptt) REVERT: E 313 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6169 (tt0) REVERT: E 342 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 361 GLU cc_start: 0.7254 (pp20) cc_final: 0.6899 (pp20) REVERT: E 367 PHE cc_start: 0.8682 (m-10) cc_final: 0.8264 (m-10) REVERT: E 385 ASN cc_start: 0.7880 (p0) cc_final: 0.7387 (t0) REVERT: E 397 ARG cc_start: 0.3764 (OUTLIER) cc_final: 0.3226 (ttt180) REVERT: E 412 ARG cc_start: 0.8263 (ttt180) cc_final: 0.7784 (ttt90) REVERT: E 414 ASP cc_start: 0.7916 (t70) cc_final: 0.7495 (t70) REVERT: E 428 TRP cc_start: 0.7432 (t-100) cc_final: 0.7117 (t-100) REVERT: E 452 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7479 (mttt) REVERT: E 454 ASN cc_start: 0.7725 (t0) cc_final: 0.7262 (t0) REVERT: E 485 GLN cc_start: 0.7899 (mt0) cc_final: 0.7553 (mt0) REVERT: E 496 MET cc_start: 0.8570 (ptp) cc_final: 0.8176 (ptp) REVERT: E 503 PHE cc_start: 0.7977 (t80) cc_final: 0.7628 (t80) REVERT: E 506 GLU cc_start: 0.7611 (pt0) cc_final: 0.6990 (pt0) REVERT: E 518 LEU cc_start: 0.7165 (mp) cc_final: 0.6772 (pt) REVERT: E 526 LYS cc_start: 0.7333 (mttp) cc_final: 0.7080 (mmtp) REVERT: E 534 LEU cc_start: 0.8032 (mt) cc_final: 0.7806 (mt) REVERT: E 623 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7161 (mtm-85) REVERT: E 624 LYS cc_start: 0.8040 (tttm) cc_final: 0.7488 (ttmt) REVERT: E 662 GLN cc_start: 0.7482 (pt0) cc_final: 0.7233 (pt0) REVERT: E 671 GLN cc_start: 0.8478 (tt0) cc_final: 0.8186 (tp40) REVERT: E 672 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7281 (tm-30) REVERT: E 689 GLU cc_start: 0.6978 (mp0) cc_final: 0.6664 (mp0) outliers start: 197 outliers final: 114 residues processed: 1193 average time/residue: 0.2768 time to fit residues: 525.1401 Evaluate side-chains 1215 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1063 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 429 GLN Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 173 PHE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 526 LYS Chi-restraints excluded: chain F residue 686 GLN Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 482 LYS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 343 LEU Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 616 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 397 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 236 optimal weight: 0.3980 chunk 315 optimal weight: 2.9990 chunk 462 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 chunk 317 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 643 ASN ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 310 GLN B 420 GLN B 448 ASN ** B 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS C 190 GLN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN H 498 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS I 429 GLN E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 542 GLN ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132892 restraints weight = 65115.043| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.91 r_work: 0.3432 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40254 Z= 0.192 Angle : 0.629 11.507 54663 Z= 0.316 Chirality : 0.045 0.379 6003 Planarity : 0.005 0.054 7119 Dihedral : 4.980 55.033 5410 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.46 % Allowed : 25.15 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 4821 helix: 1.33 (0.13), residues: 1650 sheet: -0.96 (0.21), residues: 588 loop : -1.13 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 368 TYR 0.025 0.002 TYR D 621 PHE 0.024 0.001 PHE C 100 TRP 0.023 0.002 TRP E 428 HIS 0.009 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00433 (40248) covalent geometry : angle 0.62928 (54651) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.03825 ( 12) hydrogen bonds : bond 0.03869 ( 1506) hydrogen bonds : angle 4.85558 ( 4185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1054 time to evaluate : 1.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8569 (m-80) cc_final: 0.8047 (m-80) REVERT: A 133 SER cc_start: 0.8418 (p) cc_final: 0.8186 (m) REVERT: A 210 PHE cc_start: 0.8460 (m-80) cc_final: 0.8188 (m-10) REVERT: A 213 ARG cc_start: 0.8122 (ptm160) cc_final: 0.7822 (ptp-110) REVERT: A 379 MET cc_start: 0.7951 (mpp) cc_final: 0.7690 (mpp) REVERT: A 521 MET cc_start: 0.8785 (mmp) cc_final: 0.8492 (mmm) REVERT: A 562 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8249 (mmmm) REVERT: A 574 GLU cc_start: 0.7733 (pm20) cc_final: 0.7402 (pm20) REVERT: A 805 ASP cc_start: 0.8028 (t0) cc_final: 0.7327 (t0) REVERT: A 860 ARG cc_start: 0.8567 (ptm160) cc_final: 0.8189 (mtm180) REVERT: A 904 GLU cc_start: 0.8204 (pt0) cc_final: 0.7920 (pm20) REVERT: G 187 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6999 (mmm-85) REVERT: G 283 GLU cc_start: 0.8111 (mm-30) cc_final: 0.6914 (mm-30) REVERT: G 290 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7709 (mtp85) REVERT: G 293 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6154 (tm-30) REVERT: G 332 LEU cc_start: 0.8035 (tt) cc_final: 0.7672 (pp) REVERT: G 333 MET cc_start: 0.7711 (ptm) cc_final: 0.7355 (ptm) REVERT: G 334 MET cc_start: 0.7400 (tmm) cc_final: 0.7072 (tmm) REVERT: G 344 GLU cc_start: 0.8157 (tp30) cc_final: 0.7058 (tp30) REVERT: G 347 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 356 GLN cc_start: 0.6940 (pp30) cc_final: 0.6496 (pp30) REVERT: G 360 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: G 368 ARG cc_start: 0.6872 (ttt-90) cc_final: 0.6374 (tpt170) REVERT: G 413 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7163 (mtm-85) REVERT: G 418 ASP cc_start: 0.7935 (t0) cc_final: 0.7635 (t0) REVERT: G 429 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: G 436 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7912 (tp-100) REVERT: G 448 GLN cc_start: 0.8353 (mt0) cc_final: 0.7968 (mm-40) REVERT: G 458 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7526 (mm) REVERT: G 464 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: G 465 ARG cc_start: 0.7663 (mmt90) cc_final: 0.7344 (mmt-90) REVERT: G 471 LEU cc_start: 0.8673 (mt) cc_final: 0.8384 (mm) REVERT: G 479 ARG cc_start: 0.8251 (tmt170) cc_final: 0.7972 (ptm160) REVERT: G 488 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7206 (tm) REVERT: G 502 ASN cc_start: 0.8571 (t0) cc_final: 0.7812 (t0) REVERT: G 506 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7448 (mm-30) REVERT: G 528 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.6698 (mtm110) REVERT: G 546 TYR cc_start: 0.7742 (t80) cc_final: 0.7299 (t80) REVERT: F 167 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7034 (mt) REVERT: F 170 TYR cc_start: 0.7565 (m-80) cc_final: 0.6783 (t80) REVERT: F 277 MET cc_start: 0.7195 (mmt) cc_final: 0.6309 (mmt) REVERT: F 330 ARG cc_start: 0.6461 (ttm-80) cc_final: 0.6117 (mmt180) REVERT: F 356 GLN cc_start: 0.8166 (tt0) cc_final: 0.7675 (tm-30) REVERT: F 360 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7204 (mt-10) REVERT: F 371 TYR cc_start: 0.8124 (p90) cc_final: 0.7695 (p90) REVERT: F 389 TYR cc_start: 0.7487 (t80) cc_final: 0.7121 (t80) REVERT: F 418 ASP cc_start: 0.7592 (t70) cc_final: 0.7093 (t70) REVERT: F 452 LYS cc_start: 0.8284 (mtpp) cc_final: 0.8036 (ttpt) REVERT: F 464 GLU cc_start: 0.5792 (tm-30) cc_final: 0.5372 (tm-30) REVERT: F 501 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8236 (ttm110) REVERT: F 506 GLU cc_start: 0.7677 (pt0) cc_final: 0.6815 (pt0) REVERT: F 617 TRP cc_start: 0.8189 (t60) cc_final: 0.7536 (t60) REVERT: F 668 LYS cc_start: 0.8335 (tptt) cc_final: 0.8106 (tptt) REVERT: F 672 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 676 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8061 (ttm-80) REVERT: F 684 ASP cc_start: 0.8096 (t70) cc_final: 0.7670 (t0) REVERT: F 687 SER cc_start: 0.8589 (t) cc_final: 0.8042 (t) REVERT: B 148 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 157 MET cc_start: 0.7810 (tpp) cc_final: 0.7428 (tpp) REVERT: B 158 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7612 (tptm) REVERT: B 168 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7138 (tm-30) REVERT: B 277 GLU cc_start: 0.7769 (tp30) cc_final: 0.7545 (tp30) REVERT: B 299 GLU cc_start: 0.7603 (tp30) cc_final: 0.7236 (tp30) REVERT: B 330 MET cc_start: 0.8444 (mmm) cc_final: 0.8115 (mmm) REVERT: B 358 ASN cc_start: 0.8439 (t0) cc_final: 0.7990 (t0) REVERT: B 379 MET cc_start: 0.8039 (mpp) cc_final: 0.7631 (mpp) REVERT: B 453 GLU cc_start: 0.7843 (pt0) cc_final: 0.7500 (pt0) REVERT: B 540 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7823 (mtm) REVERT: B 541 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 562 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8175 (mmmm) REVERT: B 565 LEU cc_start: 0.6883 (mt) cc_final: 0.6592 (mt) REVERT: B 570 SER cc_start: 0.8510 (t) cc_final: 0.8161 (p) REVERT: B 580 ASP cc_start: 0.7925 (t0) cc_final: 0.7651 (t0) REVERT: B 735 PHE cc_start: 0.8284 (m-80) cc_final: 0.7898 (m-80) REVERT: B 738 LYS cc_start: 0.8337 (ptmm) cc_final: 0.8110 (ptmt) REVERT: B 805 ASP cc_start: 0.7863 (t0) cc_final: 0.7213 (t0) REVERT: B 810 THR cc_start: 0.8628 (m) cc_final: 0.8338 (t) REVERT: B 828 MET cc_start: 0.7283 (ptt) cc_final: 0.7058 (ptt) REVERT: B 832 GLU cc_start: 0.8248 (pt0) cc_final: 0.7975 (pt0) REVERT: C 66 LEU cc_start: 0.8741 (mt) cc_final: 0.8328 (mp) REVERT: C 81 LYS cc_start: 0.8168 (tttt) cc_final: 0.7950 (tttt) REVERT: C 96 MET cc_start: 0.8142 (tpt) cc_final: 0.7933 (tpt) REVERT: C 107 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8568 (tp) REVERT: C 148 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 167 LEU cc_start: 0.8063 (tp) cc_final: 0.7749 (tt) REVERT: C 168 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7690 (tm-30) REVERT: C 187 LYS cc_start: 0.8418 (ptpp) cc_final: 0.8091 (ptpp) REVERT: C 210 PHE cc_start: 0.8540 (m-80) cc_final: 0.8216 (m-10) REVERT: C 213 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7540 (ptm160) REVERT: C 216 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8004 (mtmt) REVERT: C 254 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7770 (p) REVERT: C 330 MET cc_start: 0.8306 (mmm) cc_final: 0.7797 (mtt) REVERT: C 331 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 355 GLN cc_start: 0.4695 (OUTLIER) cc_final: 0.4420 (mt0) REVERT: C 365 LEU cc_start: 0.8769 (mt) cc_final: 0.8467 (mm) REVERT: C 379 MET cc_start: 0.7905 (mpp) cc_final: 0.7500 (mpp) REVERT: C 433 GLU cc_start: 0.8165 (pm20) cc_final: 0.7935 (pm20) REVERT: C 483 ASN cc_start: 0.8732 (m-40) cc_final: 0.8512 (m-40) REVERT: C 488 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8647 (t) REVERT: C 541 LEU cc_start: 0.8855 (tp) cc_final: 0.8622 (tp) REVERT: C 556 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 562 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8312 (mmmm) REVERT: C 573 TYR cc_start: 0.7543 (t80) cc_final: 0.7088 (t80) REVERT: C 611 PHE cc_start: 0.7735 (m-80) cc_final: 0.6936 (m-80) REVERT: C 644 MET cc_start: 0.8567 (mtm) cc_final: 0.7998 (mtm) REVERT: C 655 ILE cc_start: 0.8641 (mm) cc_final: 0.8329 (mm) REVERT: C 712 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7889 (ttmm) REVERT: C 762 MET cc_start: 0.8346 (mmm) cc_final: 0.8042 (mmp) REVERT: C 793 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8112 (ptp) REVERT: C 805 ASP cc_start: 0.7850 (t0) cc_final: 0.7364 (t0) REVERT: C 806 TYR cc_start: 0.8592 (t80) cc_final: 0.7678 (t80) REVERT: C 898 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7232 (mm-30) REVERT: C 904 GLU cc_start: 0.8082 (pt0) cc_final: 0.7858 (pt0) REVERT: H 187 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7092 (mmm-85) REVERT: H 257 LYS cc_start: 0.7612 (mttm) cc_final: 0.7219 (mmmt) REVERT: H 272 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7561 (tp) REVERT: H 284 LEU cc_start: 0.8163 (tp) cc_final: 0.7793 (tp) REVERT: H 314 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7068 (tt) REVERT: H 329 ARG cc_start: 0.7835 (tpp80) cc_final: 0.7353 (tpt-90) REVERT: H 344 GLU cc_start: 0.8214 (tp30) cc_final: 0.7245 (tp30) REVERT: H 347 GLN cc_start: 0.8808 (tm130) cc_final: 0.8569 (tm-30) REVERT: H 356 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6441 (tm-30) REVERT: H 413 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6851 (ttm110) REVERT: H 419 CYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7549 (m) REVERT: H 432 MET cc_start: 0.8134 (mmm) cc_final: 0.7879 (mmm) REVERT: H 444 LEU cc_start: 0.8374 (mm) cc_final: 0.7840 (mt) REVERT: H 464 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: H 470 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8047 (t-90) REVERT: H 471 LEU cc_start: 0.8392 (mt) cc_final: 0.8100 (mm) REVERT: H 488 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7252 (tm) REVERT: H 500 PHE cc_start: 0.8685 (t80) cc_final: 0.8351 (t80) REVERT: H 502 ASN cc_start: 0.8627 (t0) cc_final: 0.7865 (t0) REVERT: H 506 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7389 (mm-30) REVERT: D 167 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6623 (mt) REVERT: D 186 ASN cc_start: 0.6969 (t0) cc_final: 0.6510 (t0) REVERT: D 253 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8247 (mt) REVERT: D 277 MET cc_start: 0.7249 (mmt) cc_final: 0.6133 (mmt) REVERT: D 281 MET cc_start: 0.6994 (mmp) cc_final: 0.6529 (mmp) REVERT: D 283 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6414 (tm-30) REVERT: D 313 GLN cc_start: 0.7563 (mm-40) cc_final: 0.6743 (tt0) REVERT: D 346 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8197 (mmp) REVERT: D 349 PHE cc_start: 0.8513 (t80) cc_final: 0.8312 (t80) REVERT: D 367 PHE cc_start: 0.8618 (m-10) cc_final: 0.8260 (m-10) REVERT: D 369 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6473 (tm-30) REVERT: D 412 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8097 (ttt90) REVERT: D 416 VAL cc_start: 0.8361 (p) cc_final: 0.8054 (m) REVERT: D 425 CYS cc_start: 0.8746 (m) cc_final: 0.8359 (t) REVERT: D 439 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4165 (tp) REVERT: D 441 GLU cc_start: 0.7322 (pm20) cc_final: 0.7032 (mt-10) REVERT: D 485 GLN cc_start: 0.7944 (mt0) cc_final: 0.7485 (mt0) REVERT: D 498 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 499 ASN cc_start: 0.8031 (t0) cc_final: 0.7783 (m-40) REVERT: D 501 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8376 (ttp-170) REVERT: D 507 ARG cc_start: 0.8332 (tpt90) cc_final: 0.7802 (tpm170) REVERT: D 526 LYS cc_start: 0.7535 (mttp) cc_final: 0.7267 (mmtp) REVERT: D 539 TYR cc_start: 0.7786 (t80) cc_final: 0.7545 (t80) REVERT: D 542 GLN cc_start: 0.8300 (mp10) cc_final: 0.7897 (mp10) REVERT: D 554 MET cc_start: 0.8504 (ptp) cc_final: 0.8256 (ptp) REVERT: D 576 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6697 (mtm-85) REVERT: D 593 THR cc_start: 0.7809 (p) cc_final: 0.7537 (p) REVERT: D 594 PHE cc_start: 0.6957 (t80) cc_final: 0.6621 (t80) REVERT: D 623 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.7150 (mtm110) REVERT: D 624 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7289 (ttpt) REVERT: D 634 GLU cc_start: 0.6777 (pt0) cc_final: 0.6158 (pt0) REVERT: D 671 GLN cc_start: 0.8592 (tt0) cc_final: 0.8366 (tp40) REVERT: D 672 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 676 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: D 682 TYR cc_start: 0.8514 (m-80) cc_final: 0.8297 (m-80) REVERT: D 687 SER cc_start: 0.8629 (t) cc_final: 0.7938 (p) REVERT: I 283 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7609 (mm-30) REVERT: I 314 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7888 (tt) REVERT: I 332 LEU cc_start: 0.7874 (tt) cc_final: 0.7427 (pp) REVERT: I 344 GLU cc_start: 0.8143 (tp30) cc_final: 0.6639 (tp30) REVERT: I 347 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: I 348 ARG cc_start: 0.8162 (mtt180) cc_final: 0.6828 (mmt90) REVERT: I 350 PHE cc_start: 0.8527 (m-10) cc_final: 0.8325 (m-80) REVERT: I 361 GLU cc_start: 0.7299 (tt0) cc_final: 0.7059 (tp30) REVERT: I 368 ARG cc_start: 0.6381 (ttt-90) cc_final: 0.5924 (mmm-85) REVERT: I 419 CYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7598 (m) REVERT: I 445 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8098 (mptp) REVERT: I 464 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: I 470 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7724 (t-90) REVERT: I 488 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6959 (tm) REVERT: I 500 PHE cc_start: 0.8537 (t80) cc_final: 0.8289 (t80) REVERT: I 502 ASN cc_start: 0.8551 (t0) cc_final: 0.7600 (t0) REVERT: I 506 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7373 (mm-30) REVERT: I 526 LYS cc_start: 0.7608 (ptmt) cc_final: 0.6510 (ptmt) REVERT: I 528 ARG cc_start: 0.6820 (ptp-170) cc_final: 0.6346 (ptt-90) REVERT: I 549 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7161 (t80) REVERT: E 186 ASN cc_start: 0.6564 (t0) cc_final: 0.6345 (t0) REVERT: E 242 VAL cc_start: 0.8361 (t) cc_final: 0.8095 (p) REVERT: E 277 MET cc_start: 0.7086 (mmt) cc_final: 0.6584 (mmt) REVERT: E 281 MET cc_start: 0.6959 (ptt) cc_final: 0.6634 (ptt) REVERT: E 313 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6219 (tt0) REVERT: E 342 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 349 PHE cc_start: 0.8500 (t80) cc_final: 0.8291 (t80) REVERT: E 358 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7787 (pttt) REVERT: E 359 LEU cc_start: 0.8362 (mm) cc_final: 0.8100 (mm) REVERT: E 361 GLU cc_start: 0.7261 (pp20) cc_final: 0.6843 (pp20) REVERT: E 367 PHE cc_start: 0.8706 (m-10) cc_final: 0.8317 (m-10) REVERT: E 385 ASN cc_start: 0.7818 (p0) cc_final: 0.7338 (t0) REVERT: E 397 ARG cc_start: 0.3860 (OUTLIER) cc_final: 0.3317 (ttt180) REVERT: E 412 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7934 (ttt90) REVERT: E 414 ASP cc_start: 0.8055 (t70) cc_final: 0.7618 (t70) REVERT: E 428 TRP cc_start: 0.7416 (t-100) cc_final: 0.6989 (t-100) REVERT: E 452 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7476 (mttt) REVERT: E 454 ASN cc_start: 0.7789 (t0) cc_final: 0.7396 (t0) REVERT: E 485 GLN cc_start: 0.7922 (mt0) cc_final: 0.7597 (mt0) REVERT: E 496 MET cc_start: 0.8620 (ptp) cc_final: 0.8411 (ptp) REVERT: E 498 GLN cc_start: 0.8229 (tp40) cc_final: 0.7939 (tm-30) REVERT: E 506 GLU cc_start: 0.7666 (pt0) cc_final: 0.7003 (pt0) REVERT: E 507 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8210 (tpm170) REVERT: E 518 LEU cc_start: 0.7205 (mp) cc_final: 0.6671 (pt) REVERT: E 526 LYS cc_start: 0.7370 (mttp) cc_final: 0.7130 (mmtp) REVERT: E 554 MET cc_start: 0.8753 (mtm) cc_final: 0.8490 (mtm) REVERT: E 624 LYS cc_start: 0.8052 (tttm) cc_final: 0.7491 (ttmt) REVERT: E 662 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: E 671 GLN cc_start: 0.8444 (tt0) cc_final: 0.8200 (mm110) REVERT: E 672 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 689 GLU cc_start: 0.7117 (mp0) cc_final: 0.6762 (mp0) outliers start: 192 outliers final: 120 residues processed: 1161 average time/residue: 0.2721 time to fit residues: 500.3786 Evaluate side-chains 1210 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1051 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 429 GLN Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 449 LYS Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 526 LYS Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 427 THR Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 439 LEU Chi-restraints excluded: chain I residue 445 LYS Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 507 ARG Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 662 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 344 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 228 optimal weight: 0.0970 chunk 183 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN G 429 GLN ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 ASN F 171 HIS ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 GLN B 815 HIS C 190 GLN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** C 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134275 restraints weight = 64989.199| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.00 r_work: 0.3432 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40254 Z= 0.169 Angle : 0.631 10.770 54663 Z= 0.313 Chirality : 0.044 0.366 6003 Planarity : 0.005 0.055 7119 Dihedral : 4.948 55.179 5410 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.49 % Allowed : 25.96 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.12), residues: 4821 helix: 1.29 (0.13), residues: 1671 sheet: -0.93 (0.21), residues: 567 loop : -1.09 (0.13), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 357 TYR 0.026 0.001 TYR D 621 PHE 0.028 0.001 PHE C 687 TRP 0.021 0.001 TRP E 428 HIS 0.010 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00385 (40248) covalent geometry : angle 0.63085 (54651) SS BOND : bond 0.00208 ( 6) SS BOND : angle 1.02267 ( 12) hydrogen bonds : bond 0.03707 ( 1506) hydrogen bonds : angle 4.81948 ( 4185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1061 time to evaluate : 1.610 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: 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 74 GLU cc_start: 0.7289 (mp0) cc_final: 0.6925 (mp0) REVERT: A 78 TYR cc_start: 0.8573 (m-80) cc_final: 0.8066 (m-80) REVERT: A 81 LYS cc_start: 0.8003 (tttt) cc_final: 0.7691 (tttt) REVERT: A 133 SER cc_start: 0.8400 (p) cc_final: 0.8164 (m) REVERT: A 198 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5172 (mp0) REVERT: A 210 PHE cc_start: 0.8382 (m-80) cc_final: 0.8099 (m-10) REVERT: A 283 GLU cc_start: 0.7911 (pt0) cc_final: 0.7494 (pt0) REVERT: A 379 MET cc_start: 0.7945 (mpp) cc_final: 0.7674 (mpp) REVERT: A 521 MET cc_start: 0.8768 (mmp) cc_final: 0.8477 (mmm) REVERT: A 562 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8289 (mmmm) REVERT: A 574 GLU cc_start: 0.7728 (pm20) cc_final: 0.7411 (pm20) REVERT: A 805 ASP cc_start: 0.7990 (t0) cc_final: 0.7288 (t0) REVERT: A 860 ARG cc_start: 0.8571 (ptm160) cc_final: 0.8198 (mtm180) REVERT: A 904 GLU cc_start: 0.8203 (pt0) cc_final: 0.7952 (pm20) REVERT: G 187 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.7000 (mmm-85) REVERT: G 283 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7355 (mm-30) REVERT: G 287 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7397 (tpp80) REVERT: G 290 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7760 (mtp85) REVERT: G 293 GLU cc_start: 0.6491 (tm-30) cc_final: 0.6153 (tm-30) REVERT: G 332 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7668 (pp) REVERT: G 333 MET cc_start: 0.7708 (ptm) cc_final: 0.7358 (ptm) REVERT: G 334 MET cc_start: 0.7420 (tmm) cc_final: 0.7094 (tmm) REVERT: G 342 GLU cc_start: 0.8275 (mp0) cc_final: 0.7951 (tp30) REVERT: G 344 GLU cc_start: 0.8176 (tp30) cc_final: 0.7059 (tp30) REVERT: G 347 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8550 (tm-30) REVERT: G 352 ASP cc_start: 0.7511 (t0) cc_final: 0.6997 (t0) REVERT: G 354 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7098 (tm-30) REVERT: G 356 GLN cc_start: 0.7013 (pp30) cc_final: 0.6557 (pp30) REVERT: G 360 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: G 413 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.6801 (mtm-85) REVERT: G 418 ASP cc_start: 0.7912 (t0) cc_final: 0.7642 (t0) REVERT: G 429 GLN cc_start: 0.8343 (tt0) cc_final: 0.7939 (tt0) REVERT: G 436 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7916 (tp-100) REVERT: G 448 GLN cc_start: 0.8335 (mt0) cc_final: 0.8044 (mm110) REVERT: G 450 LEU cc_start: 0.8279 (mt) cc_final: 0.7949 (mm) REVERT: G 454 ASN cc_start: 0.7910 (m110) cc_final: 0.7532 (p0) REVERT: G 458 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7507 (mm) REVERT: G 464 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: G 465 ARG cc_start: 0.7671 (mmt90) cc_final: 0.7229 (mmt90) REVERT: G 471 LEU cc_start: 0.8670 (mt) cc_final: 0.8378 (mm) REVERT: G 479 ARG cc_start: 0.8296 (tmt170) cc_final: 0.8086 (ttt90) REVERT: G 488 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7208 (tm) REVERT: G 502 ASN cc_start: 0.8596 (t0) cc_final: 0.7836 (t0) REVERT: G 506 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7518 (mm-30) REVERT: G 528 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.7201 (ptm160) REVERT: G 546 TYR cc_start: 0.7724 (t80) cc_final: 0.7325 (t80) REVERT: F 167 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7067 (mt) REVERT: F 170 TYR cc_start: 0.7533 (m-80) cc_final: 0.6715 (t80) REVERT: F 277 MET cc_start: 0.7178 (mmt) cc_final: 0.6301 (mmt) REVERT: F 330 ARG cc_start: 0.6373 (ttm-80) cc_final: 0.6049 (mmt180) REVERT: F 346 MET cc_start: 0.8370 (mmt) cc_final: 0.7716 (mmt) REVERT: F 360 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7684 (mt-10) REVERT: F 371 TYR cc_start: 0.8106 (p90) cc_final: 0.7680 (p90) REVERT: F 389 TYR cc_start: 0.7498 (t80) cc_final: 0.7131 (t80) REVERT: F 397 ARG cc_start: 0.3865 (OUTLIER) cc_final: 0.3142 (ttt180) REVERT: F 418 ASP cc_start: 0.7596 (t70) cc_final: 0.7152 (t70) REVERT: F 428 TRP cc_start: 0.7186 (t-100) cc_final: 0.6857 (t-100) REVERT: F 464 GLU cc_start: 0.5796 (tm-30) cc_final: 0.5366 (tm-30) REVERT: F 501 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8325 (ttm110) REVERT: F 506 GLU cc_start: 0.7667 (pt0) cc_final: 0.6781 (pt0) REVERT: F 617 TRP cc_start: 0.8193 (t60) cc_final: 0.7540 (t60) REVERT: F 668 LYS cc_start: 0.8340 (tptt) cc_final: 0.8108 (tptt) REVERT: F 672 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7361 (tm-30) REVERT: F 676 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: F 684 ASP cc_start: 0.8079 (t70) cc_final: 0.7638 (t0) REVERT: F 687 SER cc_start: 0.8629 (t) cc_final: 0.8138 (t) REVERT: B 148 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7355 (p) REVERT: B 157 MET cc_start: 0.7836 (tpp) cc_final: 0.7442 (tpp) REVERT: B 158 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7508 (mmmm) REVERT: B 168 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 277 GLU cc_start: 0.7764 (tp30) cc_final: 0.7534 (tp30) REVERT: B 299 GLU cc_start: 0.7636 (tp30) cc_final: 0.7274 (tp30) REVERT: B 330 MET cc_start: 0.8457 (mmm) cc_final: 0.8129 (mmm) REVERT: B 358 ASN cc_start: 0.8452 (t0) cc_final: 0.8063 (t0) REVERT: B 379 MET cc_start: 0.8032 (mpp) cc_final: 0.7626 (mpp) REVERT: B 453 GLU cc_start: 0.7856 (pt0) cc_final: 0.7520 (pt0) REVERT: B 541 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 562 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8251 (mmmm) REVERT: B 565 LEU cc_start: 0.6857 (mt) cc_final: 0.6591 (mt) REVERT: B 570 SER cc_start: 0.8492 (t) cc_final: 0.8179 (p) REVERT: B 580 ASP cc_start: 0.7929 (t0) cc_final: 0.7616 (t0) REVERT: B 675 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 712 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7740 (ttmm) REVERT: B 735 PHE cc_start: 0.8260 (m-80) cc_final: 0.7920 (m-80) REVERT: B 738 LYS cc_start: 0.8334 (ptmm) cc_final: 0.8106 (ptmt) REVERT: B 762 MET cc_start: 0.8673 (mmm) cc_final: 0.8372 (mmm) REVERT: B 805 ASP cc_start: 0.7872 (t0) cc_final: 0.7237 (t0) REVERT: B 828 MET cc_start: 0.7251 (ptt) cc_final: 0.7002 (ptt) REVERT: B 832 GLU cc_start: 0.8239 (pt0) cc_final: 0.7973 (pt0) REVERT: C 66 LEU cc_start: 0.8737 (mt) cc_final: 0.8327 (mp) REVERT: C 74 GLU cc_start: 0.7140 (mp0) cc_final: 0.6611 (mp0) REVERT: C 81 LYS cc_start: 0.8154 (tttt) cc_final: 0.7838 (tttt) REVERT: C 96 MET cc_start: 0.8072 (tpt) cc_final: 0.7703 (tpt) REVERT: C 107 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 148 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7135 (p) REVERT: C 167 LEU cc_start: 0.8056 (tp) cc_final: 0.7749 (tt) REVERT: C 168 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 187 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8063 (ptpp) REVERT: C 213 ARG cc_start: 0.8048 (ptp-170) cc_final: 0.7518 (ptp-110) REVERT: C 216 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8004 (mtmt) REVERT: C 254 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7719 (p) REVERT: C 279 VAL cc_start: 0.8760 (t) cc_final: 0.8493 (p) REVERT: C 299 GLU cc_start: 0.7515 (tp30) cc_final: 0.7204 (tp30) REVERT: C 330 MET cc_start: 0.8290 (mmm) cc_final: 0.7758 (mtt) REVERT: C 331 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7520 (t80) REVERT: C 355 GLN cc_start: 0.4716 (OUTLIER) cc_final: 0.4434 (mt0) REVERT: C 365 LEU cc_start: 0.8756 (mt) cc_final: 0.8458 (mm) REVERT: C 379 MET cc_start: 0.7927 (mpp) cc_final: 0.7525 (mpp) REVERT: C 433 GLU cc_start: 0.8167 (pm20) cc_final: 0.7933 (pm20) REVERT: C 488 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8650 (t) REVERT: C 556 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7004 (tm-30) REVERT: C 562 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8311 (mmmm) REVERT: C 573 TYR cc_start: 0.7523 (t80) cc_final: 0.7082 (t80) REVERT: C 611 PHE cc_start: 0.7766 (m-80) cc_final: 0.6905 (m-80) REVERT: C 644 MET cc_start: 0.8522 (mtm) cc_final: 0.7976 (mtm) REVERT: C 712 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7869 (ttmm) REVERT: C 762 MET cc_start: 0.8308 (mmm) cc_final: 0.7981 (mmp) REVERT: C 793 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8134 (ptp) REVERT: C 805 ASP cc_start: 0.7701 (t0) cc_final: 0.7200 (t0) REVERT: C 806 TYR cc_start: 0.8575 (t80) cc_final: 0.7643 (t80) REVERT: C 898 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 904 GLU cc_start: 0.8082 (pt0) cc_final: 0.7848 (pt0) REVERT: H 175 GLN cc_start: 0.8521 (tt0) cc_final: 0.8236 (tt0) REVERT: H 187 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7240 (mmm-85) REVERT: H 257 LYS cc_start: 0.7575 (mttm) cc_final: 0.7200 (mmmt) REVERT: H 272 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7607 (mt) REVERT: H 284 LEU cc_start: 0.8110 (tp) cc_final: 0.7707 (tp) REVERT: H 290 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7396 (mmm-85) REVERT: H 314 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7078 (tt) REVERT: H 329 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7398 (tpt-90) REVERT: H 344 GLU cc_start: 0.8219 (tp30) cc_final: 0.7246 (tp30) REVERT: H 346 MET cc_start: 0.8502 (mtt) cc_final: 0.7953 (mmt) REVERT: H 347 GLN cc_start: 0.8811 (tm130) cc_final: 0.8559 (tm-30) REVERT: H 356 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6460 (tm-30) REVERT: H 413 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6859 (ttm110) REVERT: H 419 CYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (m) REVERT: H 444 LEU cc_start: 0.8382 (mm) cc_final: 0.7908 (mt) REVERT: H 464 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: H 470 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: H 471 LEU cc_start: 0.8379 (mt) cc_final: 0.8102 (mm) REVERT: H 488 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7193 (tm) REVERT: H 500 PHE cc_start: 0.8718 (t80) cc_final: 0.8334 (t80) REVERT: H 502 ASN cc_start: 0.8648 (t0) cc_final: 0.7881 (t0) REVERT: H 506 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7392 (mm-30) REVERT: D 253 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8198 (mt) REVERT: D 277 MET cc_start: 0.7277 (mmt) cc_final: 0.6409 (mmt) REVERT: D 313 GLN cc_start: 0.7602 (mm-40) cc_final: 0.6802 (tt0) REVERT: D 367 PHE cc_start: 0.8627 (m-10) cc_final: 0.8242 (m-10) REVERT: D 369 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6528 (tm-30) REVERT: D 412 ARG cc_start: 0.8441 (ttt90) cc_final: 0.8102 (ttt90) REVERT: D 416 VAL cc_start: 0.8304 (p) cc_final: 0.7988 (m) REVERT: D 428 TRP cc_start: 0.7105 (t-100) cc_final: 0.6641 (t-100) REVERT: D 439 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.4147 (tp) REVERT: D 441 GLU cc_start: 0.7382 (pm20) cc_final: 0.7167 (mt-10) REVERT: D 485 GLN cc_start: 0.7909 (mt0) cc_final: 0.7421 (mt0) REVERT: D 496 MET cc_start: 0.8394 (ptp) cc_final: 0.8067 (ptt) REVERT: D 498 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 499 ASN cc_start: 0.8042 (t0) cc_final: 0.7785 (m-40) REVERT: D 501 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8436 (ttp-110) REVERT: D 503 PHE cc_start: 0.8270 (t80) cc_final: 0.7945 (t80) REVERT: D 507 ARG cc_start: 0.8399 (tpt90) cc_final: 0.7858 (tpm170) REVERT: D 526 LYS cc_start: 0.7555 (mttp) cc_final: 0.7279 (mmtp) REVERT: D 576 ARG cc_start: 0.6961 (mtm-85) cc_final: 0.6687 (mtm-85) REVERT: D 593 THR cc_start: 0.7743 (p) cc_final: 0.7478 (p) REVERT: D 594 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6640 (t80) REVERT: D 623 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7162 (mtm110) REVERT: D 624 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7277 (ttpt) REVERT: D 634 GLU cc_start: 0.6794 (pt0) cc_final: 0.6167 (pt0) REVERT: D 671 GLN cc_start: 0.8605 (tt0) cc_final: 0.8388 (tp40) REVERT: D 672 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7283 (tm-30) REVERT: D 676 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: D 682 TYR cc_start: 0.8510 (m-80) cc_final: 0.8289 (m-80) REVERT: D 687 SER cc_start: 0.8623 (t) cc_final: 0.7938 (p) REVERT: I 283 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7554 (mm-30) REVERT: I 287 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6834 (tpp80) REVERT: I 314 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7897 (tt) REVERT: I 329 ARG cc_start: 0.7815 (tpp80) cc_final: 0.7047 (tpp80) REVERT: I 332 LEU cc_start: 0.7971 (tt) cc_final: 0.7483 (pp) REVERT: I 344 GLU cc_start: 0.8157 (tp30) cc_final: 0.7263 (tp30) REVERT: I 347 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: I 350 PHE cc_start: 0.8536 (m-10) cc_final: 0.8325 (m-80) REVERT: I 361 GLU cc_start: 0.7307 (tt0) cc_final: 0.7049 (tp30) REVERT: I 368 ARG cc_start: 0.6356 (ttt-90) cc_final: 0.5897 (mmm-85) REVERT: I 419 CYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7630 (m) REVERT: I 464 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: I 470 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7852 (t-90) REVERT: I 488 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6950 (tm) REVERT: I 500 PHE cc_start: 0.8533 (t80) cc_final: 0.8261 (t80) REVERT: I 502 ASN cc_start: 0.8558 (t0) cc_final: 0.7603 (t0) REVERT: I 506 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7387 (mm-30) REVERT: I 549 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7190 (t80) REVERT: E 167 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6848 (mp) REVERT: E 186 ASN cc_start: 0.6539 (t0) cc_final: 0.6288 (t0) REVERT: E 242 VAL cc_start: 0.8386 (t) cc_final: 0.8120 (p) REVERT: E 261 GLU cc_start: 0.2784 (mp0) cc_final: 0.2299 (pm20) REVERT: E 277 MET cc_start: 0.7147 (mmt) cc_final: 0.6695 (mmt) REVERT: E 281 MET cc_start: 0.7004 (ptt) cc_final: 0.6663 (ptt) REVERT: E 313 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6234 (tt0) REVERT: E 342 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7670 (mm-30) REVERT: E 349 PHE cc_start: 0.8513 (t80) cc_final: 0.8312 (t80) REVERT: E 358 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7796 (pttt) REVERT: E 359 LEU cc_start: 0.8368 (mm) cc_final: 0.8129 (mm) REVERT: E 361 GLU cc_start: 0.7304 (pp20) cc_final: 0.6837 (pp20) REVERT: E 367 PHE cc_start: 0.8630 (m-10) cc_final: 0.8393 (m-10) REVERT: E 371 TYR cc_start: 0.8101 (p90) cc_final: 0.7445 (p90) REVERT: E 385 ASN cc_start: 0.7811 (p0) cc_final: 0.7236 (t0) REVERT: E 397 ARG cc_start: 0.3908 (OUTLIER) cc_final: 0.3358 (ttt180) REVERT: E 412 ARG cc_start: 0.8237 (ttt180) cc_final: 0.7859 (ttt90) REVERT: E 428 TRP cc_start: 0.7382 (t-100) cc_final: 0.6943 (t-100) REVERT: E 452 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7513 (mttt) REVERT: E 454 ASN cc_start: 0.7759 (t0) cc_final: 0.7378 (t0) REVERT: E 485 GLN cc_start: 0.7931 (mt0) cc_final: 0.7633 (mt0) REVERT: E 498 GLN cc_start: 0.8235 (tp40) cc_final: 0.7944 (tm-30) REVERT: E 506 GLU cc_start: 0.7697 (pt0) cc_final: 0.6899 (pt0) REVERT: E 526 LYS cc_start: 0.7414 (mttp) cc_final: 0.7155 (mmtp) REVERT: E 534 LEU cc_start: 0.8213 (mt) cc_final: 0.8000 (mm) REVERT: E 542 GLN cc_start: 0.8519 (mp10) cc_final: 0.8188 (mm-40) REVERT: E 596 LEU cc_start: 0.7434 (mt) cc_final: 0.6793 (pp) REVERT: E 624 LYS cc_start: 0.8026 (tttm) cc_final: 0.7467 (ttmt) REVERT: E 671 GLN cc_start: 0.8459 (tt0) cc_final: 0.8203 (mm110) REVERT: E 672 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 687 SER cc_start: 0.8373 (t) cc_final: 0.7565 (t) REVERT: E 689 GLU cc_start: 0.7229 (mp0) cc_final: 0.6641 (mp0) outliers start: 193 outliers final: 124 residues processed: 1174 average time/residue: 0.2770 time to fit residues: 516.1073 Evaluate side-chains 1211 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1049 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain G residue 175 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 470 HIS Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 526 LYS Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 554 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 333 MET Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 458 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 57 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 354 optimal weight: 1.9990 chunk 369 optimal weight: 0.9980 chunk 348 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 277 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 175 GLN F 502 ASN ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 GLN B 815 HIS C 190 GLN ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** C 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 HIS ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS ** I 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.178287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134359 restraints weight = 65279.083| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.00 r_work: 0.3426 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 40254 Z= 0.170 Angle : 0.641 10.787 54663 Z= 0.318 Chirality : 0.045 0.391 6003 Planarity : 0.005 0.055 7119 Dihedral : 4.938 55.221 5410 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.42 % Allowed : 26.38 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.12), residues: 4821 helix: 1.31 (0.13), residues: 1653 sheet: -0.92 (0.21), residues: 588 loop : -1.12 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 357 TYR 0.029 0.001 TYR D 621 PHE 0.036 0.001 PHE G 349 TRP 0.020 0.001 TRP E 428 HIS 0.010 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00389 (40248) covalent geometry : angle 0.64139 (54651) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.99909 ( 12) hydrogen bonds : bond 0.03693 ( 1506) hydrogen bonds : angle 4.80540 ( 4185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1070 time to evaluate : 1.605 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: 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 74 GLU cc_start: 0.7314 (mp0) cc_final: 0.7104 (mp0) REVERT: A 78 TYR cc_start: 0.8590 (m-80) cc_final: 0.8087 (m-80) REVERT: A 81 LYS cc_start: 0.7973 (tttt) cc_final: 0.7738 (tttt) REVERT: A 133 SER cc_start: 0.8383 (p) cc_final: 0.8160 (m) REVERT: A 283 GLU cc_start: 0.7972 (pt0) cc_final: 0.7608 (pm20) REVERT: A 379 MET cc_start: 0.7910 (mpp) cc_final: 0.7627 (mpp) REVERT: A 521 MET cc_start: 0.8742 (mmp) cc_final: 0.8459 (mmm) REVERT: A 562 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8298 (mmmm) REVERT: A 805 ASP cc_start: 0.8011 (t0) cc_final: 0.7525 (t0) REVERT: A 860 ARG cc_start: 0.8563 (ptm160) cc_final: 0.8210 (mtm180) REVERT: A 903 ASP cc_start: 0.7570 (p0) cc_final: 0.6834 (p0) REVERT: A 904 GLU cc_start: 0.8233 (pt0) cc_final: 0.7974 (pm20) REVERT: G 187 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7069 (mmm-85) REVERT: G 287 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7417 (tpp80) REVERT: G 290 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7711 (mtp85) REVERT: G 293 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6157 (tm-30) REVERT: G 332 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7645 (pp) REVERT: G 333 MET cc_start: 0.7716 (ptm) cc_final: 0.7368 (ptm) REVERT: G 334 MET cc_start: 0.7393 (tmm) cc_final: 0.7049 (tmm) REVERT: G 344 GLU cc_start: 0.8140 (tp30) cc_final: 0.7002 (tp30) REVERT: G 347 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8556 (tm-30) REVERT: G 352 ASP cc_start: 0.7586 (t0) cc_final: 0.7038 (t0) REVERT: G 354 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7077 (tm-30) REVERT: G 356 GLN cc_start: 0.7003 (pp30) cc_final: 0.6545 (pp30) REVERT: G 360 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: G 368 ARG cc_start: 0.6882 (ttt-90) cc_final: 0.6423 (tpt170) REVERT: G 408 LYS cc_start: 0.7880 (tppt) cc_final: 0.7517 (tppt) REVERT: G 413 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: G 418 ASP cc_start: 0.7902 (t0) cc_final: 0.7570 (t0) REVERT: G 429 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: G 436 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7967 (tp-100) REVERT: G 450 LEU cc_start: 0.8277 (mt) cc_final: 0.8058 (mm) REVERT: G 454 ASN cc_start: 0.7812 (m110) cc_final: 0.7473 (p0) REVERT: G 458 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (mm) REVERT: G 464 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: G 465 ARG cc_start: 0.7668 (mmt90) cc_final: 0.7207 (mmt90) REVERT: G 471 LEU cc_start: 0.8667 (mt) cc_final: 0.8377 (mm) REVERT: G 488 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7241 (tm) REVERT: G 502 ASN cc_start: 0.8602 (t0) cc_final: 0.7831 (t0) REVERT: G 506 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7502 (mm-30) REVERT: G 528 ARG cc_start: 0.7436 (ptp-170) cc_final: 0.7187 (ptp-170) REVERT: G 546 TYR cc_start: 0.7737 (t80) cc_final: 0.7319 (t80) REVERT: F 167 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7041 (mt) REVERT: F 170 TYR cc_start: 0.7588 (m-80) cc_final: 0.6722 (t80) REVERT: F 277 MET cc_start: 0.7172 (mmt) cc_final: 0.6247 (mmt) REVERT: F 330 ARG cc_start: 0.6355 (ttm-80) cc_final: 0.6071 (mmt180) REVERT: F 346 MET cc_start: 0.8409 (mmt) cc_final: 0.7593 (mmt) REVERT: F 360 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7685 (mt-10) REVERT: F 362 THR cc_start: 0.8327 (t) cc_final: 0.8070 (m) REVERT: F 371 TYR cc_start: 0.8106 (p90) cc_final: 0.7607 (p90) REVERT: F 389 TYR cc_start: 0.7515 (t80) cc_final: 0.7111 (t80) REVERT: F 397 ARG cc_start: 0.3889 (OUTLIER) cc_final: 0.3160 (ttt180) REVERT: F 418 ASP cc_start: 0.7573 (t70) cc_final: 0.7132 (t70) REVERT: F 430 THR cc_start: 0.8398 (t) cc_final: 0.7801 (t) REVERT: F 464 GLU cc_start: 0.5815 (tm-30) cc_final: 0.5364 (tm-30) REVERT: F 501 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8327 (ttm110) REVERT: F 506 GLU cc_start: 0.7676 (pt0) cc_final: 0.6892 (pt0) REVERT: F 593 THR cc_start: 0.7862 (p) cc_final: 0.7229 (t) REVERT: F 595 GLU cc_start: 0.4174 (pm20) cc_final: 0.3628 (pm20) REVERT: F 617 TRP cc_start: 0.8188 (t60) cc_final: 0.7527 (t60) REVERT: F 668 LYS cc_start: 0.8256 (tptt) cc_final: 0.8020 (tptt) REVERT: F 672 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7333 (tm-30) REVERT: F 676 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: F 684 ASP cc_start: 0.8087 (t70) cc_final: 0.7645 (t70) REVERT: F 687 SER cc_start: 0.8637 (t) cc_final: 0.8084 (t) REVERT: B 148 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7339 (p) REVERT: B 157 MET cc_start: 0.7864 (tpp) cc_final: 0.7449 (tpp) REVERT: B 158 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7481 (tptp) REVERT: B 168 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 277 GLU cc_start: 0.7761 (tp30) cc_final: 0.7506 (tp30) REVERT: B 299 GLU cc_start: 0.7644 (tp30) cc_final: 0.7296 (tp30) REVERT: B 330 MET cc_start: 0.8464 (mmm) cc_final: 0.8129 (mmm) REVERT: B 358 ASN cc_start: 0.8489 (t0) cc_final: 0.8130 (t0) REVERT: B 379 MET cc_start: 0.8045 (mpp) cc_final: 0.7636 (mpp) REVERT: B 453 GLU cc_start: 0.7884 (pt0) cc_final: 0.7541 (pt0) REVERT: B 540 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7856 (mtm) REVERT: B 541 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8516 (tt) REVERT: B 562 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8254 (mmmm) REVERT: B 565 LEU cc_start: 0.6855 (mt) cc_final: 0.6434 (mm) REVERT: B 570 SER cc_start: 0.8563 (t) cc_final: 0.8218 (p) REVERT: B 580 ASP cc_start: 0.7945 (t0) cc_final: 0.7630 (t0) REVERT: B 601 SER cc_start: 0.8931 (t) cc_final: 0.8631 (p) REVERT: B 675 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 712 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7693 (ttmm) REVERT: B 735 PHE cc_start: 0.8231 (m-80) cc_final: 0.7880 (m-80) REVERT: B 738 LYS cc_start: 0.8359 (ptmm) cc_final: 0.8145 (ptmt) REVERT: B 762 MET cc_start: 0.8690 (mmm) cc_final: 0.8448 (mmm) REVERT: B 805 ASP cc_start: 0.7854 (t0) cc_final: 0.7203 (t0) REVERT: B 832 GLU cc_start: 0.8228 (pt0) cc_final: 0.7915 (pt0) REVERT: C 66 LEU cc_start: 0.8732 (mt) cc_final: 0.8295 (mp) REVERT: C 73 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7861 (ptp90) REVERT: C 81 LYS cc_start: 0.8200 (tttt) cc_final: 0.7769 (tttp) REVERT: C 96 MET cc_start: 0.8080 (tpt) cc_final: 0.7709 (tpt) REVERT: C 107 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8561 (tp) REVERT: C 148 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.7154 (p) REVERT: C 167 LEU cc_start: 0.7991 (tp) cc_final: 0.7683 (tt) REVERT: C 168 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 187 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8079 (ptpp) REVERT: C 213 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7721 (ptm160) REVERT: C 216 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7988 (mtmt) REVERT: C 254 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7685 (p) REVERT: C 279 VAL cc_start: 0.8758 (t) cc_final: 0.8493 (p) REVERT: C 299 GLU cc_start: 0.7507 (tp30) cc_final: 0.7158 (tp30) REVERT: C 330 MET cc_start: 0.8307 (mmm) cc_final: 0.7771 (mtt) REVERT: C 331 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 355 GLN cc_start: 0.4733 (OUTLIER) cc_final: 0.4452 (mt0) REVERT: C 365 LEU cc_start: 0.8784 (mt) cc_final: 0.8479 (mm) REVERT: C 379 MET cc_start: 0.7967 (mpp) cc_final: 0.7553 (mpp) REVERT: C 556 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: C 562 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8313 (mmmm) REVERT: C 573 TYR cc_start: 0.7534 (t80) cc_final: 0.7063 (t80) REVERT: C 574 GLU cc_start: 0.8001 (pm20) cc_final: 0.7727 (pm20) REVERT: C 611 PHE cc_start: 0.7764 (m-80) cc_final: 0.6892 (m-80) REVERT: C 712 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7894 (ttmm) REVERT: C 762 MET cc_start: 0.8313 (mmm) cc_final: 0.8029 (mmp) REVERT: C 805 ASP cc_start: 0.7848 (t0) cc_final: 0.7337 (t0) REVERT: C 806 TYR cc_start: 0.8581 (t80) cc_final: 0.7651 (t80) REVERT: C 828 MET cc_start: 0.7807 (ptt) cc_final: 0.7421 (ptt) REVERT: C 898 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 904 GLU cc_start: 0.8163 (pt0) cc_final: 0.7895 (pt0) REVERT: H 175 GLN cc_start: 0.8505 (tt0) cc_final: 0.8182 (tt0) REVERT: H 187 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.7250 (mmm-85) REVERT: H 290 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7400 (mmm-85) REVERT: H 314 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7017 (tt) REVERT: H 329 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7413 (tpt-90) REVERT: H 344 GLU cc_start: 0.8229 (tp30) cc_final: 0.7395 (tp30) REVERT: H 346 MET cc_start: 0.8458 (mtt) cc_final: 0.7840 (mmt) REVERT: H 356 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6520 (tm-30) REVERT: H 413 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6862 (ttm110) REVERT: H 419 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7521 (m) REVERT: H 444 LEU cc_start: 0.8380 (mm) cc_final: 0.7916 (mt) REVERT: H 464 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: H 465 ARG cc_start: 0.7536 (mmt90) cc_final: 0.7285 (tpt90) REVERT: H 470 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8107 (t-90) REVERT: H 471 LEU cc_start: 0.8481 (mt) cc_final: 0.8248 (mm) REVERT: H 488 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7193 (tm) REVERT: H 500 PHE cc_start: 0.8659 (t80) cc_final: 0.8258 (t80) REVERT: H 502 ASN cc_start: 0.8647 (t0) cc_final: 0.7904 (t0) REVERT: H 506 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7398 (mm-30) REVERT: D 167 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6770 (mp) REVERT: D 186 ASN cc_start: 0.7057 (t160) cc_final: 0.6763 (t0) REVERT: D 197 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5643 (ptp-170) REVERT: D 253 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8191 (mt) REVERT: D 277 MET cc_start: 0.7386 (mmt) cc_final: 0.6545 (mmt) REVERT: D 313 GLN cc_start: 0.7623 (mm-40) cc_final: 0.6814 (tt0) REVERT: D 346 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8348 (mmp) REVERT: D 367 PHE cc_start: 0.8643 (m-10) cc_final: 0.8269 (m-10) REVERT: D 369 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6516 (tm-30) REVERT: D 412 ARG cc_start: 0.8453 (ttt90) cc_final: 0.8114 (ttt90) REVERT: D 416 VAL cc_start: 0.8267 (p) cc_final: 0.7953 (m) REVERT: D 439 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.4123 (tp) REVERT: D 485 GLN cc_start: 0.7922 (mt0) cc_final: 0.7512 (mt0) REVERT: D 496 MET cc_start: 0.8413 (ptp) cc_final: 0.8072 (ptt) REVERT: D 498 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 499 ASN cc_start: 0.8046 (t0) cc_final: 0.7794 (m-40) REVERT: D 501 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8476 (ttp-110) REVERT: D 503 PHE cc_start: 0.8311 (t80) cc_final: 0.7984 (t80) REVERT: D 507 ARG cc_start: 0.8426 (tpt90) cc_final: 0.7864 (tpm170) REVERT: D 526 LYS cc_start: 0.7627 (mttp) cc_final: 0.7116 (mmtp) REVERT: D 542 GLN cc_start: 0.8396 (mp10) cc_final: 0.7882 (mp10) REVERT: D 593 THR cc_start: 0.7802 (p) cc_final: 0.7569 (p) REVERT: D 594 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6772 (t80) REVERT: D 623 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.7157 (mtm110) REVERT: D 624 LYS cc_start: 0.7584 (ttpp) cc_final: 0.7256 (ttpt) REVERT: D 634 GLU cc_start: 0.6795 (pt0) cc_final: 0.6138 (pt0) REVERT: D 659 ILE cc_start: 0.7866 (tt) cc_final: 0.7605 (mt) REVERT: D 671 GLN cc_start: 0.8575 (tt0) cc_final: 0.8345 (tp40) REVERT: D 672 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 676 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: D 682 TYR cc_start: 0.8522 (m-80) cc_final: 0.8284 (m-80) REVERT: D 687 SER cc_start: 0.8670 (t) cc_final: 0.7973 (p) REVERT: I 283 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7456 (mm-30) REVERT: I 287 ARG cc_start: 0.7459 (ttm110) cc_final: 0.6825 (tpp80) REVERT: I 314 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7887 (tt) REVERT: I 329 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7094 (tpp80) REVERT: I 332 LEU cc_start: 0.7939 (tt) cc_final: 0.7377 (pp) REVERT: I 347 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: I 348 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7518 (mtt180) REVERT: I 350 PHE cc_start: 0.8601 (m-10) cc_final: 0.8379 (m-80) REVERT: I 361 GLU cc_start: 0.7320 (tt0) cc_final: 0.7073 (tp30) REVERT: I 368 ARG cc_start: 0.6432 (ttt-90) cc_final: 0.5937 (mmm-85) REVERT: I 419 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7590 (m) REVERT: I 445 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (mptp) REVERT: I 464 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: I 470 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7876 (t-90) REVERT: I 488 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6965 (tm) REVERT: I 500 PHE cc_start: 0.8563 (t80) cc_final: 0.8295 (t80) REVERT: I 502 ASN cc_start: 0.8562 (t0) cc_final: 0.7631 (t0) REVERT: I 506 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7404 (mm-30) REVERT: I 549 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7281 (t80) REVERT: E 167 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7127 (mt) REVERT: E 186 ASN cc_start: 0.6515 (t0) cc_final: 0.6293 (t0) REVERT: E 261 GLU cc_start: 0.3222 (mp0) cc_final: 0.2589 (pm20) REVERT: E 277 MET cc_start: 0.7140 (mmt) cc_final: 0.6676 (mmt) REVERT: E 281 MET cc_start: 0.7016 (ptt) cc_final: 0.6686 (ptt) REVERT: E 313 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6183 (tt0) REVERT: E 342 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 349 PHE cc_start: 0.8601 (t80) cc_final: 0.8396 (t80) REVERT: E 361 GLU cc_start: 0.7264 (pp20) cc_final: 0.6848 (pp20) REVERT: E 367 PHE cc_start: 0.8671 (m-10) cc_final: 0.8420 (m-10) REVERT: E 371 TYR cc_start: 0.8113 (p90) cc_final: 0.7442 (p90) REVERT: E 397 ARG cc_start: 0.3948 (OUTLIER) cc_final: 0.3375 (ttt180) REVERT: E 412 ARG cc_start: 0.8215 (ttt180) cc_final: 0.7836 (ttt90) REVERT: E 428 TRP cc_start: 0.7309 (t-100) cc_final: 0.6860 (t-100) REVERT: E 429 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8018 (mm-40) REVERT: E 452 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7545 (mttt) REVERT: E 454 ASN cc_start: 0.7751 (t0) cc_final: 0.7378 (t0) REVERT: E 498 GLN cc_start: 0.8208 (tp40) cc_final: 0.7892 (tm-30) REVERT: E 506 GLU cc_start: 0.7716 (pt0) cc_final: 0.6983 (pt0) REVERT: E 507 ARG cc_start: 0.8499 (tpm170) cc_final: 0.8218 (tpm170) REVERT: E 526 LYS cc_start: 0.7458 (mttp) cc_final: 0.7175 (mmtp) REVERT: E 534 LEU cc_start: 0.8179 (mt) cc_final: 0.7951 (mm) REVERT: E 624 LYS cc_start: 0.8051 (tttm) cc_final: 0.7489 (ttmt) REVERT: E 670 ARG cc_start: 0.7796 (tpp-160) cc_final: 0.6924 (mtt-85) REVERT: E 671 GLN cc_start: 0.8466 (tt0) cc_final: 0.8168 (mm110) REVERT: E 672 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7332 (tm-30) REVERT: E 689 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6970 (mp0) outliers start: 190 outliers final: 117 residues processed: 1183 average time/residue: 0.2749 time to fit residues: 513.2530 Evaluate side-chains 1223 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1064 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 429 GLN Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 526 LYS Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 333 MET Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 445 LYS Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 689 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 101 optimal weight: 3.9990 chunk 349 optimal weight: 4.9990 chunk 455 optimal weight: 4.9990 chunk 291 optimal weight: 0.3980 chunk 269 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 175 GLN ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 553 GLN B 815 HIS C 190 GLN C 511 ASN C 591 ASN ** C 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN H 436 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN I 264 HIS E 171 HIS E 347 GLN ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 662 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135017 restraints weight = 65546.972| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.02 r_work: 0.3441 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40254 Z= 0.141 Angle : 0.646 11.595 54663 Z= 0.317 Chirality : 0.044 0.466 6003 Planarity : 0.005 0.054 7119 Dihedral : 4.880 55.646 5410 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.18 % Allowed : 27.08 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.12), residues: 4821 helix: 1.32 (0.13), residues: 1653 sheet: -0.84 (0.21), residues: 588 loop : -1.11 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 357 TYR 0.031 0.001 TYR D 621 PHE 0.035 0.001 PHE G 349 TRP 0.026 0.001 TRP F 428 HIS 0.012 0.001 HIS D 550 Details of bonding type rmsd covalent geometry : bond 0.00326 (40248) covalent geometry : angle 0.64588 (54651) SS BOND : bond 0.00207 ( 6) SS BOND : angle 1.00836 ( 12) hydrogen bonds : bond 0.03545 ( 1506) hydrogen bonds : angle 4.77826 ( 4185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1071 time to evaluate : 1.528 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: 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 74 GLU cc_start: 0.7305 (mp0) cc_final: 0.7080 (mp0) REVERT: A 78 TYR cc_start: 0.8576 (m-80) cc_final: 0.8118 (m-80) REVERT: A 81 LYS cc_start: 0.8017 (tttt) cc_final: 0.7797 (tttt) REVERT: A 133 SER cc_start: 0.8433 (p) cc_final: 0.8203 (m) REVERT: A 283 GLU cc_start: 0.7968 (pt0) cc_final: 0.7602 (pm20) REVERT: A 338 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5975 (mtp) REVERT: A 379 MET cc_start: 0.8009 (mpp) cc_final: 0.7800 (mpp) REVERT: A 521 MET cc_start: 0.8710 (mmp) cc_final: 0.8397 (mmm) REVERT: A 541 LEU cc_start: 0.8750 (tp) cc_final: 0.8517 (tt) REVERT: A 574 GLU cc_start: 0.7824 (pm20) cc_final: 0.7270 (pm20) REVERT: A 805 ASP cc_start: 0.8021 (t0) cc_final: 0.7540 (t0) REVERT: A 860 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8165 (mtm180) REVERT: A 903 ASP cc_start: 0.7554 (p0) cc_final: 0.6893 (p0) REVERT: A 904 GLU cc_start: 0.8232 (pt0) cc_final: 0.8000 (pm20) REVERT: G 187 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.7035 (mmm-85) REVERT: G 287 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7426 (tpp80) REVERT: G 290 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7752 (mtp85) REVERT: G 293 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6175 (tm-30) REVERT: G 332 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7472 (pp) REVERT: G 333 MET cc_start: 0.7699 (ptm) cc_final: 0.7366 (ptm) REVERT: G 334 MET cc_start: 0.7392 (tmm) cc_final: 0.7023 (tmm) REVERT: G 344 GLU cc_start: 0.8137 (tp30) cc_final: 0.6996 (tp30) REVERT: G 347 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8561 (tm-30) REVERT: G 352 ASP cc_start: 0.7614 (t0) cc_final: 0.7100 (t0) REVERT: G 354 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7207 (tm-30) REVERT: G 356 GLN cc_start: 0.6965 (pp30) cc_final: 0.6453 (pp30) REVERT: G 357 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7669 (mtp-110) REVERT: G 360 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: G 368 ARG cc_start: 0.6900 (ttt-90) cc_final: 0.6398 (tpt170) REVERT: G 408 LYS cc_start: 0.7871 (tppt) cc_final: 0.7521 (tppt) REVERT: G 418 ASP cc_start: 0.7905 (t0) cc_final: 0.7574 (t0) REVERT: G 429 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: G 436 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7913 (tp-100) REVERT: G 450 LEU cc_start: 0.8278 (mt) cc_final: 0.8051 (mm) REVERT: G 454 ASN cc_start: 0.7877 (m110) cc_final: 0.7486 (p0) REVERT: G 458 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7485 (mm) REVERT: G 465 ARG cc_start: 0.7726 (mmt90) cc_final: 0.7295 (mmt-90) REVERT: G 471 LEU cc_start: 0.8656 (mt) cc_final: 0.8416 (mm) REVERT: G 486 GLN cc_start: 0.7963 (mm110) cc_final: 0.7008 (mm110) REVERT: G 488 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7248 (tm) REVERT: G 502 ASN cc_start: 0.8583 (t0) cc_final: 0.7844 (t0) REVERT: G 506 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 528 ARG cc_start: 0.7436 (ptp-170) cc_final: 0.6685 (ptm-80) REVERT: G 546 TYR cc_start: 0.7723 (t80) cc_final: 0.7298 (t80) REVERT: F 167 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.6959 (mp) REVERT: F 170 TYR cc_start: 0.7587 (m-80) cc_final: 0.6733 (t80) REVERT: F 277 MET cc_start: 0.7097 (mmt) cc_final: 0.6216 (mmt) REVERT: F 330 ARG cc_start: 0.6299 (ttm-80) cc_final: 0.6026 (mmt180) REVERT: F 346 MET cc_start: 0.8118 (mmt) cc_final: 0.7500 (mmt) REVERT: F 360 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7689 (mt-10) REVERT: F 389 TYR cc_start: 0.7485 (t80) cc_final: 0.7091 (t80) REVERT: F 397 ARG cc_start: 0.3918 (OUTLIER) cc_final: 0.3195 (ttt180) REVERT: F 418 ASP cc_start: 0.7550 (t70) cc_final: 0.7029 (t70) REVERT: F 464 GLU cc_start: 0.5813 (tm-30) cc_final: 0.5362 (tm-30) REVERT: F 501 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8184 (ttm110) REVERT: F 506 GLU cc_start: 0.7686 (pt0) cc_final: 0.6842 (pt0) REVERT: F 617 TRP cc_start: 0.8127 (t60) cc_final: 0.7515 (t60) REVERT: F 668 LYS cc_start: 0.8242 (tptt) cc_final: 0.8008 (tptt) REVERT: F 672 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 676 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8055 (ttm-80) REVERT: F 684 ASP cc_start: 0.7998 (t70) cc_final: 0.7553 (t0) REVERT: F 687 SER cc_start: 0.8666 (t) cc_final: 0.8167 (t) REVERT: B 148 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7376 (p) REVERT: B 157 MET cc_start: 0.7886 (tpp) cc_final: 0.7532 (tpp) REVERT: B 158 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7665 (tptm) REVERT: B 168 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7209 (tm-30) REVERT: B 277 GLU cc_start: 0.7753 (tp30) cc_final: 0.7488 (tp30) REVERT: B 299 GLU cc_start: 0.7649 (tp30) cc_final: 0.7344 (tp30) REVERT: B 330 MET cc_start: 0.8465 (mmm) cc_final: 0.8109 (mmm) REVERT: B 358 ASN cc_start: 0.8387 (t0) cc_final: 0.8095 (t0) REVERT: B 379 MET cc_start: 0.8017 (mpp) cc_final: 0.7608 (mpp) REVERT: B 453 GLU cc_start: 0.7955 (pt0) cc_final: 0.7620 (pt0) REVERT: B 541 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 562 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8255 (mmmm) REVERT: B 565 LEU cc_start: 0.6816 (mt) cc_final: 0.6416 (mm) REVERT: B 570 SER cc_start: 0.8568 (t) cc_final: 0.8221 (p) REVERT: B 580 ASP cc_start: 0.7858 (t0) cc_final: 0.7564 (t0) REVERT: B 601 SER cc_start: 0.8912 (t) cc_final: 0.8615 (p) REVERT: B 675 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 712 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7685 (ttmm) REVERT: B 735 PHE cc_start: 0.8247 (m-80) cc_final: 0.7938 (m-80) REVERT: B 738 LYS cc_start: 0.8287 (ptmm) cc_final: 0.8062 (ptmt) REVERT: B 762 MET cc_start: 0.8665 (mmm) cc_final: 0.8436 (mmm) REVERT: B 805 ASP cc_start: 0.7848 (t0) cc_final: 0.7285 (t0) REVERT: B 828 MET cc_start: 0.7216 (ptt) cc_final: 0.6985 (ptt) REVERT: B 832 GLU cc_start: 0.8223 (pt0) cc_final: 0.7906 (pt0) REVERT: B 904 GLU cc_start: 0.8269 (pt0) cc_final: 0.7879 (pm20) REVERT: C 66 LEU cc_start: 0.8719 (mt) cc_final: 0.8294 (mp) REVERT: C 73 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7899 (ptp90) REVERT: C 81 LYS cc_start: 0.8190 (tttt) cc_final: 0.7816 (tttp) REVERT: C 96 MET cc_start: 0.8041 (tpt) cc_final: 0.7636 (tpt) REVERT: C 107 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8548 (tp) REVERT: C 135 TRP cc_start: 0.8590 (p90) cc_final: 0.8336 (p90) REVERT: C 148 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7172 (p) REVERT: C 154 ILE cc_start: 0.8390 (mt) cc_final: 0.8189 (mm) REVERT: C 167 LEU cc_start: 0.8011 (tp) cc_final: 0.7709 (tt) REVERT: C 168 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 213 ARG cc_start: 0.8089 (ptp-170) cc_final: 0.7675 (ptm160) REVERT: C 254 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7731 (p) REVERT: C 279 VAL cc_start: 0.8767 (t) cc_final: 0.8526 (p) REVERT: C 299 GLU cc_start: 0.7525 (tp30) cc_final: 0.7227 (tp30) REVERT: C 330 MET cc_start: 0.8257 (mmm) cc_final: 0.7756 (mtt) REVERT: C 331 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 355 GLN cc_start: 0.4737 (OUTLIER) cc_final: 0.4444 (mt0) REVERT: C 365 LEU cc_start: 0.8748 (mt) cc_final: 0.8448 (mm) REVERT: C 379 MET cc_start: 0.7955 (mpp) cc_final: 0.7539 (mpp) REVERT: C 556 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: C 562 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8302 (mmmm) REVERT: C 564 LEU cc_start: 0.8314 (tp) cc_final: 0.8088 (tt) REVERT: C 574 GLU cc_start: 0.7963 (pm20) cc_final: 0.7736 (pm20) REVERT: C 611 PHE cc_start: 0.7717 (m-80) cc_final: 0.6820 (m-80) REVERT: C 644 MET cc_start: 0.8387 (mtm) cc_final: 0.7843 (mtm) REVERT: C 712 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7883 (ttmm) REVERT: C 762 MET cc_start: 0.8392 (mmm) cc_final: 0.8041 (mmp) REVERT: C 805 ASP cc_start: 0.7845 (t0) cc_final: 0.7343 (t0) REVERT: C 898 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 904 GLU cc_start: 0.8162 (pt0) cc_final: 0.7910 (pt0) REVERT: H 175 GLN cc_start: 0.8483 (tt0) cc_final: 0.8187 (tt0) REVERT: H 187 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7219 (mmm-85) REVERT: H 252 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: H 257 LYS cc_start: 0.7489 (mttm) cc_final: 0.7188 (mmmt) REVERT: H 283 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7002 (mm-30) REVERT: H 290 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7399 (mmm-85) REVERT: H 314 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7045 (tt) REVERT: H 329 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7591 (tpt-90) REVERT: H 344 GLU cc_start: 0.8211 (tp30) cc_final: 0.7351 (tp30) REVERT: H 346 MET cc_start: 0.8442 (mtt) cc_final: 0.7832 (mmt) REVERT: H 356 GLN cc_start: 0.7148 (tm-30) cc_final: 0.6570 (tm-30) REVERT: H 413 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6833 (ttm110) REVERT: H 419 CYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7518 (m) REVERT: H 444 LEU cc_start: 0.8380 (mm) cc_final: 0.7902 (mt) REVERT: H 445 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7713 (mptp) REVERT: H 448 GLN cc_start: 0.8214 (mt0) cc_final: 0.7990 (mm-40) REVERT: H 464 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: H 470 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8124 (t-90) REVERT: H 471 LEU cc_start: 0.8468 (mt) cc_final: 0.8261 (mm) REVERT: H 488 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7209 (tm) REVERT: H 500 PHE cc_start: 0.8623 (t80) cc_final: 0.8249 (t80) REVERT: H 502 ASN cc_start: 0.8642 (t0) cc_final: 0.7919 (t0) REVERT: H 506 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7372 (mm-30) REVERT: D 167 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6777 (mp) REVERT: D 186 ASN cc_start: 0.7071 (t160) cc_final: 0.6795 (t0) REVERT: D 188 SER cc_start: 0.8308 (p) cc_final: 0.7853 (m) REVERT: D 253 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8175 (mt) REVERT: D 277 MET cc_start: 0.7387 (mmt) cc_final: 0.6559 (mmt) REVERT: D 313 GLN cc_start: 0.7467 (mm-40) cc_final: 0.6640 (tt0) REVERT: D 346 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8283 (mmp) REVERT: D 349 PHE cc_start: 0.8542 (t80) cc_final: 0.8240 (t80) REVERT: D 362 THR cc_start: 0.8361 (t) cc_final: 0.8129 (m) REVERT: D 367 PHE cc_start: 0.8632 (m-10) cc_final: 0.8281 (m-10) REVERT: D 369 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6535 (tm-30) REVERT: D 412 ARG cc_start: 0.8442 (ttt90) cc_final: 0.8116 (ttt90) REVERT: D 416 VAL cc_start: 0.8278 (p) cc_final: 0.7979 (m) REVERT: D 439 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.4030 (tp) REVERT: D 454 ASN cc_start: 0.8017 (m-40) cc_final: 0.7654 (m-40) REVERT: D 485 GLN cc_start: 0.7863 (mt0) cc_final: 0.7501 (mt0) REVERT: D 496 MET cc_start: 0.8371 (ptp) cc_final: 0.8043 (ptt) REVERT: D 498 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 499 ASN cc_start: 0.7997 (t0) cc_final: 0.7747 (m-40) REVERT: D 503 PHE cc_start: 0.8305 (t80) cc_final: 0.7874 (t80) REVERT: D 507 ARG cc_start: 0.8409 (tpt90) cc_final: 0.7842 (tpm170) REVERT: D 526 LYS cc_start: 0.7604 (mttp) cc_final: 0.7381 (mmtp) REVERT: D 593 THR cc_start: 0.7853 (p) cc_final: 0.7642 (p) REVERT: D 594 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6676 (t80) REVERT: D 623 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7148 (mtm110) REVERT: D 624 LYS cc_start: 0.7594 (ttpp) cc_final: 0.7259 (ttpt) REVERT: D 634 GLU cc_start: 0.6865 (pt0) cc_final: 0.6216 (pt0) REVERT: D 671 GLN cc_start: 0.8573 (tt0) cc_final: 0.8341 (tp40) REVERT: D 672 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7309 (tm-30) REVERT: D 676 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8010 (ttm-80) REVERT: D 682 TYR cc_start: 0.8511 (m-80) cc_final: 0.8260 (m-80) REVERT: D 687 SER cc_start: 0.8666 (t) cc_final: 0.7981 (p) REVERT: I 275 LYS cc_start: 0.7049 (mttm) cc_final: 0.6810 (mmmm) REVERT: I 283 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7481 (mm-30) REVERT: I 287 ARG cc_start: 0.7462 (ttm110) cc_final: 0.6859 (tpp80) REVERT: I 292 LEU cc_start: 0.8168 (tp) cc_final: 0.7746 (pp) REVERT: I 314 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7885 (tt) REVERT: I 329 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7129 (tpp80) REVERT: I 332 LEU cc_start: 0.7949 (tt) cc_final: 0.7379 (pp) REVERT: I 347 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: I 348 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7564 (mtt180) REVERT: I 350 PHE cc_start: 0.8577 (m-10) cc_final: 0.8349 (m-80) REVERT: I 361 GLU cc_start: 0.7305 (tt0) cc_final: 0.7057 (tp30) REVERT: I 419 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7617 (m) REVERT: I 464 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: I 488 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6964 (tm) REVERT: I 500 PHE cc_start: 0.8550 (t80) cc_final: 0.8259 (t80) REVERT: I 502 ASN cc_start: 0.8550 (t0) cc_final: 0.7649 (t0) REVERT: I 506 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7406 (mm-30) REVERT: I 528 ARG cc_start: 0.6844 (ptp-170) cc_final: 0.6229 (ptt-90) REVERT: I 549 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7263 (t80) REVERT: E 167 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7126 (mt) REVERT: E 186 ASN cc_start: 0.6552 (t0) cc_final: 0.6285 (t0) REVERT: E 277 MET cc_start: 0.7097 (mmt) cc_final: 0.6607 (mmt) REVERT: E 281 MET cc_start: 0.6938 (ptt) cc_final: 0.6578 (ptt) REVERT: E 313 GLN cc_start: 0.7023 (mm-40) cc_final: 0.6182 (tt0) REVERT: E 342 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 349 PHE cc_start: 0.8595 (t80) cc_final: 0.8217 (t80) REVERT: E 358 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7784 (pttt) REVERT: E 359 LEU cc_start: 0.8325 (mm) cc_final: 0.8091 (mm) REVERT: E 361 GLU cc_start: 0.7296 (pp20) cc_final: 0.6863 (pp20) REVERT: E 367 PHE cc_start: 0.8666 (m-10) cc_final: 0.8457 (m-10) REVERT: E 397 ARG cc_start: 0.3934 (OUTLIER) cc_final: 0.3362 (ttt180) REVERT: E 410 GLU cc_start: 0.6962 (tp30) cc_final: 0.6271 (tp30) REVERT: E 412 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7842 (ttt90) REVERT: E 428 TRP cc_start: 0.7272 (t-100) cc_final: 0.6867 (t-100) REVERT: E 429 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7943 (mm-40) REVERT: E 452 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7602 (mttt) REVERT: E 454 ASN cc_start: 0.7890 (t0) cc_final: 0.7540 (t0) REVERT: E 498 GLN cc_start: 0.8205 (tp40) cc_final: 0.7897 (tm-30) REVERT: E 506 GLU cc_start: 0.7693 (pt0) cc_final: 0.6956 (pt0) REVERT: E 526 LYS cc_start: 0.7462 (mttp) cc_final: 0.7190 (mmtp) REVERT: E 530 CYS cc_start: 0.7944 (t) cc_final: 0.7659 (p) REVERT: E 542 GLN cc_start: 0.8548 (mp10) cc_final: 0.8225 (mm-40) REVERT: E 624 LYS cc_start: 0.8036 (tttm) cc_final: 0.7474 (ttmt) REVERT: E 662 GLN cc_start: 0.7490 (pt0) cc_final: 0.7227 (pm20) REVERT: E 670 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7013 (tpp80) REVERT: E 671 GLN cc_start: 0.8462 (tt0) cc_final: 0.8203 (mm110) REVERT: E 672 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 689 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6964 (mp0) outliers start: 180 outliers final: 122 residues processed: 1174 average time/residue: 0.2682 time to fit residues: 496.5418 Evaluate side-chains 1220 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1059 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 429 GLN Chi-restraints excluded: chain G residue 432 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 333 MET Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 464 GLU Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 689 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 44 optimal weight: 0.1980 chunk 401 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 460 optimal weight: 6.9990 chunk 430 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 482 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 438 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN F 171 HIS F 186 ASN F 537 HIS ** F 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 553 GLN ** B 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 815 HIS C 190 GLN C 591 ASN ** C 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.178986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135557 restraints weight = 65189.301| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.97 r_work: 0.3438 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40254 Z= 0.145 Angle : 0.660 11.570 54663 Z= 0.324 Chirality : 0.045 0.415 6003 Planarity : 0.005 0.130 7119 Dihedral : 4.877 55.598 5410 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.81 % Allowed : 27.80 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.12), residues: 4821 helix: 1.33 (0.13), residues: 1653 sheet: -0.81 (0.21), residues: 588 loop : -1.11 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 465 TYR 0.029 0.001 TYR D 621 PHE 0.032 0.001 PHE G 349 TRP 0.051 0.002 TRP F 428 HIS 0.010 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00336 (40248) covalent geometry : angle 0.66027 (54651) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.97846 ( 12) hydrogen bonds : bond 0.03559 ( 1506) hydrogen bonds : angle 4.77575 ( 4185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9642 Ramachandran restraints generated. 4821 Oldfield, 0 Emsley, 4821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1063 time to evaluate : 1.286 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: 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 74 GLU cc_start: 0.7303 (mp0) cc_final: 0.7069 (mp0) REVERT: A 78 TYR cc_start: 0.8569 (m-80) cc_final: 0.8066 (m-80) REVERT: A 81 LYS cc_start: 0.8011 (tttt) cc_final: 0.7752 (tttt) REVERT: A 133 SER cc_start: 0.8438 (p) cc_final: 0.8206 (m) REVERT: A 198 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5210 (mp0) REVERT: A 283 GLU cc_start: 0.7973 (pt0) cc_final: 0.7591 (pm20) REVERT: A 338 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5977 (mtp) REVERT: A 379 MET cc_start: 0.8023 (mpp) cc_final: 0.7811 (mpp) REVERT: A 521 MET cc_start: 0.8691 (mmp) cc_final: 0.8382 (mmm) REVERT: A 734 GLU cc_start: 0.7955 (pm20) cc_final: 0.7686 (pm20) REVERT: A 805 ASP cc_start: 0.8027 (t0) cc_final: 0.7541 (t0) REVERT: A 860 ARG cc_start: 0.8517 (ptm160) cc_final: 0.8172 (mtm180) REVERT: A 895 MET cc_start: 0.8536 (mtt) cc_final: 0.8164 (mtm) REVERT: A 903 ASP cc_start: 0.7533 (p0) cc_final: 0.6899 (p0) REVERT: A 904 GLU cc_start: 0.8241 (pt0) cc_final: 0.7889 (pm20) REVERT: G 187 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7017 (mmm-85) REVERT: G 287 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7435 (tpp80) REVERT: G 290 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7775 (mtp85) REVERT: G 293 GLU cc_start: 0.6542 (tm-30) cc_final: 0.6178 (tm-30) REVERT: G 332 LEU cc_start: 0.8014 (tt) cc_final: 0.7481 (pp) REVERT: G 333 MET cc_start: 0.7693 (ptm) cc_final: 0.7370 (ptm) REVERT: G 334 MET cc_start: 0.7390 (tmm) cc_final: 0.7003 (tmm) REVERT: G 344 GLU cc_start: 0.8136 (tp30) cc_final: 0.6995 (tp30) REVERT: G 347 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8558 (tm-30) REVERT: G 352 ASP cc_start: 0.7634 (t0) cc_final: 0.7123 (t0) REVERT: G 354 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6983 (tm-30) REVERT: G 356 GLN cc_start: 0.6973 (pp30) cc_final: 0.6462 (pp30) REVERT: G 357 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7606 (ttp80) REVERT: G 360 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: G 408 LYS cc_start: 0.7870 (tppt) cc_final: 0.7525 (tppt) REVERT: G 413 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7168 (mtm-85) REVERT: G 418 ASP cc_start: 0.7914 (t0) cc_final: 0.7583 (t0) REVERT: G 429 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: G 436 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7903 (tp-100) REVERT: G 450 LEU cc_start: 0.8273 (mt) cc_final: 0.8044 (mm) REVERT: G 454 ASN cc_start: 0.7867 (m110) cc_final: 0.7476 (p0) REVERT: G 458 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7461 (mm) REVERT: G 465 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7186 (mmt90) REVERT: G 471 LEU cc_start: 0.8655 (mt) cc_final: 0.8425 (mm) REVERT: G 486 GLN cc_start: 0.7963 (mm110) cc_final: 0.7005 (mm110) REVERT: G 488 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7260 (tm) REVERT: G 502 ASN cc_start: 0.8583 (t0) cc_final: 0.7855 (t0) REVERT: G 506 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7577 (mm-30) REVERT: G 528 ARG cc_start: 0.7447 (ptp-170) cc_final: 0.6748 (ptp-170) REVERT: G 546 TYR cc_start: 0.7700 (t80) cc_final: 0.7235 (t80) REVERT: F 167 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6978 (mp) REVERT: F 170 TYR cc_start: 0.7543 (m-80) cc_final: 0.6701 (t80) REVERT: F 277 MET cc_start: 0.7105 (mmt) cc_final: 0.6231 (mmt) REVERT: F 330 ARG cc_start: 0.6324 (ttm-80) cc_final: 0.6048 (mmt180) REVERT: F 346 MET cc_start: 0.7882 (mmt) cc_final: 0.7213 (mmt) REVERT: F 360 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7669 (mt-10) REVERT: F 389 TYR cc_start: 0.7475 (t80) cc_final: 0.7085 (t80) REVERT: F 397 ARG cc_start: 0.3970 (OUTLIER) cc_final: 0.3259 (ttt180) REVERT: F 418 ASP cc_start: 0.7556 (t70) cc_final: 0.7037 (t70) REVERT: F 464 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5359 (tm-30) REVERT: F 501 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8175 (ttm110) REVERT: F 506 GLU cc_start: 0.7687 (pt0) cc_final: 0.6900 (pt0) REVERT: F 593 THR cc_start: 0.7944 (p) cc_final: 0.7118 (p) REVERT: F 617 TRP cc_start: 0.8111 (t60) cc_final: 0.7511 (t60) REVERT: F 668 LYS cc_start: 0.8247 (tptt) cc_final: 0.8008 (tptt) REVERT: F 672 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7330 (tm-30) REVERT: F 676 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8029 (ttm-80) REVERT: F 684 ASP cc_start: 0.8000 (t70) cc_final: 0.7544 (t0) REVERT: F 687 SER cc_start: 0.8666 (t) cc_final: 0.8179 (t) REVERT: B 117 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8644 (m) REVERT: B 148 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7413 (p) REVERT: B 150 ASN cc_start: 0.8441 (m-40) cc_final: 0.8239 (m110) REVERT: B 157 MET cc_start: 0.7885 (tpp) cc_final: 0.7525 (tpp) REVERT: B 158 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7562 (tptm) REVERT: B 168 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 186 ASP cc_start: 0.7590 (t0) cc_final: 0.7099 (t0) REVERT: B 277 GLU cc_start: 0.7750 (tp30) cc_final: 0.7492 (tp30) REVERT: B 299 GLU cc_start: 0.7634 (tp30) cc_final: 0.7346 (tp30) REVERT: B 330 MET cc_start: 0.8463 (mmm) cc_final: 0.8104 (mmm) REVERT: B 358 ASN cc_start: 0.8373 (t0) cc_final: 0.8074 (t0) REVERT: B 379 MET cc_start: 0.8005 (mpp) cc_final: 0.7587 (mpp) REVERT: B 453 GLU cc_start: 0.7873 (pt0) cc_final: 0.7529 (pt0) REVERT: B 541 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (tt) REVERT: B 562 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8272 (mmmm) REVERT: B 565 LEU cc_start: 0.6809 (mt) cc_final: 0.6408 (mm) REVERT: B 570 SER cc_start: 0.8575 (t) cc_final: 0.8228 (p) REVERT: B 580 ASP cc_start: 0.7849 (t0) cc_final: 0.7551 (t0) REVERT: B 601 SER cc_start: 0.8910 (t) cc_final: 0.8612 (p) REVERT: B 675 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 712 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7683 (ttmm) REVERT: B 735 PHE cc_start: 0.8249 (m-80) cc_final: 0.7940 (m-80) REVERT: B 738 LYS cc_start: 0.8298 (ptmm) cc_final: 0.8071 (ptmt) REVERT: B 762 MET cc_start: 0.8666 (mmm) cc_final: 0.8430 (mmm) REVERT: B 805 ASP cc_start: 0.7825 (t0) cc_final: 0.7257 (t0) REVERT: B 828 MET cc_start: 0.7224 (ptt) cc_final: 0.6976 (ptt) REVERT: B 832 GLU cc_start: 0.8234 (pt0) cc_final: 0.7894 (pt0) REVERT: B 904 GLU cc_start: 0.8251 (pt0) cc_final: 0.7865 (pm20) REVERT: C 66 LEU cc_start: 0.8718 (mt) cc_final: 0.8293 (mp) REVERT: C 73 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7899 (ptp90) REVERT: C 81 LYS cc_start: 0.8176 (tttt) cc_final: 0.7807 (tttp) REVERT: C 96 MET cc_start: 0.8044 (tpt) cc_final: 0.7627 (tpt) REVERT: C 107 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8553 (tp) REVERT: C 135 TRP cc_start: 0.8590 (p90) cc_final: 0.8333 (p90) REVERT: C 148 THR cc_start: 0.7440 (OUTLIER) cc_final: 0.7163 (p) REVERT: C 167 LEU cc_start: 0.8031 (tp) cc_final: 0.7729 (tt) REVERT: C 168 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 213 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7662 (ptm160) REVERT: C 254 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7750 (p) REVERT: C 279 VAL cc_start: 0.8765 (t) cc_final: 0.8525 (p) REVERT: C 299 GLU cc_start: 0.7529 (tp30) cc_final: 0.7251 (tp30) REVERT: C 330 MET cc_start: 0.8307 (mmm) cc_final: 0.7765 (mtt) REVERT: C 331 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 365 LEU cc_start: 0.8748 (mt) cc_final: 0.8447 (mm) REVERT: C 379 MET cc_start: 0.7938 (mpp) cc_final: 0.7519 (mpp) REVERT: C 556 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: C 562 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8280 (mmmm) REVERT: C 564 LEU cc_start: 0.8313 (tp) cc_final: 0.8082 (tt) REVERT: C 574 GLU cc_start: 0.7870 (pm20) cc_final: 0.7659 (pm20) REVERT: C 611 PHE cc_start: 0.7713 (m-80) cc_final: 0.6812 (m-80) REVERT: C 644 MET cc_start: 0.8399 (mtm) cc_final: 0.7842 (mtm) REVERT: C 712 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7887 (ttmm) REVERT: C 762 MET cc_start: 0.8316 (mmm) cc_final: 0.8028 (mmp) REVERT: C 805 ASP cc_start: 0.7854 (t0) cc_final: 0.7348 (t0) REVERT: C 898 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7316 (mm-30) REVERT: C 904 GLU cc_start: 0.8154 (pt0) cc_final: 0.7900 (pt0) REVERT: H 175 GLN cc_start: 0.8470 (tt0) cc_final: 0.8167 (tt0) REVERT: H 187 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7187 (mmm-85) REVERT: H 252 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7807 (ttp-110) REVERT: H 257 LYS cc_start: 0.7545 (mttm) cc_final: 0.7304 (mmmt) REVERT: H 283 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7219 (mm-30) REVERT: H 290 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7430 (mmm-85) REVERT: H 314 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7050 (tt) REVERT: H 329 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7465 (tpt-90) REVERT: H 344 GLU cc_start: 0.8353 (tp30) cc_final: 0.7342 (tp30) REVERT: H 346 MET cc_start: 0.8436 (mtt) cc_final: 0.7810 (mmt) REVERT: H 356 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6732 (tm-30) REVERT: H 360 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6434 (mt-10) REVERT: H 413 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6833 (ttm110) REVERT: H 419 CYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7478 (m) REVERT: H 444 LEU cc_start: 0.8371 (mm) cc_final: 0.7897 (mt) REVERT: H 445 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7705 (mptp) REVERT: H 450 LEU cc_start: 0.8074 (mm) cc_final: 0.7674 (mt) REVERT: H 464 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: H 470 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8073 (t-90) REVERT: H 471 LEU cc_start: 0.8424 (mt) cc_final: 0.8198 (mm) REVERT: H 488 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7254 (tm) REVERT: H 500 PHE cc_start: 0.8627 (t80) cc_final: 0.8241 (t80) REVERT: H 502 ASN cc_start: 0.8643 (t0) cc_final: 0.7919 (t0) REVERT: H 506 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7377 (mm-30) REVERT: H 542 GLN cc_start: 0.8307 (mt0) cc_final: 0.8078 (mt0) REVERT: D 167 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6773 (mp) REVERT: D 186 ASN cc_start: 0.7074 (t160) cc_final: 0.6796 (t0) REVERT: D 188 SER cc_start: 0.8317 (p) cc_final: 0.7866 (m) REVERT: D 253 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8167 (mt) REVERT: D 277 MET cc_start: 0.7371 (mmt) cc_final: 0.6550 (mmt) REVERT: D 313 GLN cc_start: 0.7500 (mm-40) cc_final: 0.6650 (tt0) REVERT: D 346 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8281 (mmp) REVERT: D 349 PHE cc_start: 0.8522 (t80) cc_final: 0.8199 (t80) REVERT: D 367 PHE cc_start: 0.8611 (m-10) cc_final: 0.8271 (m-10) REVERT: D 369 GLN cc_start: 0.7175 (tm-30) cc_final: 0.6532 (tm-30) REVERT: D 412 ARG cc_start: 0.8431 (ttt90) cc_final: 0.8105 (ttt90) REVERT: D 416 VAL cc_start: 0.8351 (p) cc_final: 0.8073 (m) REVERT: D 454 ASN cc_start: 0.8019 (m-40) cc_final: 0.7562 (t0) REVERT: D 485 GLN cc_start: 0.7988 (mt0) cc_final: 0.7589 (mt0) REVERT: D 496 MET cc_start: 0.8369 (ptp) cc_final: 0.8037 (ptt) REVERT: D 498 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 499 ASN cc_start: 0.8003 (t0) cc_final: 0.7745 (m-40) REVERT: D 503 PHE cc_start: 0.8284 (t80) cc_final: 0.7876 (t80) REVERT: D 507 ARG cc_start: 0.8405 (tpt90) cc_final: 0.7834 (tpm170) REVERT: D 526 LYS cc_start: 0.7613 (mttp) cc_final: 0.7375 (mmtp) REVERT: D 542 GLN cc_start: 0.8267 (mp-120) cc_final: 0.7811 (mp10) REVERT: D 593 THR cc_start: 0.7837 (p) cc_final: 0.7624 (p) REVERT: D 594 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6712 (t80) REVERT: D 623 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7183 (mtm110) REVERT: D 624 LYS cc_start: 0.7596 (ttpp) cc_final: 0.7259 (ttpt) REVERT: D 634 GLU cc_start: 0.6765 (pt0) cc_final: 0.6125 (pt0) REVERT: D 671 GLN cc_start: 0.8588 (tt0) cc_final: 0.8350 (tp40) REVERT: D 672 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 676 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: D 682 TYR cc_start: 0.8511 (m-80) cc_final: 0.8257 (m-80) REVERT: D 687 SER cc_start: 0.8672 (t) cc_final: 0.7989 (p) REVERT: I 275 LYS cc_start: 0.7049 (mttm) cc_final: 0.6815 (mmmm) REVERT: I 283 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7478 (mm-30) REVERT: I 287 ARG cc_start: 0.7455 (ttm110) cc_final: 0.6851 (tpp80) REVERT: I 292 LEU cc_start: 0.8169 (tp) cc_final: 0.7745 (pp) REVERT: I 314 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7873 (tt) REVERT: I 329 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7157 (tpp80) REVERT: I 332 LEU cc_start: 0.7978 (tt) cc_final: 0.7399 (pp) REVERT: I 347 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: I 348 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7451 (mtt180) REVERT: I 350 PHE cc_start: 0.8571 (m-10) cc_final: 0.8342 (m-80) REVERT: I 361 GLU cc_start: 0.7302 (tt0) cc_final: 0.7052 (tp30) REVERT: I 419 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7579 (m) REVERT: I 488 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6995 (tm) REVERT: I 500 PHE cc_start: 0.8546 (t80) cc_final: 0.8274 (t80) REVERT: I 502 ASN cc_start: 0.8539 (t0) cc_final: 0.7718 (t0) REVERT: I 506 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7385 (mm-30) REVERT: I 528 ARG cc_start: 0.6860 (ptp-170) cc_final: 0.6234 (ptt-90) REVERT: I 549 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7252 (t80) REVERT: E 167 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7137 (mt) REVERT: E 186 ASN cc_start: 0.6534 (t0) cc_final: 0.6252 (t0) REVERT: E 277 MET cc_start: 0.7086 (mmt) cc_final: 0.6594 (mmt) REVERT: E 281 MET cc_start: 0.6931 (ptt) cc_final: 0.6566 (ptt) REVERT: E 313 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6188 (tt0) REVERT: E 342 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 349 PHE cc_start: 0.8615 (t80) cc_final: 0.8204 (t80) REVERT: E 358 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7793 (pttt) REVERT: E 361 GLU cc_start: 0.7288 (pp20) cc_final: 0.6855 (pp20) REVERT: E 367 PHE cc_start: 0.8640 (m-10) cc_final: 0.8432 (m-10) REVERT: E 397 ARG cc_start: 0.3940 (OUTLIER) cc_final: 0.3374 (ttt180) REVERT: E 410 GLU cc_start: 0.6952 (tp30) cc_final: 0.6266 (tp30) REVERT: E 412 ARG cc_start: 0.8228 (ttt180) cc_final: 0.7868 (ttt90) REVERT: E 428 TRP cc_start: 0.7275 (t-100) cc_final: 0.6869 (t-100) REVERT: E 429 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7932 (mm-40) REVERT: E 450 LEU cc_start: 0.8110 (mt) cc_final: 0.7855 (mt) REVERT: E 452 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7602 (mttt) REVERT: E 454 ASN cc_start: 0.7883 (t0) cc_final: 0.7538 (t0) REVERT: E 498 GLN cc_start: 0.8205 (tp40) cc_final: 0.7926 (tp40) REVERT: E 506 GLU cc_start: 0.7684 (pt0) cc_final: 0.6958 (pt0) REVERT: E 518 LEU cc_start: 0.7110 (mt) cc_final: 0.6783 (pt) REVERT: E 526 LYS cc_start: 0.7468 (mttp) cc_final: 0.7194 (mmtp) REVERT: E 530 CYS cc_start: 0.7939 (t) cc_final: 0.7652 (p) REVERT: E 542 GLN cc_start: 0.8537 (mp10) cc_final: 0.8211 (mm-40) REVERT: E 623 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7420 (mtm110) REVERT: E 624 LYS cc_start: 0.8045 (tttm) cc_final: 0.7471 (ttmt) REVERT: E 671 GLN cc_start: 0.8466 (tt0) cc_final: 0.8185 (mm110) REVERT: E 672 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7338 (tm-30) REVERT: E 689 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6964 (mp0) outliers start: 164 outliers final: 119 residues processed: 1159 average time/residue: 0.2377 time to fit residues: 437.1814 Evaluate side-chains 1231 residues out of total 4302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1075 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 429 GLN Chi-restraints excluded: chain G residue 432 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 458 LEU Chi-restraints excluded: chain G residue 464 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain G residue 554 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 197 ARG Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 397 ARG Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 689 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 898 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 407 CYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 357 ARG Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 434 VAL Chi-restraints excluded: chain H residue 439 LEU Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 464 GLU Chi-restraints excluded: chain H residue 470 HIS Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 257 LYS Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 523 VAL Chi-restraints excluded: chain D residue 594 PHE Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 686 GLN Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain I residue 175 GLN Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 333 MET Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 347 GLN Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 430 THR Chi-restraints excluded: chain I residue 470 HIS Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain I residue 493 SER Chi-restraints excluded: chain I residue 538 CYS Chi-restraints excluded: chain I residue 540 LEU Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 549 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 HIS Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 397 ARG Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 689 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 59 optimal weight: 0.0870 chunk 222 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 484 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 447 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 chunk 378 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 425 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 186 ASN F 662 GLN B 303 ASN B 553 GLN B 815 HIS C 190 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN C 837 ASN H 347 GLN ** H 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 429 GLN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN I 264 HIS ** I 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.179078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135028 restraints weight = 65500.742| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.00 r_work: 0.3448 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40254 Z= 0.138 Angle : 0.664 13.167 54663 Z= 0.323 Chirality : 0.044 0.361 6003 Planarity : 0.005 0.066 7119 Dihedral : 4.755 54.100 5407 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.93 % Allowed : 27.75 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.12), residues: 4821 helix: 1.33 (0.13), residues: 1650 sheet: -0.84 (0.21), residues: 594 loop : -1.10 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 465 TYR 0.028 0.001 TYR D 621 PHE 0.037 0.001 PHE G 349 TRP 0.053 0.002 TRP F 428 HIS 0.010 0.001 HIS I 264 Details of bonding type rmsd covalent geometry : bond 0.00321 (40248) covalent geometry : angle 0.66397 (54651) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.96422 ( 12) hydrogen bonds : bond 0.03520 ( 1506) hydrogen bonds : angle 4.75164 ( 4185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13542.03 seconds wall clock time: 231 minutes 40.78 seconds (13900.78 seconds total)