Starting phenix.real_space_refine on Sun Feb 8 04:37:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.map" model { file = "/net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nlu_49522/02_2026/9nlu_49522.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 170 5.16 5 C 24900 2.51 5 N 6872 2.21 5 O 7763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39736 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3994 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 491} Chain breaks: 2 Chain: "B" Number of atoms: 5726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 731, 5715 Classifications: {'peptide': 731} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 701} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 731, 5715 Classifications: {'peptide': 731} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 701} Chain breaks: 1 bond proxies already assigned to first conformer: 5795 Chain: "C" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5736 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 705} Chain breaks: 2 Chain: "D" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5699 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 700} Chain breaks: 2 Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5575 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 685} Chain breaks: 3 Chain: "F" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3809 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 469} Chain breaks: 3 Chain: "G" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2264 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Chain: "H" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2158 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 271} Chain breaks: 3 Chain: "I" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain breaks: 1 Chain: "J" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "K" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 698 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "L" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1015 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'TRANS': 128} Chain breaks: 1 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 396 " occ=0.30 ... (20 atoms not shown) pdb=" NH2BARG B 396 " occ=0.70 Time building chain proxies: 10.82, per 1000 atoms: 0.27 Number of scatterers: 39736 At special positions: 0 Unit cell: (172.072, 236.736, 149.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 170 16.00 P 31 15.00 O 7763 8.00 N 6872 7.00 C 24900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9432 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 26 sheets defined 57.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.557A pdb=" N ILE A 266 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.566A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.669A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 454 Processing helix chain 'A' and resid 460 through 478 Processing helix chain 'A' and resid 498 through 509 removed outlier: 3.685A pdb=" N PHE A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.676A pdb=" N LEU A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 551 removed outlier: 3.582A pdb=" N SER A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 590 through 595 removed outlier: 3.643A pdb=" N LEU A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 removed outlier: 3.667A pdb=" N PHE A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.573A pdb=" N LEU A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 745 through 758 removed outlier: 3.849A pdb=" N GLU A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 103 through 109 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 262 through 270 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.925A pdb=" N ILE B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.571A pdb=" N ALA B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.868A pdb=" N VAL B 354 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.533A pdb=" N LEU B 405 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 406 " --> pdb=" O ALA B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 402 through 406' Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.523A pdb=" N ASN B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 490 through 495 removed outlier: 3.601A pdb=" N ALA B 493 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 3.530A pdb=" N PHE B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 532 through 551 removed outlier: 4.093A pdb=" N ASN B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.857A pdb=" N LEU B 573 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 Processing helix chain 'B' and resid 640 through 651 removed outlier: 3.875A pdb=" N LEU B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.657A pdb=" N CYS B 681 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'B' and resid 693 through 705 removed outlier: 3.685A pdb=" N LEU B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 723 removed outlier: 3.815A pdb=" N ARG B 721 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.891A pdb=" N HIS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.377A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 43 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 136 through 147 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.502A pdb=" N ILE C 266 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 327 through 337 Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.019A pdb=" N VAL C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 446 through 454 Processing helix chain 'C' and resid 458 through 476 removed outlier: 3.581A pdb=" N ILE C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 removed outlier: 3.562A pdb=" N PHE C 502 " --> pdb=" O THR C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 523 removed outlier: 3.708A pdb=" N ASP C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.730A pdb=" N SER C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 3.898A pdb=" N LEU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 598 through 613 removed outlier: 3.599A pdb=" N ALA C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 630 removed outlier: 3.516A pdb=" N LEU C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 625 through 630' Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.514A pdb=" N LEU C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 removed outlier: 3.543A pdb=" N ASP C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 705 removed outlier: 3.535A pdb=" N ASN C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.998A pdb=" N ARG C 721 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER C 722 " --> pdb=" O GLU C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 741 removed outlier: 3.541A pdb=" N THR C 735 " --> pdb=" O LYS C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 135 through 147 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 256 through 259 removed outlier: 3.784A pdb=" N ARG D 259 " --> pdb=" O PHE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.679A pdb=" N ILE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.815A pdb=" N ALA D 336 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.973A pdb=" N SER D 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.522A pdb=" N VAL D 354 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.752A pdb=" N ASP D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.643A pdb=" N ARG D 406 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 454 Processing helix chain 'D' and resid 458 through 479 removed outlier: 4.049A pdb=" N ILE D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY D 464 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 478 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 498 through 506 removed outlier: 4.133A pdb=" N PHE D 502 " --> pdb=" O THR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.902A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.923A pdb=" N LEU D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.824A pdb=" N LEU D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 625 through 630 removed outlier: 3.557A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.694A pdb=" N LEU D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 677 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.820A pdb=" N CYS D 681 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 693 through 705 removed outlier: 3.904A pdb=" N LEU D 697 " --> pdb=" O ASN D 693 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 729 through 744 removed outlier: 4.265A pdb=" N HIS D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 744 " --> pdb=" O ALA D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 758 removed outlier: 4.471A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 135 through 147 Processing helix chain 'E' and resid 245 through 256 Processing helix chain 'E' and resid 257 through 260 Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.444A pdb=" N ILE E 266 " --> pdb=" O PRO E 262 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 267 " --> pdb=" O PRO E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 removed outlier: 4.319A pdb=" N GLY E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 327 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.782A pdb=" N VAL E 354 " --> pdb=" O LEU E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.776A pdb=" N VAL E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 400 removed outlier: 3.592A pdb=" N LEU E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 420 through 438 removed outlier: 4.968A pdb=" N LYS E 434 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N MET E 435 " --> pdb=" O GLN E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'E' and resid 458 through 475 removed outlier: 3.579A pdb=" N PHE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 509 removed outlier: 3.562A pdb=" N PHE E 502 " --> pdb=" O THR E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 524 removed outlier: 3.510A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 552 removed outlier: 4.133A pdb=" N ASN E 536 " --> pdb=" O SER E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 582 removed outlier: 3.662A pdb=" N GLY E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 595 removed outlier: 3.703A pdb=" N LEU E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 614 Processing helix chain 'E' and resid 625 through 630 Processing helix chain 'E' and resid 640 through 651 removed outlier: 3.620A pdb=" N LEU E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 677 Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.713A pdb=" N CYS E 681 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 678 through 682' Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.644A pdb=" N LEU E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 708 through 723 removed outlier: 3.530A pdb=" N ILE E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 721 " --> pdb=" O ASN E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 741 Processing helix chain 'E' and resid 747 through 758 removed outlier: 4.270A pdb=" N GLU E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.525A pdb=" N PHE F 252 " --> pdb=" O PHE F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 262 through 270 removed outlier: 3.761A pdb=" N ILE F 266 " --> pdb=" O PRO F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 298 removed outlier: 3.759A pdb=" N GLY F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 317 through 327 removed outlier: 4.025A pdb=" N PHE F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 337 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.204A pdb=" N VAL F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 removed outlier: 4.083A pdb=" N VAL F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP F 380 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 400 removed outlier: 3.581A pdb=" N LEU F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 438 removed outlier: 5.056A pdb=" N LYS F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N MET F 435 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN F 438 " --> pdb=" O LYS F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'F' and resid 458 through 478 removed outlier: 3.517A pdb=" N ALA F 473 " --> pdb=" O ALA F 469 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 495 Processing helix chain 'F' and resid 498 through 506 removed outlier: 3.673A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 506 " --> pdb=" O PHE F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.627A pdb=" N CYS F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 552 removed outlier: 4.052A pdb=" N ASN F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 582 removed outlier: 3.912A pdb=" N GLY F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 595 removed outlier: 3.954A pdb=" N LEU F 594 " --> pdb=" O SER F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.712A pdb=" N ALA F 604 " --> pdb=" O SER F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 630 Processing helix chain 'F' and resid 640 through 651 removed outlier: 3.610A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 676 Processing helix chain 'F' and resid 677 through 682 removed outlier: 4.009A pdb=" N SER F 680 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 704 removed outlier: 3.643A pdb=" N LEU F 697 " --> pdb=" O ASN F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 708 through 721 removed outlier: 4.190A pdb=" N ILE F 716 " --> pdb=" O ARG F 712 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN F 717 " --> pdb=" O VAL F 713 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG F 721 " --> pdb=" O ASN F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 744 removed outlier: 4.314A pdb=" N HIS F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 744 " --> pdb=" O ALA F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 757 removed outlier: 4.509A pdb=" N LEU F 750 " --> pdb=" O PRO F 746 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 21 through 26 removed outlier: 3.914A pdb=" N PHE G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 50 Processing helix chain 'G' and resid 52 through 71 Processing helix chain 'G' and resid 72 through 91 Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 112 through 130 Processing helix chain 'G' and resid 133 through 151 Processing helix chain 'G' and resid 153 through 171 Processing helix chain 'G' and resid 173 through 189 Processing helix chain 'G' and resid 196 through 212 Processing helix chain 'G' and resid 214 through 229 Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 235 through 251 Processing helix chain 'G' and resid 252 through 267 removed outlier: 3.666A pdb=" N PHE G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 290 Processing helix chain 'H' and resid 3 through 15 Processing helix chain 'H' and resid 21 through 26 removed outlier: 3.919A pdb=" N PHE H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 47 Processing helix chain 'H' and resid 53 through 71 Processing helix chain 'H' and resid 72 through 91 Processing helix chain 'H' and resid 92 through 110 Processing helix chain 'H' and resid 116 through 130 Processing helix chain 'H' and resid 133 through 151 Processing helix chain 'H' and resid 153 through 171 Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 198 through 212 Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 251 Processing helix chain 'H' and resid 252 through 267 removed outlier: 3.670A pdb=" N PHE H 266 " --> pdb=" O GLU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 292 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 21 through 26 removed outlier: 3.915A pdb=" N PHE I 25 " --> pdb=" O PHE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 50 Processing helix chain 'I' and resid 52 through 71 Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 92 through 110 Processing helix chain 'I' and resid 112 through 130 Processing helix chain 'I' and resid 133 through 151 Processing helix chain 'I' and resid 153 through 171 Processing helix chain 'I' and resid 173 through 188 Processing helix chain 'I' and resid 196 through 212 removed outlier: 3.733A pdb=" N ASP I 200 " --> pdb=" O TRP I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 229 Processing helix chain 'I' and resid 229 through 234 Processing helix chain 'I' and resid 235 through 251 Processing helix chain 'I' and resid 252 through 267 removed outlier: 3.663A pdb=" N PHE I 266 " --> pdb=" O GLU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 292 Processing helix chain 'J' and resid 28 through 86 Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.648A pdb=" N THR K 188 " --> pdb=" O GLU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 257 removed outlier: 3.894A pdb=" N GLU K 226 " --> pdb=" O ILE K 222 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN K 227 " --> pdb=" O GLU K 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 499 Processing helix chain 'L' and resid 590 through 649 removed outlier: 3.595A pdb=" N GLY L 649 " --> pdb=" O ASN L 645 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.179A pdb=" N LYS A 304 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASP A 349 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 306 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 277 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR A 394 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 279 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 589 removed outlier: 6.260A pdb=" N PHE A 585 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 622 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 587 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 662 " --> pdb=" O ASN A 619 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 558 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 665 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 560 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR A 667 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 562 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 684 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 47 removed outlier: 7.175A pdb=" N ILE B 79 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS B 30 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 162 removed outlier: 3.750A pdb=" N SER B 122 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 118 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL B 174 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 116 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 176 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 114 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.204A pdb=" N PHE B 134 " --> pdb=" O LYS B 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.579A pdb=" N PHE B 152 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 196 " --> pdb=" O PHE B 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.718A pdb=" N MET B 393 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 277 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N THR B 394 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 279 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 585 through 589 removed outlier: 6.646A pdb=" N PHE B 585 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL B 622 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG B 587 " --> pdb=" O VAL B 622 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 662 " --> pdb=" O ASN B 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 7.194A pdb=" N ILE C 79 " --> pdb=" O HIS C 28 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS C 30 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 159 removed outlier: 3.732A pdb=" N SER C 122 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP C 118 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C 174 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 116 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA C 176 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU C 114 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.217A pdb=" N PHE C 134 " --> pdb=" O LYS C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 152 removed outlier: 3.599A pdb=" N PHE C 152 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 196 " --> pdb=" O PHE C 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.610A pdb=" N MET C 393 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 277 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR C 394 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 279 " --> pdb=" O THR C 394 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 586 through 589 removed outlier: 6.643A pdb=" N LEU C 621 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR C 666 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 623 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 684 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 7.172A pdb=" N ILE D 79 " --> pdb=" O HIS D 28 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS D 30 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 157 through 159 removed outlier: 3.773A pdb=" N SER D 122 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP D 118 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL D 174 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER D 116 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA D 176 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU D 114 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 152 removed outlier: 3.604A pdb=" N PHE D 152 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 196 " --> pdb=" O PHE D 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 304 through 306 removed outlier: 3.744A pdb=" N MET D 393 " --> pdb=" O PHE D 348 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 277 " --> pdb=" O GLY D 392 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR D 394 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 279 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 278 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 585 through 589 removed outlier: 3.807A pdb=" N PHE D 585 " --> pdb=" O LEU D 618 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 558 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N THR D 665 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 560 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 684 " --> pdb=" O SER D 559 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 7.179A pdb=" N ILE E 79 " --> pdb=" O HIS E 28 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LYS E 30 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 157 through 162 removed outlier: 3.721A pdb=" N SER E 122 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP E 118 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL E 174 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 116 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA E 176 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU E 114 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 152 removed outlier: 3.609A pdb=" N PHE E 152 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY E 196 " --> pdb=" O PHE E 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 304 through 307 removed outlier: 6.137A pdb=" N LYS E 304 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP E 349 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 306 " --> pdb=" O ASP E 349 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 389 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 346 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 393 " --> pdb=" O PHE E 348 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY E 276 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL E 414 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 278 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 585 through 589 removed outlier: 6.420A pdb=" N VAL E 558 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR E 665 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU E 560 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR E 667 " --> pdb=" O LEU E 560 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE E 562 " --> pdb=" O THR E 667 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 684 " --> pdb=" O SER E 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 276 through 280 removed outlier: 6.600A pdb=" N LEU F 277 " --> pdb=" O GLY F 392 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR F 394 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU F 279 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS F 344 " --> pdb=" O LEU F 389 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE F 391 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE F 346 " --> pdb=" O ILE F 391 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET F 393 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE F 348 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS F 304 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP F 349 " --> pdb=" O LYS F 304 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL F 306 " --> pdb=" O ASP F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 585 through 589 removed outlier: 4.054A pdb=" N PHE F 585 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL F 558 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR F 665 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU F 560 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR F 667 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE F 562 " --> pdb=" O THR F 667 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN F 684 " --> pdb=" O SER F 559 " (cutoff:3.500A) 2078 hydrogen bonds defined for protein. 6081 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: 9.41 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6963 1.32 - 1.44: 9718 1.44 - 1.57: 23323 1.57 - 1.69: 34 1.69 - 1.82: 293 Bond restraints: 40331 Sorted by residual: bond pdb=" CG LYS D 128 " pdb=" CD LYS D 128 " ideal model delta sigma weight residual 1.520 1.389 0.131 3.00e-02 1.11e+03 1.89e+01 bond pdb=" CG ARG G 114 " pdb=" CD ARG G 114 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.15e+01 bond pdb=" CB LYS G 199 " pdb=" CG LYS G 199 " ideal model delta sigma weight residual 1.520 1.425 0.095 3.00e-02 1.11e+03 9.99e+00 bond pdb=" C GLN K 225 " pdb=" N GLU K 226 " ideal model delta sigma weight residual 1.334 1.295 0.039 1.27e-02 6.20e+03 9.51e+00 bond pdb=" CB PHE G 113 " pdb=" CG PHE G 113 " ideal model delta sigma weight residual 1.502 1.433 0.069 2.30e-02 1.89e+03 8.97e+00 ... (remaining 40326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 53288 2.32 - 4.63: 997 4.63 - 6.95: 118 6.95 - 9.27: 16 9.27 - 11.58: 3 Bond angle restraints: 54422 Sorted by residual: angle pdb=" C GLU K 218 " pdb=" CA GLU K 218 " pdb=" CB GLU K 218 " ideal model delta sigma weight residual 110.88 102.27 8.61 1.57e+00 4.06e-01 3.01e+01 angle pdb=" N GLU K 226 " pdb=" CA GLU K 226 " pdb=" CB GLU K 226 " ideal model delta sigma weight residual 110.01 103.10 6.91 1.45e+00 4.76e-01 2.27e+01 angle pdb=" CA LYS D 128 " pdb=" CB LYS D 128 " pdb=" CG LYS D 128 " ideal model delta sigma weight residual 114.10 105.14 8.96 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N ARG J 44 " pdb=" CA ARG J 44 " pdb=" CB ARG J 44 " ideal model delta sigma weight residual 110.12 103.74 6.38 1.47e+00 4.63e-01 1.89e+01 angle pdb=" C GLY E 514 " pdb=" N ILE E 515 " pdb=" CA ILE E 515 " ideal model delta sigma weight residual 121.97 129.54 -7.57 1.80e+00 3.09e-01 1.77e+01 ... (remaining 54417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.51: 23732 29.51 - 59.01: 1094 59.01 - 88.52: 93 88.52 - 118.03: 4 118.03 - 147.53: 1 Dihedral angle restraints: 24924 sinusoidal: 10378 harmonic: 14546 Sorted by residual: dihedral pdb=" C2' ADP E 801 " pdb=" C1' ADP E 801 " pdb=" N9 ADP E 801 " pdb=" C4 ADP E 801 " ideal model delta sinusoidal sigma weight residual 91.55 -120.92 -147.53 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 38.82 -98.82 1 2.00e+01 2.50e-03 2.77e+01 dihedral pdb=" CA ALA D 228 " pdb=" C ALA D 228 " pdb=" N VAL D 229 " pdb=" CA VAL D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 24921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4930 0.055 - 0.110: 1027 0.110 - 0.164: 190 0.164 - 0.219: 15 0.219 - 0.274: 1 Chirality restraints: 6163 Sorted by residual: chirality pdb=" CA ARG D 124 " pdb=" N ARG D 124 " pdb=" C ARG D 124 " pdb=" CB ARG D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA PRO G 230 " pdb=" N PRO G 230 " pdb=" C PRO G 230 " pdb=" CB PRO G 230 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ARG L 607 " pdb=" N ARG L 607 " pdb=" C ARG L 607 " pdb=" CB ARG L 607 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 6160 not shown) Planarity restraints: 7056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 215 " -0.033 2.00e-02 2.50e+03 6.61e-02 4.36e+01 pdb=" CG ASN K 215 " 0.114 2.00e-02 2.50e+03 pdb=" OD1 ASN K 215 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN K 215 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 44 " -0.268 9.50e-02 1.11e+02 1.27e-01 3.11e+01 pdb=" NE ARG J 44 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG J 44 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG J 44 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG J 44 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 196 " 0.037 2.00e-02 2.50e+03 3.30e-02 2.73e+01 pdb=" CG TRP G 196 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP G 196 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 196 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP G 196 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP G 196 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP G 196 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 196 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 196 " -0.051 2.00e-02 2.50e+03 pdb=" CH2 TRP G 196 " 0.020 2.00e-02 2.50e+03 ... (remaining 7053 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 16895 2.93 - 3.42: 39670 3.42 - 3.91: 61250 3.91 - 4.41: 69607 4.41 - 4.90: 115637 Nonbonded interactions: 303059 Sorted by model distance: nonbonded pdb=" O VAL E 713 " pdb=" OD1 ASN E 717 " model vdw 2.436 3.040 nonbonded pdb=" O4' ATP A 802 " pdb=" O5' ATP A 802 " model vdw 2.439 2.432 nonbonded pdb=" OD1 ASN C 205 " pdb=" NH1 ARG C 223 " model vdw 2.447 3.120 nonbonded pdb=" O ASP B 658 " pdb=" OD1 ASP B 658 " model vdw 2.450 3.040 nonbonded pdb=" O ASP L 453 " pdb=" N GLU L 455 " model vdw 2.458 3.120 ... (remaining 303054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 245 through 357 or resid 366 through 412 or resid 420 thro \ ugh 758)) selection = (chain 'F' and (resid 245 through 478 or resid 491 through 758)) } ncs_group { reference = (chain 'B' and (resid 18 through 91 or resid 95 through 160 or resid 166 through \ 207 or resid 228 through 395 or resid 397 through 741 or resid 746 through 758 \ or resid 802)) selection = (chain 'C' and (resid 18 through 91 or resid 95 through 160 or resid 166 through \ 207 or resid 228 through 395 or resid 397 through 478 or resid 489 through 758 \ or resid 802)) selection = (chain 'D' and (resid 18 through 91 or resid 95 through 207 or resid 228 through \ 395 or resid 397 through 478 or resid 489 through 741 or resid 746 through 758 \ or resid 802)) selection = (chain 'E' and (resid 18 through 160 or resid 166 through 395 or resid 397 throu \ gh 478 or resid 489 through 758 or resid 802)) } ncs_group { reference = (chain 'G' and (resid 1 through 47 or resid 52 through 110 or resid 115 through \ 188 or resid 198 through 290)) selection = (chain 'H' and resid 1 through 290) selection = (chain 'I' and (resid 1 through 47 or resid 52 through 110 or resid 115 through \ 188 or resid 198 through 290)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 41.360 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 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 0.131 40331 Z= 0.278 Angle : 0.805 11.583 54422 Z= 0.457 Chirality : 0.047 0.274 6163 Planarity : 0.007 0.127 7056 Dihedral : 15.810 147.533 15492 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 0.83 % Allowed : 10.52 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.12), residues: 4979 helix: 1.34 (0.10), residues: 2532 sheet: -0.05 (0.19), residues: 614 loop : -1.18 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.002 ARG J 44 TYR 0.047 0.004 TYR I 174 PHE 0.045 0.003 PHE G 113 TRP 0.057 0.004 TRP G 196 HIS 0.010 0.002 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00558 (40331) covalent geometry : angle 0.80546 (54422) hydrogen bonds : bond 0.14420 ( 2078) hydrogen bonds : angle 5.30507 ( 6081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1003 time to evaluate : 1.601 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.5731 (m-80) cc_final: 0.5293 (m-80) REVERT: B 137 ASP cc_start: 0.8501 (m-30) cc_final: 0.7791 (m-30) REVERT: B 223 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5221 (tpp-160) REVERT: B 400 ILE cc_start: 0.7013 (mm) cc_final: 0.6655 (mm) REVERT: C 87 THR cc_start: 0.9146 (m) cc_final: 0.8762 (p) REVERT: C 160 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: C 385 LEU cc_start: 0.7582 (tp) cc_final: 0.7163 (tt) REVERT: C 608 ASN cc_start: 0.8136 (t0) cc_final: 0.7016 (t0) REVERT: D 22 MET cc_start: 0.1829 (ptp) cc_final: -0.1663 (tmm) REVERT: D 122 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.8160 (p) REVERT: D 160 MET cc_start: 0.2865 (OUTLIER) cc_final: 0.2019 (mmm) REVERT: D 577 ILE cc_start: 0.9039 (mt) cc_final: 0.8799 (tp) REVERT: G 1 MET cc_start: 0.1506 (mtt) cc_final: 0.0720 (ptp) REVERT: H 22 MET cc_start: -0.2492 (mtm) cc_final: -0.2861 (mpp) outliers start: 36 outliers final: 9 residues processed: 1032 average time/residue: 0.2791 time to fit residues: 447.4666 Evaluate side-chains 552 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 539 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 548 GLN B 387 ASN B 456 ASN B 475 ASN B 608 ASN C 215 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 717 ASN C 756 GLN ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN E 727 ASN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 748 ASN G 150 GLN G 173 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 GLN K 171 GLN K 175 GLN K 215 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.106739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.084306 restraints weight = 512738.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.083548 restraints weight = 234042.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.084412 restraints weight = 129820.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.084763 restraints weight = 83199.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.085156 restraints weight = 61794.904| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40331 Z= 0.198 Angle : 0.674 9.197 54422 Z= 0.355 Chirality : 0.043 0.219 6163 Planarity : 0.005 0.126 7056 Dihedral : 8.744 137.079 5698 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.12), residues: 4979 helix: 1.82 (0.10), residues: 2606 sheet: -0.12 (0.18), residues: 642 loop : -0.87 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 82 TYR 0.045 0.002 TYR I 31 PHE 0.040 0.002 PHE A 261 TRP 0.060 0.002 TRP I 147 HIS 0.011 0.001 HIS F 563 Details of bonding type rmsd covalent geometry : bond 0.00422 (40331) covalent geometry : angle 0.67438 (54422) hydrogen bonds : bond 0.04702 ( 2078) hydrogen bonds : angle 4.40306 ( 6081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 632 time to evaluate : 1.542 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: 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 321 GLU cc_start: 0.9743 (tp30) cc_final: 0.9494 (tp30) REVERT: A 352 ASP cc_start: 0.9364 (p0) cc_final: 0.9088 (p0) REVERT: A 606 ILE cc_start: 0.9807 (mt) cc_final: 0.9563 (mt) REVERT: A 610 PHE cc_start: 0.9186 (m-80) cc_final: 0.8694 (m-80) REVERT: A 631 ASP cc_start: 0.9635 (m-30) cc_final: 0.9276 (t0) REVERT: A 644 LEU cc_start: 0.9812 (tp) cc_final: 0.9545 (tp) REVERT: A 662 LEU cc_start: 0.9802 (tp) cc_final: 0.9405 (tp) REVERT: A 664 MET cc_start: 0.9300 (ptp) cc_final: 0.8999 (ptp) REVERT: B 19 MET cc_start: -0.0627 (ttm) cc_final: -0.1419 (ttm) REVERT: B 22 MET cc_start: 0.6423 (tmm) cc_final: 0.6087 (tmm) REVERT: B 256 PHE cc_start: 0.9497 (m-80) cc_final: 0.9078 (m-80) REVERT: B 304 LYS cc_start: 0.9395 (mtpt) cc_final: 0.8585 (mptt) REVERT: B 321 GLU cc_start: 0.9838 (tt0) cc_final: 0.9410 (tp30) REVERT: B 398 ASP cc_start: 0.9694 (m-30) cc_final: 0.9451 (p0) REVERT: B 410 PHE cc_start: 0.9334 (m-10) cc_final: 0.9052 (m-80) REVERT: B 495 LEU cc_start: 0.8012 (mt) cc_final: 0.7710 (mt) REVERT: B 519 ASP cc_start: 0.9564 (t70) cc_final: 0.9242 (t0) REVERT: B 520 LEU cc_start: 0.9442 (mt) cc_final: 0.9235 (mp) REVERT: B 597 MET cc_start: 0.9505 (mtp) cc_final: 0.9143 (mtp) REVERT: B 673 LEU cc_start: 0.9795 (mt) cc_final: 0.9548 (mt) REVERT: B 676 MET cc_start: 0.9206 (mtm) cc_final: 0.8983 (ptp) REVERT: B 678 ILE cc_start: 0.9686 (tp) cc_final: 0.9405 (tp) REVERT: B 701 MET cc_start: 0.8994 (mtm) cc_final: 0.8772 (ptp) REVERT: C 19 MET cc_start: 0.0545 (mmt) cc_final: -0.2554 (ttm) REVERT: C 22 MET cc_start: 0.1492 (ptt) cc_final: 0.0734 (ptp) REVERT: C 87 THR cc_start: 0.9724 (m) cc_final: 0.9456 (p) REVERT: C 157 TYR cc_start: 0.9481 (m-80) cc_final: 0.9222 (m-10) REVERT: C 278 LEU cc_start: 0.9279 (mt) cc_final: 0.8687 (mt) REVERT: C 293 LYS cc_start: 0.9754 (mmtt) cc_final: 0.9530 (mmtm) REVERT: C 312 LEU cc_start: 0.9652 (mp) cc_final: 0.9126 (tp) REVERT: C 349 ASP cc_start: 0.9444 (t0) cc_final: 0.9119 (t0) REVERT: C 410 PHE cc_start: 0.9631 (m-80) cc_final: 0.8989 (m-80) REVERT: C 428 PHE cc_start: 0.9359 (m-80) cc_final: 0.8735 (m-10) REVERT: C 607 ASP cc_start: 0.9609 (t0) cc_final: 0.9364 (t0) REVERT: C 610 PHE cc_start: 0.9612 (m-80) cc_final: 0.9178 (m-80) REVERT: C 611 ARG cc_start: 0.9239 (mtm110) cc_final: 0.8990 (mtm110) REVERT: C 648 LYS cc_start: 0.9502 (tptt) cc_final: 0.9297 (tptt) REVERT: C 701 MET cc_start: 0.8467 (ptt) cc_final: 0.8105 (ptt) REVERT: D 22 MET cc_start: 0.8090 (ptp) cc_final: 0.2887 (tmm) REVERT: D 250 LYS cc_start: 0.9809 (ttmm) cc_final: 0.9552 (ptpp) REVERT: D 311 ILE cc_start: 0.9203 (mm) cc_final: 0.8917 (tp) REVERT: D 322 ASN cc_start: 0.9656 (m110) cc_final: 0.9377 (m110) REVERT: D 348 PHE cc_start: 0.9321 (m-80) cc_final: 0.9119 (t80) REVERT: D 349 ASP cc_start: 0.8659 (t0) cc_final: 0.8236 (t0) REVERT: D 351 LEU cc_start: 0.9651 (mp) cc_final: 0.9178 (mp) REVERT: D 391 ILE cc_start: 0.9688 (mm) cc_final: 0.9473 (mp) REVERT: D 393 MET cc_start: 0.8911 (mtp) cc_final: 0.8609 (mtp) REVERT: D 399 LEU cc_start: 0.9587 (mt) cc_final: 0.9267 (mp) REVERT: D 400 ILE cc_start: 0.9449 (mm) cc_final: 0.8919 (mm) REVERT: D 428 PHE cc_start: 0.9026 (m-80) cc_final: 0.8724 (m-80) REVERT: D 439 ASN cc_start: 0.9538 (t0) cc_final: 0.9308 (p0) REVERT: D 528 MET cc_start: 0.9524 (mmp) cc_final: 0.8917 (mmp) REVERT: D 529 MET cc_start: 0.8726 (mpp) cc_final: 0.7672 (ttp) REVERT: D 573 LEU cc_start: 0.9721 (mm) cc_final: 0.9486 (mm) REVERT: D 629 LEU cc_start: 0.9671 (mt) cc_final: 0.9459 (mt) REVERT: E 346 ILE cc_start: 0.9738 (pt) cc_final: 0.9517 (mp) REVERT: E 441 MET cc_start: 0.9165 (ppp) cc_final: 0.8804 (tpp) REVERT: E 513 PHE cc_start: 0.8730 (t80) cc_final: 0.8276 (t80) REVERT: E 597 MET cc_start: 0.9342 (mtp) cc_final: 0.8813 (mtp) REVERT: E 602 LYS cc_start: 0.9845 (mttp) cc_final: 0.9562 (mmtm) REVERT: E 605 TYR cc_start: 0.9444 (t80) cc_final: 0.9052 (t80) REVERT: E 624 ASP cc_start: 0.9328 (t0) cc_final: 0.8981 (p0) REVERT: E 691 MET cc_start: 0.6609 (ppp) cc_final: 0.6387 (ppp) REVERT: F 334 TYR cc_start: 0.9356 (t80) cc_final: 0.9136 (t80) REVERT: F 441 MET cc_start: 0.8762 (ppp) cc_final: 0.8426 (ppp) REVERT: L 634 ASP cc_start: 0.7656 (t70) cc_final: 0.7022 (m-30) REVERT: L 642 MET cc_start: 0.0506 (tmm) cc_final: -0.0676 (tmm) outliers start: 6 outliers final: 2 residues processed: 633 average time/residue: 0.2688 time to fit residues: 269.7220 Evaluate side-chains 464 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 185 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 400 optimal weight: 50.0000 chunk 162 optimal weight: 5.9990 chunk 357 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN B 299 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 475 ASN B 541 ASN ** C 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 HIS D 344 HIS ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN E 699 ASN E 736 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.103222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.080677 restraints weight = 435381.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.082164 restraints weight = 215281.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.083084 restraints weight = 129373.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.082882 restraints weight = 94714.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.083079 restraints weight = 65679.887| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 40331 Z= 0.174 Angle : 0.620 9.232 54422 Z= 0.326 Chirality : 0.042 0.174 6163 Planarity : 0.005 0.142 7056 Dihedral : 8.502 125.972 5698 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 4979 helix: 1.85 (0.10), residues: 2627 sheet: -0.00 (0.18), residues: 636 loop : -0.69 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 254 TYR 0.033 0.002 TYR D 315 PHE 0.036 0.002 PHE B 457 TRP 0.016 0.001 TRP I 147 HIS 0.008 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00370 (40331) covalent geometry : angle 0.61958 (54422) hydrogen bonds : bond 0.04096 ( 2078) hydrogen bonds : angle 4.24185 ( 6081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 1.631 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: 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 352 ASP cc_start: 0.9406 (p0) cc_final: 0.9135 (p0) REVERT: A 404 LEU cc_start: 0.9590 (mm) cc_final: 0.9191 (mm) REVERT: A 435 MET cc_start: 0.9620 (ppp) cc_final: 0.9217 (ppp) REVERT: A 441 MET cc_start: 0.9638 (ppp) cc_final: 0.9340 (ptm) REVERT: A 621 LEU cc_start: 0.9687 (tp) cc_final: 0.9483 (tp) REVERT: A 662 LEU cc_start: 0.9839 (tp) cc_final: 0.9427 (tp) REVERT: A 664 MET cc_start: 0.9431 (ptp) cc_final: 0.9020 (ptp) REVERT: A 691 MET cc_start: 0.7343 (ttt) cc_final: 0.6231 (tmm) REVERT: B 256 PHE cc_start: 0.9604 (m-80) cc_final: 0.9159 (m-80) REVERT: B 355 PHE cc_start: 0.9223 (m-80) cc_final: 0.8941 (m-80) REVERT: B 398 ASP cc_start: 0.9673 (m-30) cc_final: 0.9448 (p0) REVERT: B 463 GLU cc_start: 0.9558 (tt0) cc_final: 0.9289 (tm-30) REVERT: B 495 LEU cc_start: 0.8089 (mt) cc_final: 0.7710 (mt) REVERT: B 519 ASP cc_start: 0.9563 (t70) cc_final: 0.9231 (t0) REVERT: B 587 ARG cc_start: 0.9337 (ttm170) cc_final: 0.9023 (mmt90) REVERT: B 588 LEU cc_start: 0.9221 (tp) cc_final: 0.8944 (tp) REVERT: B 597 MET cc_start: 0.9467 (mtp) cc_final: 0.9214 (mtp) REVERT: B 603 ILE cc_start: 0.9788 (pt) cc_final: 0.9534 (pt) REVERT: B 607 ASP cc_start: 0.9383 (m-30) cc_final: 0.8715 (m-30) REVERT: B 611 ARG cc_start: 0.9358 (ptp-110) cc_final: 0.9070 (ptt-90) REVERT: B 648 LYS cc_start: 0.9797 (ttmt) cc_final: 0.9559 (mtmm) REVERT: B 678 ILE cc_start: 0.9717 (tp) cc_final: 0.9395 (tp) REVERT: C 19 MET cc_start: 0.2513 (mmt) cc_final: -0.0134 (ttm) REVERT: C 87 THR cc_start: 0.9821 (m) cc_final: 0.9569 (p) REVERT: C 157 TYR cc_start: 0.9582 (m-80) cc_final: 0.9294 (m-80) REVERT: C 269 LEU cc_start: 0.9521 (mt) cc_final: 0.9238 (mt) REVERT: C 277 LEU cc_start: 0.9811 (tp) cc_final: 0.9580 (tp) REVERT: C 278 LEU cc_start: 0.9186 (mt) cc_final: 0.8496 (mt) REVERT: C 293 LYS cc_start: 0.9749 (mmtt) cc_final: 0.9538 (mmtm) REVERT: C 304 LYS cc_start: 0.9051 (mppt) cc_final: 0.8726 (mmtm) REVERT: C 348 PHE cc_start: 0.9611 (m-80) cc_final: 0.9389 (t80) REVERT: C 349 ASP cc_start: 0.9494 (t0) cc_final: 0.9194 (t0) REVERT: C 355 PHE cc_start: 0.9496 (m-80) cc_final: 0.8946 (m-80) REVERT: C 410 PHE cc_start: 0.9569 (m-80) cc_final: 0.8805 (m-80) REVERT: C 428 PHE cc_start: 0.9392 (m-80) cc_final: 0.8709 (m-10) REVERT: C 519 ASP cc_start: 0.9427 (m-30) cc_final: 0.9204 (m-30) REVERT: C 589 ILE cc_start: 0.9832 (mp) cc_final: 0.9557 (mp) REVERT: C 607 ASP cc_start: 0.9621 (t0) cc_final: 0.9346 (t0) REVERT: C 611 ARG cc_start: 0.9265 (mtm110) cc_final: 0.8991 (mtm110) REVERT: C 624 ASP cc_start: 0.9273 (t0) cc_final: 0.8489 (p0) REVERT: C 701 MET cc_start: 0.8756 (ptt) cc_final: 0.8352 (ptt) REVERT: D 22 MET cc_start: 0.7406 (ptp) cc_final: 0.6590 (tmm) REVERT: D 277 LEU cc_start: 0.9892 (tp) cc_final: 0.9653 (tp) REVERT: D 312 LEU cc_start: 0.8849 (tp) cc_final: 0.8616 (tp) REVERT: D 315 TYR cc_start: 0.9681 (m-10) cc_final: 0.9386 (m-80) REVERT: D 322 ASN cc_start: 0.9601 (m110) cc_final: 0.9382 (m110) REVERT: D 348 PHE cc_start: 0.9534 (m-10) cc_final: 0.9166 (t80) REVERT: D 349 ASP cc_start: 0.8725 (t0) cc_final: 0.8390 (t0) REVERT: D 355 PHE cc_start: 0.9436 (m-80) cc_final: 0.9059 (m-80) REVERT: D 391 ILE cc_start: 0.9706 (mm) cc_final: 0.9368 (mm) REVERT: D 393 MET cc_start: 0.9042 (mtp) cc_final: 0.8627 (mtp) REVERT: D 396 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6986 (tmm-80) REVERT: D 410 PHE cc_start: 0.9728 (m-10) cc_final: 0.9373 (m-80) REVERT: D 428 PHE cc_start: 0.9126 (m-80) cc_final: 0.8837 (m-80) REVERT: E 306 VAL cc_start: 0.9652 (m) cc_final: 0.9270 (p) REVERT: E 321 GLU cc_start: 0.9773 (mp0) cc_final: 0.9335 (mp0) REVERT: E 513 PHE cc_start: 0.8802 (t80) cc_final: 0.8318 (t80) REVERT: E 624 ASP cc_start: 0.9360 (t0) cc_final: 0.9022 (p0) REVERT: E 646 MET cc_start: 0.9433 (tmm) cc_final: 0.9217 (tmm) REVERT: E 648 LYS cc_start: 0.9481 (tptt) cc_final: 0.9182 (tptt) REVERT: F 334 TYR cc_start: 0.9286 (t80) cc_final: 0.9051 (t80) REVERT: G 1 MET cc_start: 0.6402 (ptp) cc_final: 0.6160 (ptp) REVERT: G 242 LYS cc_start: 0.9503 (tppt) cc_final: 0.9292 (ptpt) REVERT: L 642 MET cc_start: -0.0417 (tmm) cc_final: -0.0715 (tmm) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.2539 time to fit residues: 222.0217 Evaluate side-chains 420 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 237 optimal weight: 0.8980 chunk 473 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 489 optimal weight: 50.0000 chunk 377 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 373 ASN ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 215 ASN D 608 ASN E 84 ASN ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 GLN K 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.101131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.078044 restraints weight = 467798.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.077927 restraints weight = 220909.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.078008 restraints weight = 123572.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.078392 restraints weight = 82134.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.078546 restraints weight = 61095.977| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40331 Z= 0.167 Angle : 0.592 9.278 54422 Z= 0.313 Chirality : 0.041 0.204 6163 Planarity : 0.004 0.073 7056 Dihedral : 8.356 117.140 5698 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4979 helix: 1.81 (0.10), residues: 2638 sheet: 0.04 (0.18), residues: 626 loop : -0.59 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 10 TYR 0.020 0.001 TYR A 315 PHE 0.025 0.002 PHE C 248 TRP 0.014 0.001 TRP C 632 HIS 0.007 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00351 (40331) covalent geometry : angle 0.59216 (54422) hydrogen bonds : bond 0.03819 ( 2078) hydrogen bonds : angle 4.14614 ( 6081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 512 time to evaluate : 1.974 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: 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 278 LEU cc_start: 0.9565 (mt) cc_final: 0.9357 (mt) REVERT: A 352 ASP cc_start: 0.9426 (p0) cc_final: 0.9150 (p0) REVERT: A 370 ASN cc_start: 0.9578 (m110) cc_final: 0.9376 (m110) REVERT: A 529 MET cc_start: 0.7337 (ttt) cc_final: 0.6162 (tmm) REVERT: A 621 LEU cc_start: 0.9717 (tp) cc_final: 0.9291 (tp) REVERT: A 662 LEU cc_start: 0.9837 (tp) cc_final: 0.9404 (tp) REVERT: A 664 MET cc_start: 0.9524 (ptp) cc_final: 0.9163 (mpp) REVERT: A 691 MET cc_start: 0.7242 (ttt) cc_final: 0.6104 (tmm) REVERT: B 256 PHE cc_start: 0.9603 (m-80) cc_final: 0.9151 (m-80) REVERT: B 304 LYS cc_start: 0.9309 (mtpt) cc_final: 0.8699 (mptt) REVERT: B 355 PHE cc_start: 0.9305 (m-80) cc_final: 0.8972 (m-80) REVERT: B 400 ILE cc_start: 0.9312 (mm) cc_final: 0.9096 (mm) REVERT: B 495 LEU cc_start: 0.8127 (mt) cc_final: 0.7763 (mt) REVERT: B 519 ASP cc_start: 0.9559 (t70) cc_final: 0.9242 (t0) REVERT: B 603 ILE cc_start: 0.9761 (pt) cc_final: 0.9453 (pt) REVERT: B 607 ASP cc_start: 0.9384 (m-30) cc_final: 0.8700 (m-30) REVERT: B 608 ASN cc_start: 0.9532 (m110) cc_final: 0.8778 (m110) REVERT: B 611 ARG cc_start: 0.9293 (ptp-110) cc_final: 0.9066 (ptt-90) REVERT: B 678 ILE cc_start: 0.9550 (tp) cc_final: 0.9304 (tp) REVERT: C 19 MET cc_start: -0.0164 (mmt) cc_final: -0.2837 (ttm) REVERT: C 277 LEU cc_start: 0.9793 (tp) cc_final: 0.9538 (tp) REVERT: C 278 LEU cc_start: 0.9228 (mt) cc_final: 0.8496 (mt) REVERT: C 293 LYS cc_start: 0.9766 (mmtt) cc_final: 0.9565 (mmtm) REVERT: C 349 ASP cc_start: 0.9425 (t0) cc_final: 0.9029 (t0) REVERT: C 410 PHE cc_start: 0.9483 (m-80) cc_final: 0.8705 (m-80) REVERT: C 428 PHE cc_start: 0.9385 (m-80) cc_final: 0.8704 (m-10) REVERT: C 607 ASP cc_start: 0.9582 (t0) cc_final: 0.9290 (t0) REVERT: C 611 ARG cc_start: 0.9266 (mtm110) cc_final: 0.8986 (mtm110) REVERT: C 624 ASP cc_start: 0.9230 (t0) cc_final: 0.8650 (p0) REVERT: C 647 LEU cc_start: 0.9859 (mt) cc_final: 0.9637 (mt) REVERT: C 701 MET cc_start: 0.8797 (ptt) cc_final: 0.8447 (ptt) REVERT: D 22 MET cc_start: 0.8109 (ptp) cc_final: 0.3961 (tmm) REVERT: D 312 LEU cc_start: 0.8945 (tp) cc_final: 0.8692 (tp) REVERT: D 348 PHE cc_start: 0.9552 (m-10) cc_final: 0.9171 (t80) REVERT: D 349 ASP cc_start: 0.8725 (t0) cc_final: 0.8388 (t0) REVERT: D 355 PHE cc_start: 0.9408 (m-80) cc_final: 0.9060 (m-80) REVERT: D 375 LEU cc_start: 0.9649 (pp) cc_final: 0.8952 (pp) REVERT: D 393 MET cc_start: 0.9054 (mtp) cc_final: 0.8797 (mtp) REVERT: D 400 ILE cc_start: 0.9565 (mm) cc_final: 0.9350 (mm) REVERT: D 428 PHE cc_start: 0.9129 (m-80) cc_final: 0.8819 (m-80) REVERT: D 608 ASN cc_start: 0.9725 (m-40) cc_final: 0.9420 (m110) REVERT: D 662 LEU cc_start: 0.9408 (tp) cc_final: 0.9016 (tp) REVERT: E 513 PHE cc_start: 0.8821 (t80) cc_final: 0.8225 (t80) REVERT: E 597 MET cc_start: 0.9387 (mtp) cc_final: 0.9048 (mtp) REVERT: E 602 LYS cc_start: 0.9801 (mtmm) cc_final: 0.9590 (mttm) REVERT: E 647 LEU cc_start: 0.9880 (mt) cc_final: 0.9600 (mt) REVERT: F 334 TYR cc_start: 0.9423 (t80) cc_final: 0.9188 (t80) REVERT: F 520 LEU cc_start: 0.9388 (tp) cc_final: 0.9018 (mp) REVERT: F 602 LYS cc_start: 0.9819 (mttt) cc_final: 0.9552 (mttt) REVERT: G 1 MET cc_start: 0.6580 (ptp) cc_final: 0.6376 (ptp) REVERT: L 450 MET cc_start: 0.2572 (ptp) cc_final: 0.2191 (ptp) REVERT: L 642 MET cc_start: -0.0390 (tmm) cc_final: -0.0659 (tmm) outliers start: 2 outliers final: 0 residues processed: 513 average time/residue: 0.2582 time to fit residues: 214.2720 Evaluate side-chains 403 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 178 optimal weight: 7.9990 chunk 335 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 442 optimal weight: 30.0000 chunk 489 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 322 ASN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN B 475 ASN B 756 GLN C 84 ASN C 322 ASN C 446 ASN C 619 ASN D 84 ASN D 548 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 GLN ** L 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 603 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.095919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.072564 restraints weight = 488650.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.073872 restraints weight = 238504.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.074234 restraints weight = 148148.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.074646 restraints weight = 101715.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.074594 restraints weight = 80235.940| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40331 Z= 0.222 Angle : 0.657 8.629 54422 Z= 0.347 Chirality : 0.042 0.176 6163 Planarity : 0.005 0.081 7056 Dihedral : 8.467 108.743 5698 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4979 helix: 1.49 (0.10), residues: 2661 sheet: -0.08 (0.18), residues: 627 loop : -0.57 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 409 TYR 0.047 0.002 TYR B 57 PHE 0.023 0.002 PHE D 610 TRP 0.020 0.002 TRP C 632 HIS 0.005 0.001 HIS F 742 Details of bonding type rmsd covalent geometry : bond 0.00454 (40331) covalent geometry : angle 0.65731 (54422) hydrogen bonds : bond 0.03909 ( 2078) hydrogen bonds : angle 4.30396 ( 6081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 1.567 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: 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 278 LEU cc_start: 0.9516 (mt) cc_final: 0.9269 (mt) REVERT: A 331 GLU cc_start: 0.9832 (pt0) cc_final: 0.9618 (pt0) REVERT: A 389 LEU cc_start: 0.9662 (tp) cc_final: 0.9459 (tp) REVERT: A 404 LEU cc_start: 0.9519 (mm) cc_final: 0.9283 (mm) REVERT: A 621 LEU cc_start: 0.9766 (tp) cc_final: 0.9346 (tp) REVERT: A 662 LEU cc_start: 0.9853 (tp) cc_final: 0.9554 (tp) REVERT: A 664 MET cc_start: 0.9613 (ptp) cc_final: 0.9264 (mpp) REVERT: A 691 MET cc_start: 0.7745 (ttt) cc_final: 0.6575 (tmm) REVERT: B 256 PHE cc_start: 0.9632 (m-80) cc_final: 0.9266 (m-80) REVERT: B 304 LYS cc_start: 0.9318 (mtpt) cc_final: 0.8773 (mptt) REVERT: B 327 PHE cc_start: 0.9626 (m-80) cc_final: 0.9331 (m-80) REVERT: B 355 PHE cc_start: 0.9488 (m-80) cc_final: 0.9139 (m-80) REVERT: B 399 LEU cc_start: 0.9474 (tt) cc_final: 0.9243 (tt) REVERT: B 495 LEU cc_start: 0.8345 (mt) cc_final: 0.7807 (mt) REVERT: B 519 ASP cc_start: 0.9589 (t70) cc_final: 0.9226 (t0) REVERT: B 588 LEU cc_start: 0.9253 (tp) cc_final: 0.8753 (tp) REVERT: B 597 MET cc_start: 0.9391 (mtp) cc_final: 0.9132 (mtp) REVERT: B 603 ILE cc_start: 0.9755 (pt) cc_final: 0.9456 (pt) REVERT: B 607 ASP cc_start: 0.9364 (m-30) cc_final: 0.8737 (m-30) REVERT: B 608 ASN cc_start: 0.9563 (m110) cc_final: 0.8782 (m-40) REVERT: B 611 ARG cc_start: 0.9359 (ptp-110) cc_final: 0.9130 (ptt-90) REVERT: B 682 PHE cc_start: 0.9249 (m-80) cc_final: 0.8958 (m-80) REVERT: C 19 MET cc_start: 0.4880 (mmt) cc_final: 0.2022 (ttp) REVERT: C 278 LEU cc_start: 0.9198 (mt) cc_final: 0.8557 (mt) REVERT: C 348 PHE cc_start: 0.9679 (m-80) cc_final: 0.9323 (t80) REVERT: C 349 ASP cc_start: 0.9490 (t0) cc_final: 0.9272 (t0) REVERT: C 393 MET cc_start: 0.8299 (tpp) cc_final: 0.7495 (mmm) REVERT: C 410 PHE cc_start: 0.9422 (m-80) cc_final: 0.8638 (m-80) REVERT: C 428 PHE cc_start: 0.8996 (m-10) cc_final: 0.8737 (m-10) REVERT: C 607 ASP cc_start: 0.9568 (t0) cc_final: 0.9311 (t0) REVERT: C 611 ARG cc_start: 0.9304 (mtm110) cc_final: 0.9051 (mtm110) REVERT: C 624 ASP cc_start: 0.9172 (t0) cc_final: 0.8795 (p0) REVERT: C 701 MET cc_start: 0.9029 (ptt) cc_final: 0.8652 (ptt) REVERT: D 22 MET cc_start: 0.6917 (ptp) cc_final: 0.6558 (tmm) REVERT: D 277 LEU cc_start: 0.9905 (tp) cc_final: 0.9645 (tp) REVERT: D 312 LEU cc_start: 0.8952 (tp) cc_final: 0.8710 (tp) REVERT: D 348 PHE cc_start: 0.9636 (m-10) cc_final: 0.9140 (t80) REVERT: D 349 ASP cc_start: 0.8809 (t0) cc_final: 0.8494 (t0) REVERT: D 355 PHE cc_start: 0.9327 (m-80) cc_final: 0.8461 (m-80) REVERT: D 393 MET cc_start: 0.9148 (mtp) cc_final: 0.8720 (mtp) REVERT: D 410 PHE cc_start: 0.9749 (m-10) cc_final: 0.9477 (m-80) REVERT: D 428 PHE cc_start: 0.9334 (m-80) cc_final: 0.8982 (m-80) REVERT: D 528 MET cc_start: 0.9567 (mmp) cc_final: 0.9176 (mmp) REVERT: D 644 LEU cc_start: 0.9788 (tp) cc_final: 0.9544 (tp) REVERT: D 662 LEU cc_start: 0.9529 (tp) cc_final: 0.9191 (tp) REVERT: E 513 PHE cc_start: 0.8870 (t80) cc_final: 0.8156 (t80) REVERT: E 597 MET cc_start: 0.9366 (mtp) cc_final: 0.9059 (mtp) REVERT: E 631 ASP cc_start: 0.9380 (m-30) cc_final: 0.9176 (m-30) REVERT: F 334 TYR cc_start: 0.9264 (t80) cc_final: 0.9048 (t80) REVERT: F 520 LEU cc_start: 0.9468 (tp) cc_final: 0.9071 (mp) REVERT: F 602 LYS cc_start: 0.9802 (mttt) cc_final: 0.9549 (mttm) REVERT: G 1 MET cc_start: 0.6592 (ptp) cc_final: 0.6374 (ptp) REVERT: H 1 MET cc_start: 0.8545 (mtp) cc_final: 0.8243 (ttt) REVERT: L 450 MET cc_start: 0.2397 (ptp) cc_final: 0.2119 (ptp) REVERT: L 642 MET cc_start: -0.0352 (tmm) cc_final: -0.0600 (tmm) outliers start: 1 outliers final: 0 residues processed: 472 average time/residue: 0.2512 time to fit residues: 193.1424 Evaluate side-chains 369 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 455 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 279 optimal weight: 50.0000 chunk 161 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 292 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 ASN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** I 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 GLN L 597 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.076105 restraints weight = 491125.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.076911 restraints weight = 220849.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 85)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.076331 restraints weight = 118546.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.076563 restraints weight = 80096.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076824 restraints weight = 61677.025| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40331 Z= 0.120 Angle : 0.565 10.241 54422 Z= 0.295 Chirality : 0.041 0.247 6163 Planarity : 0.004 0.064 7056 Dihedral : 8.148 103.313 5698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.36 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.12), residues: 4979 helix: 1.78 (0.10), residues: 2651 sheet: 0.15 (0.18), residues: 621 loop : -0.49 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 324 TYR 0.041 0.001 TYR E 57 PHE 0.032 0.001 PHE D 610 TRP 0.015 0.001 TRP C 632 HIS 0.004 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00259 (40331) covalent geometry : angle 0.56521 (54422) hydrogen bonds : bond 0.03531 ( 2078) hydrogen bonds : angle 4.03012 ( 6081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.847 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: 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 278 LEU cc_start: 0.9579 (mt) cc_final: 0.9341 (mt) REVERT: A 321 GLU cc_start: 0.9743 (tp30) cc_final: 0.9445 (tp30) REVERT: A 529 MET cc_start: 0.7382 (ttt) cc_final: 0.6726 (tmm) REVERT: A 662 LEU cc_start: 0.9837 (tp) cc_final: 0.9552 (tp) REVERT: A 664 MET cc_start: 0.9632 (ptp) cc_final: 0.9282 (mpp) REVERT: A 691 MET cc_start: 0.7633 (ttt) cc_final: 0.6655 (tmm) REVERT: B 19 MET cc_start: -0.2598 (ttm) cc_final: -0.4582 (tmm) REVERT: B 256 PHE cc_start: 0.9616 (m-80) cc_final: 0.9220 (m-80) REVERT: B 278 LEU cc_start: 0.9695 (mm) cc_final: 0.8970 (mm) REVERT: B 304 LYS cc_start: 0.9376 (mtpt) cc_final: 0.8869 (mptt) REVERT: B 327 PHE cc_start: 0.9642 (m-80) cc_final: 0.9363 (m-80) REVERT: B 355 PHE cc_start: 0.9350 (m-80) cc_final: 0.8971 (m-80) REVERT: B 382 VAL cc_start: 0.9511 (m) cc_final: 0.9004 (p) REVERT: B 400 ILE cc_start: 0.9354 (mm) cc_final: 0.9148 (mm) REVERT: B 495 LEU cc_start: 0.8262 (mt) cc_final: 0.7681 (mt) REVERT: B 519 ASP cc_start: 0.9535 (t70) cc_final: 0.9174 (t0) REVERT: B 588 LEU cc_start: 0.9199 (tp) cc_final: 0.8782 (tp) REVERT: B 603 ILE cc_start: 0.9759 (pt) cc_final: 0.9497 (pt) REVERT: B 607 ASP cc_start: 0.9388 (m-30) cc_final: 0.9112 (m-30) REVERT: B 608 ASN cc_start: 0.9563 (m110) cc_final: 0.9325 (m110) REVERT: B 682 PHE cc_start: 0.9310 (m-80) cc_final: 0.8999 (m-80) REVERT: C 19 MET cc_start: -0.0604 (mmt) cc_final: -0.4290 (ttp) REVERT: C 244 LEU cc_start: 0.9747 (mp) cc_final: 0.9425 (pt) REVERT: C 248 PHE cc_start: 0.9587 (m-80) cc_final: 0.9153 (m-80) REVERT: C 269 LEU cc_start: 0.9532 (mt) cc_final: 0.9323 (mt) REVERT: C 277 LEU cc_start: 0.9811 (tp) cc_final: 0.9608 (tp) REVERT: C 278 LEU cc_start: 0.9291 (mt) cc_final: 0.8677 (mt) REVERT: C 348 PHE cc_start: 0.9652 (m-80) cc_final: 0.9324 (t80) REVERT: C 349 ASP cc_start: 0.9474 (t0) cc_final: 0.9267 (t0) REVERT: C 410 PHE cc_start: 0.9424 (m-80) cc_final: 0.8651 (m-80) REVERT: C 428 PHE cc_start: 0.8887 (m-10) cc_final: 0.8621 (m-10) REVERT: C 519 ASP cc_start: 0.9642 (m-30) cc_final: 0.9280 (m-30) REVERT: C 607 ASP cc_start: 0.9587 (t0) cc_final: 0.9245 (t0) REVERT: C 611 ARG cc_start: 0.9293 (mtm110) cc_final: 0.8938 (mtm110) REVERT: C 624 ASP cc_start: 0.9091 (t0) cc_final: 0.8685 (p0) REVERT: C 701 MET cc_start: 0.8939 (ptt) cc_final: 0.8638 (ptt) REVERT: D 22 MET cc_start: 0.7771 (ptp) cc_final: 0.4636 (tmm) REVERT: D 277 LEU cc_start: 0.9835 (tp) cc_final: 0.9556 (pp) REVERT: D 312 LEU cc_start: 0.8988 (tp) cc_final: 0.8755 (tp) REVERT: D 348 PHE cc_start: 0.9601 (m-10) cc_final: 0.9152 (t80) REVERT: D 349 ASP cc_start: 0.8714 (t0) cc_final: 0.8455 (t0) REVERT: D 351 LEU cc_start: 0.9684 (mp) cc_final: 0.9065 (mp) REVERT: D 355 PHE cc_start: 0.9262 (m-80) cc_final: 0.8454 (m-80) REVERT: D 391 ILE cc_start: 0.9636 (mm) cc_final: 0.9300 (mm) REVERT: D 393 MET cc_start: 0.9041 (mtp) cc_final: 0.8716 (mtp) REVERT: D 528 MET cc_start: 0.9556 (mmp) cc_final: 0.9060 (mmp) REVERT: D 644 LEU cc_start: 0.9721 (tp) cc_final: 0.9480 (tp) REVERT: D 648 LYS cc_start: 0.9073 (ptpp) cc_final: 0.8588 (ptpp) REVERT: D 662 LEU cc_start: 0.9474 (tp) cc_final: 0.9144 (tp) REVERT: E 19 MET cc_start: 0.8294 (mmm) cc_final: 0.7973 (mmt) REVERT: E 440 MET cc_start: 0.8886 (pmm) cc_final: 0.8671 (pmm) REVERT: E 513 PHE cc_start: 0.8729 (t80) cc_final: 0.8055 (t80) REVERT: E 602 LYS cc_start: 0.9823 (mtmm) cc_final: 0.9603 (mttm) REVERT: F 334 TYR cc_start: 0.9391 (t80) cc_final: 0.9145 (t80) REVERT: F 602 LYS cc_start: 0.9800 (mttt) cc_final: 0.9560 (mttm) REVERT: F 647 LEU cc_start: 0.9890 (mt) cc_final: 0.9480 (mt) REVERT: G 1 MET cc_start: 0.6699 (ptp) cc_final: 0.6475 (ptp) REVERT: H 1 MET cc_start: 0.8576 (mtp) cc_final: 0.8327 (ttt) REVERT: L 450 MET cc_start: -0.1062 (ptp) cc_final: -0.1590 (ptp) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.2515 time to fit residues: 200.8241 Evaluate side-chains 384 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 7.9990 chunk 326 optimal weight: 0.9980 chunk 272 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 463 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 189 optimal weight: 0.0170 chunk 249 optimal weight: 5.9990 chunk 407 optimal weight: 30.0000 chunk 342 optimal weight: 7.9990 overall best weight: 4.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS I 195 GLN ** I 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.096849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.073393 restraints weight = 506483.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.074560 restraints weight = 236246.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.076263 restraints weight = 130875.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.075610 restraints weight = 90325.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.075706 restraints weight = 67301.532| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40331 Z= 0.162 Angle : 0.579 9.644 54422 Z= 0.304 Chirality : 0.040 0.218 6163 Planarity : 0.004 0.063 7056 Dihedral : 8.097 101.979 5698 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4979 helix: 1.78 (0.10), residues: 2667 sheet: 0.11 (0.18), residues: 627 loop : -0.47 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 324 TYR 0.024 0.001 TYR E 57 PHE 0.029 0.001 PHE C 355 TRP 0.019 0.001 TRP C 632 HIS 0.005 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00339 (40331) covalent geometry : angle 0.57937 (54422) hydrogen bonds : bond 0.03485 ( 2078) hydrogen bonds : angle 4.10329 ( 6081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.684 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: 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 278 LEU cc_start: 0.9571 (mt) cc_final: 0.9327 (mt) REVERT: A 357 GLN cc_start: 0.8944 (tp40) cc_final: 0.8697 (tp40) REVERT: A 358 ARG cc_start: 0.9028 (ptt-90) cc_final: 0.8698 (ptt-90) REVERT: A 529 MET cc_start: 0.7416 (ttt) cc_final: 0.6843 (tmm) REVERT: A 610 PHE cc_start: 0.9424 (m-80) cc_final: 0.8948 (m-80) REVERT: A 662 LEU cc_start: 0.9847 (tp) cc_final: 0.9620 (tp) REVERT: A 664 MET cc_start: 0.9666 (ptp) cc_final: 0.9356 (mpp) REVERT: A 691 MET cc_start: 0.7610 (ttt) cc_final: 0.6519 (tmm) REVERT: B 19 MET cc_start: 0.3973 (ttm) cc_final: 0.3713 (ttm) REVERT: B 256 PHE cc_start: 0.9631 (m-80) cc_final: 0.9272 (m-80) REVERT: B 278 LEU cc_start: 0.9687 (mm) cc_final: 0.9234 (mm) REVERT: B 304 LYS cc_start: 0.9324 (mtpt) cc_final: 0.8867 (mptt) REVERT: B 327 PHE cc_start: 0.9622 (m-80) cc_final: 0.9410 (m-80) REVERT: B 355 PHE cc_start: 0.9417 (m-80) cc_final: 0.9045 (m-80) REVERT: B 378 LYS cc_start: 0.9710 (mmmm) cc_final: 0.9297 (mmmm) REVERT: B 382 VAL cc_start: 0.9528 (m) cc_final: 0.9018 (p) REVERT: B 399 LEU cc_start: 0.9423 (tt) cc_final: 0.9212 (tt) REVERT: B 400 ILE cc_start: 0.9395 (mm) cc_final: 0.9178 (mm) REVERT: B 495 LEU cc_start: 0.8033 (mt) cc_final: 0.7484 (mt) REVERT: B 519 ASP cc_start: 0.9568 (t70) cc_final: 0.9217 (t0) REVERT: B 588 LEU cc_start: 0.9190 (tp) cc_final: 0.8831 (tp) REVERT: B 603 ILE cc_start: 0.9760 (pt) cc_final: 0.9456 (pt) REVERT: B 607 ASP cc_start: 0.9382 (m-30) cc_final: 0.8655 (m-30) REVERT: B 608 ASN cc_start: 0.9561 (m110) cc_final: 0.8891 (m110) REVERT: B 611 ARG cc_start: 0.9401 (ptp-110) cc_final: 0.9109 (ptt-90) REVERT: B 682 PHE cc_start: 0.9357 (m-80) cc_final: 0.9013 (m-80) REVERT: C 19 MET cc_start: 0.2814 (mmt) cc_final: -0.0471 (ttp) REVERT: C 244 LEU cc_start: 0.9699 (mp) cc_final: 0.9291 (mt) REVERT: C 248 PHE cc_start: 0.9559 (m-80) cc_final: 0.9233 (m-80) REVERT: C 278 LEU cc_start: 0.9249 (mt) cc_final: 0.8674 (mt) REVERT: C 348 PHE cc_start: 0.9649 (m-80) cc_final: 0.9295 (t80) REVERT: C 410 PHE cc_start: 0.9395 (m-80) cc_final: 0.9071 (m-80) REVERT: C 428 PHE cc_start: 0.8949 (m-10) cc_final: 0.8691 (m-10) REVERT: C 607 ASP cc_start: 0.9572 (t0) cc_final: 0.9321 (t0) REVERT: C 611 ARG cc_start: 0.9286 (mtm110) cc_final: 0.9021 (mtm110) REVERT: C 624 ASP cc_start: 0.9066 (t0) cc_final: 0.8728 (p0) REVERT: C 701 MET cc_start: 0.9030 (ptt) cc_final: 0.8726 (ptt) REVERT: D 22 MET cc_start: 0.6801 (ptp) cc_final: 0.6345 (tmm) REVERT: D 312 LEU cc_start: 0.9061 (tp) cc_final: 0.8816 (tp) REVERT: D 348 PHE cc_start: 0.9577 (m-10) cc_final: 0.9154 (t80) REVERT: D 349 ASP cc_start: 0.8753 (t0) cc_final: 0.8432 (t0) REVERT: D 351 LEU cc_start: 0.9674 (mp) cc_final: 0.9063 (mp) REVERT: D 355 PHE cc_start: 0.9267 (m-80) cc_final: 0.8450 (m-80) REVERT: D 393 MET cc_start: 0.8977 (mtp) cc_final: 0.8753 (mtp) REVERT: D 528 MET cc_start: 0.9551 (mmp) cc_final: 0.9093 (mmp) REVERT: D 608 ASN cc_start: 0.9624 (m110) cc_final: 0.9236 (m110) REVERT: D 662 LEU cc_start: 0.9592 (tp) cc_final: 0.9295 (tp) REVERT: E 19 MET cc_start: 0.8141 (mmm) cc_final: 0.7800 (mmt) REVERT: E 349 ASP cc_start: 0.8838 (t70) cc_final: 0.8594 (t0) REVERT: E 513 PHE cc_start: 0.8971 (t80) cc_final: 0.8282 (t80) REVERT: E 648 LYS cc_start: 0.9522 (tptt) cc_final: 0.9285 (tptt) REVERT: F 334 TYR cc_start: 0.9219 (t80) cc_final: 0.8999 (t80) REVERT: F 602 LYS cc_start: 0.9785 (mttt) cc_final: 0.9566 (mttm) REVERT: G 1 MET cc_start: 0.6737 (ptp) cc_final: 0.6509 (ptp) REVERT: G 110 ARG cc_start: 0.8634 (tmt170) cc_final: 0.8384 (mmm-85) REVERT: H 1 MET cc_start: 0.8544 (mtp) cc_final: 0.8342 (ttt) REVERT: L 450 MET cc_start: 0.0647 (ptp) cc_final: 0.0409 (ptp) REVERT: L 642 MET cc_start: -0.0460 (tmm) cc_final: -0.0705 (ppp) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.2550 time to fit residues: 192.6205 Evaluate side-chains 380 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 480 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 496 optimal weight: 5.9990 chunk 404 optimal weight: 50.0000 chunk 316 optimal weight: 4.9990 chunk 379 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 449 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 165 HIS ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 HIS ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** I 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 597 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.097994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.074766 restraints weight = 468617.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.074867 restraints weight = 212815.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.075537 restraints weight = 118750.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075921 restraints weight = 80022.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.076056 restraints weight = 59148.754| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40331 Z= 0.121 Angle : 0.558 10.194 54422 Z= 0.291 Chirality : 0.040 0.185 6163 Planarity : 0.004 0.079 7056 Dihedral : 7.966 99.405 5698 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.12), residues: 4979 helix: 1.85 (0.10), residues: 2667 sheet: 0.21 (0.19), residues: 613 loop : -0.41 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 324 TYR 0.018 0.001 TYR E 57 PHE 0.031 0.001 PHE D 610 TRP 0.015 0.001 TRP C 632 HIS 0.005 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00259 (40331) covalent geometry : angle 0.55835 (54422) hydrogen bonds : bond 0.03378 ( 2078) hydrogen bonds : angle 3.98310 ( 6081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.708 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: 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 321 GLU cc_start: 0.9763 (tp30) cc_final: 0.9458 (tp30) REVERT: A 357 GLN cc_start: 0.9056 (tp40) cc_final: 0.8828 (tp40) REVERT: A 358 ARG cc_start: 0.9083 (ptt-90) cc_final: 0.8764 (ptt-90) REVERT: A 529 MET cc_start: 0.7365 (ttt) cc_final: 0.6703 (tmm) REVERT: A 664 MET cc_start: 0.9674 (ptp) cc_final: 0.9361 (mpp) REVERT: A 691 MET cc_start: 0.7978 (ttt) cc_final: 0.6642 (tpp) REVERT: B 19 MET cc_start: 0.0367 (ttm) cc_final: -0.0714 (ttm) REVERT: B 256 PHE cc_start: 0.9633 (m-80) cc_final: 0.9267 (m-80) REVERT: B 278 LEU cc_start: 0.9692 (mm) cc_final: 0.9183 (mm) REVERT: B 304 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8874 (mptt) REVERT: B 327 PHE cc_start: 0.9603 (m-80) cc_final: 0.9358 (m-80) REVERT: B 355 PHE cc_start: 0.9354 (m-80) cc_final: 0.8981 (m-80) REVERT: B 378 LYS cc_start: 0.9753 (mmmm) cc_final: 0.9321 (mmmm) REVERT: B 382 VAL cc_start: 0.9483 (m) cc_final: 0.9063 (p) REVERT: B 384 GLN cc_start: 0.9444 (mm110) cc_final: 0.9219 (mm110) REVERT: B 400 ILE cc_start: 0.9381 (mm) cc_final: 0.9175 (mm) REVERT: B 404 LEU cc_start: 0.9763 (mm) cc_final: 0.9561 (mm) REVERT: B 495 LEU cc_start: 0.7995 (mt) cc_final: 0.7429 (mt) REVERT: B 519 ASP cc_start: 0.9555 (t70) cc_final: 0.9204 (t0) REVERT: B 588 LEU cc_start: 0.9153 (tp) cc_final: 0.8810 (tp) REVERT: B 603 ILE cc_start: 0.9769 (pt) cc_final: 0.9473 (pt) REVERT: B 607 ASP cc_start: 0.9361 (m-30) cc_final: 0.8537 (m-30) REVERT: B 608 ASN cc_start: 0.9578 (m110) cc_final: 0.8932 (m110) REVERT: B 611 ARG cc_start: 0.9379 (ptp-110) cc_final: 0.9034 (ptt-90) REVERT: B 644 LEU cc_start: 0.9762 (tp) cc_final: 0.9499 (tp) REVERT: B 682 PHE cc_start: 0.9369 (m-80) cc_final: 0.8994 (m-80) REVERT: B 701 MET cc_start: 0.8882 (ptp) cc_final: 0.8673 (ptp) REVERT: C 19 MET cc_start: 0.0446 (mmt) cc_final: -0.2384 (mtm) REVERT: C 244 LEU cc_start: 0.9670 (mp) cc_final: 0.9268 (mt) REVERT: C 248 PHE cc_start: 0.9554 (m-80) cc_final: 0.9208 (m-80) REVERT: C 277 LEU cc_start: 0.9808 (tp) cc_final: 0.9606 (tp) REVERT: C 278 LEU cc_start: 0.9295 (mt) cc_final: 0.8788 (mt) REVERT: C 348 PHE cc_start: 0.9662 (m-80) cc_final: 0.9332 (t80) REVERT: C 355 PHE cc_start: 0.9456 (m-80) cc_final: 0.9062 (m-80) REVERT: C 393 MET cc_start: 0.7682 (mmm) cc_final: 0.7389 (mmt) REVERT: C 410 PHE cc_start: 0.9528 (m-80) cc_final: 0.8935 (m-80) REVERT: C 428 PHE cc_start: 0.8884 (m-10) cc_final: 0.8591 (m-10) REVERT: C 607 ASP cc_start: 0.9570 (t0) cc_final: 0.9340 (t0) REVERT: C 621 LEU cc_start: 0.9598 (mm) cc_final: 0.9336 (mm) REVERT: C 624 ASP cc_start: 0.9028 (t0) cc_final: 0.8641 (p0) REVERT: C 701 MET cc_start: 0.9019 (ptt) cc_final: 0.8784 (ptt) REVERT: D 22 MET cc_start: 0.7370 (ptp) cc_final: 0.6150 (tmm) REVERT: D 312 LEU cc_start: 0.9133 (tp) cc_final: 0.8909 (tp) REVERT: D 348 PHE cc_start: 0.9577 (m-10) cc_final: 0.9159 (t80) REVERT: D 349 ASP cc_start: 0.8733 (t0) cc_final: 0.8451 (t0) REVERT: D 351 LEU cc_start: 0.9687 (mp) cc_final: 0.9068 (mp) REVERT: D 355 PHE cc_start: 0.9236 (m-80) cc_final: 0.8426 (m-80) REVERT: D 528 MET cc_start: 0.9520 (mmp) cc_final: 0.8994 (mmp) REVERT: D 662 LEU cc_start: 0.9550 (tp) cc_final: 0.9240 (tp) REVERT: D 676 MET cc_start: 0.9403 (mpp) cc_final: 0.9154 (ptp) REVERT: E 19 MET cc_start: 0.8081 (mmm) cc_final: 0.7724 (mmt) REVERT: E 349 ASP cc_start: 0.8844 (t70) cc_final: 0.8597 (t0) REVERT: E 513 PHE cc_start: 0.8845 (t80) cc_final: 0.8173 (t80) REVERT: F 334 TYR cc_start: 0.9266 (t80) cc_final: 0.9037 (t80) REVERT: F 602 LYS cc_start: 0.9778 (mttt) cc_final: 0.9198 (mttt) REVERT: G 1 MET cc_start: 0.6734 (ptp) cc_final: 0.6509 (ptp) REVERT: H 1 MET cc_start: 0.8477 (mtp) cc_final: 0.8253 (ttt) REVERT: L 450 MET cc_start: -0.0284 (ptp) cc_final: -0.1433 (ptp) REVERT: L 634 ASP cc_start: 0.7381 (t70) cc_final: 0.6962 (m-30) REVERT: L 642 MET cc_start: -0.0494 (tmm) cc_final: -0.0723 (ppp) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.2627 time to fit residues: 199.7343 Evaluate side-chains 381 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 150 optimal weight: 0.0070 chunk 131 optimal weight: 30.0000 chunk 251 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 285 optimal weight: 6.9990 chunk 278 optimal weight: 50.0000 chunk 194 optimal weight: 5.9990 overall best weight: 4.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN F 438 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.096269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.072688 restraints weight = 572965.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.072264 restraints weight = 246422.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.072880 restraints weight = 133773.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.073138 restraints weight = 84811.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.073344 restraints weight = 64771.690| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40331 Z= 0.150 Angle : 0.589 9.869 54422 Z= 0.307 Chirality : 0.041 0.183 6163 Planarity : 0.004 0.062 7056 Dihedral : 7.940 97.508 5698 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 0.02 % Allowed : 0.53 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.12), residues: 4979 helix: 1.77 (0.10), residues: 2683 sheet: 0.09 (0.18), residues: 633 loop : -0.43 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 324 TYR 0.017 0.001 TYR I 66 PHE 0.021 0.001 PHE D 610 TRP 0.022 0.001 TRP C 632 HIS 0.006 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00318 (40331) covalent geometry : angle 0.58868 (54422) hydrogen bonds : bond 0.03424 ( 2078) hydrogen bonds : angle 4.11709 ( 6081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.532 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: 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 278 LEU cc_start: 0.9419 (mt) cc_final: 0.9142 (mt) REVERT: A 321 GLU cc_start: 0.9776 (tp30) cc_final: 0.9483 (tp30) REVERT: A 357 GLN cc_start: 0.9014 (tp40) cc_final: 0.8777 (tp-100) REVERT: A 358 ARG cc_start: 0.9097 (ptt-90) cc_final: 0.8797 (ptt-90) REVERT: A 529 MET cc_start: 0.7436 (ttt) cc_final: 0.6800 (tmm) REVERT: A 610 PHE cc_start: 0.9461 (m-80) cc_final: 0.8966 (m-80) REVERT: A 644 LEU cc_start: 0.9843 (tp) cc_final: 0.9615 (tp) REVERT: A 648 LYS cc_start: 0.9549 (ptpp) cc_final: 0.8960 (ptpp) REVERT: A 664 MET cc_start: 0.9686 (ptp) cc_final: 0.9317 (tpt) REVERT: B 256 PHE cc_start: 0.9626 (m-80) cc_final: 0.9252 (m-80) REVERT: B 278 LEU cc_start: 0.9701 (mm) cc_final: 0.9153 (mm) REVERT: B 304 LYS cc_start: 0.9357 (mtpt) cc_final: 0.8911 (mptt) REVERT: B 327 PHE cc_start: 0.9594 (m-80) cc_final: 0.8940 (m-80) REVERT: B 355 PHE cc_start: 0.9420 (m-80) cc_final: 0.9055 (m-80) REVERT: B 378 LYS cc_start: 0.9750 (mmmm) cc_final: 0.9438 (mtpt) REVERT: B 382 VAL cc_start: 0.9397 (m) cc_final: 0.8999 (p) REVERT: B 384 GLN cc_start: 0.9375 (mm110) cc_final: 0.9170 (mm110) REVERT: B 399 LEU cc_start: 0.9387 (tt) cc_final: 0.9184 (tt) REVERT: B 400 ILE cc_start: 0.9376 (mm) cc_final: 0.9162 (mm) REVERT: B 495 LEU cc_start: 0.8081 (mt) cc_final: 0.7528 (mt) REVERT: B 588 LEU cc_start: 0.9105 (tp) cc_final: 0.8764 (tp) REVERT: B 603 ILE cc_start: 0.9777 (pt) cc_final: 0.9497 (pt) REVERT: B 607 ASP cc_start: 0.9397 (m-30) cc_final: 0.9146 (m-30) REVERT: B 608 ASN cc_start: 0.9575 (m110) cc_final: 0.9348 (m110) REVERT: B 682 PHE cc_start: 0.9412 (m-80) cc_final: 0.9014 (m-80) REVERT: C 19 MET cc_start: 0.0297 (mmt) cc_final: -0.2583 (mtm) REVERT: C 244 LEU cc_start: 0.9685 (mp) cc_final: 0.9485 (mt) REVERT: C 278 LEU cc_start: 0.9270 (mt) cc_final: 0.8776 (mt) REVERT: C 348 PHE cc_start: 0.9639 (m-80) cc_final: 0.9258 (t80) REVERT: C 355 PHE cc_start: 0.9536 (m-80) cc_final: 0.9121 (m-80) REVERT: C 385 LEU cc_start: 0.9575 (tt) cc_final: 0.9168 (mt) REVERT: C 393 MET cc_start: 0.7672 (mmm) cc_final: 0.7416 (mmt) REVERT: C 410 PHE cc_start: 0.9525 (m-80) cc_final: 0.8996 (m-80) REVERT: C 428 PHE cc_start: 0.8916 (m-10) cc_final: 0.8632 (m-10) REVERT: C 607 ASP cc_start: 0.9643 (t0) cc_final: 0.9346 (t0) REVERT: C 621 LEU cc_start: 0.9603 (mm) cc_final: 0.9289 (mm) REVERT: C 624 ASP cc_start: 0.9041 (t0) cc_final: 0.8707 (p0) REVERT: C 701 MET cc_start: 0.9062 (ptt) cc_final: 0.8816 (ptt) REVERT: D 22 MET cc_start: 0.7747 (ptp) cc_final: 0.5648 (tmm) REVERT: D 312 LEU cc_start: 0.9156 (tp) cc_final: 0.8923 (tp) REVERT: D 348 PHE cc_start: 0.9713 (m-10) cc_final: 0.9509 (m-80) REVERT: D 349 ASP cc_start: 0.8713 (t0) cc_final: 0.8195 (t0) REVERT: D 355 PHE cc_start: 0.9251 (m-80) cc_final: 0.9038 (m-80) REVERT: D 528 MET cc_start: 0.9507 (mmp) cc_final: 0.8952 (mmp) REVERT: D 662 LEU cc_start: 0.9591 (tp) cc_final: 0.9290 (tp) REVERT: E 19 MET cc_start: 0.7924 (mmm) cc_final: 0.7592 (mmt) REVERT: E 335 ARG cc_start: 0.9426 (mtm110) cc_final: 0.9180 (ptt-90) REVERT: E 349 ASP cc_start: 0.8879 (t70) cc_final: 0.8675 (t0) REVERT: E 513 PHE cc_start: 0.8861 (t80) cc_final: 0.8136 (t80) REVERT: E 597 MET cc_start: 0.9443 (mtp) cc_final: 0.9231 (mtp) REVERT: E 661 LEU cc_start: 0.9637 (tp) cc_final: 0.9312 (tt) REVERT: F 334 TYR cc_start: 0.9384 (t80) cc_final: 0.9141 (t80) REVERT: F 438 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7992 (t0) REVERT: F 440 MET cc_start: 0.8441 (ptt) cc_final: 0.7379 (ptt) REVERT: F 602 LYS cc_start: 0.9778 (mttt) cc_final: 0.9538 (mttm) REVERT: G 1 MET cc_start: 0.6758 (ptp) cc_final: 0.6528 (ptp) REVERT: H 1 MET cc_start: 0.8530 (mtp) cc_final: 0.8319 (ttt) REVERT: L 450 MET cc_start: -0.0459 (ptp) cc_final: -0.1554 (ptp) REVERT: L 634 ASP cc_start: 0.7290 (t70) cc_final: 0.6878 (m-30) REVERT: L 642 MET cc_start: -0.0414 (tmm) cc_final: -0.0640 (ppp) outliers start: 1 outliers final: 0 residues processed: 460 average time/residue: 0.2464 time to fit residues: 184.2577 Evaluate side-chains 380 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 394 optimal weight: 8.9990 chunk 398 optimal weight: 40.0000 chunk 242 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.071813 restraints weight = 431957.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.071802 restraints weight = 200077.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.071882 restraints weight = 115481.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.072162 restraints weight = 79864.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.072289 restraints weight = 62369.318| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40331 Z= 0.162 Angle : 0.597 9.620 54422 Z= 0.313 Chirality : 0.041 0.267 6163 Planarity : 0.004 0.063 7056 Dihedral : 7.967 96.459 5698 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 4979 helix: 1.71 (0.10), residues: 2678 sheet: -0.00 (0.18), residues: 635 loop : -0.45 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 324 TYR 0.016 0.001 TYR I 66 PHE 0.026 0.001 PHE D 610 TRP 0.022 0.001 TRP C 632 HIS 0.006 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00341 (40331) covalent geometry : angle 0.59695 (54422) hydrogen bonds : bond 0.03419 ( 2078) hydrogen bonds : angle 4.16916 ( 6081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9958 Ramachandran restraints generated. 4979 Oldfield, 0 Emsley, 4979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.748 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: 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 321 GLU cc_start: 0.9794 (tp30) cc_final: 0.9518 (tp30) REVERT: A 357 GLN cc_start: 0.8977 (tp40) cc_final: 0.8718 (tp40) REVERT: A 358 ARG cc_start: 0.9092 (ptt-90) cc_final: 0.8807 (ptt-90) REVERT: A 529 MET cc_start: 0.7437 (ttt) cc_final: 0.6813 (tmm) REVERT: A 610 PHE cc_start: 0.9525 (m-80) cc_final: 0.9040 (m-80) REVERT: A 664 MET cc_start: 0.9703 (ptp) cc_final: 0.9329 (tpt) REVERT: A 691 MET cc_start: 0.8271 (ttt) cc_final: 0.6965 (tpp) REVERT: B 19 MET cc_start: -0.1733 (ttm) cc_final: -0.3940 (tmm) REVERT: B 256 PHE cc_start: 0.9693 (m-80) cc_final: 0.9273 (m-80) REVERT: B 277 LEU cc_start: 0.9771 (tp) cc_final: 0.9556 (tp) REVERT: B 278 LEU cc_start: 0.9730 (mm) cc_final: 0.9186 (mm) REVERT: B 304 LYS cc_start: 0.9370 (mtpt) cc_final: 0.8955 (mptt) REVERT: B 327 PHE cc_start: 0.9603 (m-80) cc_final: 0.9253 (m-80) REVERT: B 355 PHE cc_start: 0.9490 (m-80) cc_final: 0.9201 (m-80) REVERT: B 378 LYS cc_start: 0.9742 (mmmm) cc_final: 0.9386 (mtpp) REVERT: B 399 LEU cc_start: 0.9412 (tt) cc_final: 0.9209 (tt) REVERT: B 400 ILE cc_start: 0.9413 (mm) cc_final: 0.9200 (mm) REVERT: B 588 LEU cc_start: 0.8981 (tp) cc_final: 0.8708 (tp) REVERT: B 603 ILE cc_start: 0.9777 (pt) cc_final: 0.9474 (pt) REVERT: B 607 ASP cc_start: 0.9448 (m-30) cc_final: 0.8742 (m-30) REVERT: B 608 ASN cc_start: 0.9615 (m110) cc_final: 0.8989 (m110) REVERT: B 611 ARG cc_start: 0.9426 (ptp-110) cc_final: 0.9182 (ptt-90) REVERT: B 612 ASP cc_start: 0.9516 (t70) cc_final: 0.9289 (t0) REVERT: B 682 PHE cc_start: 0.9473 (m-80) cc_final: 0.9055 (m-80) REVERT: C 19 MET cc_start: 0.1534 (mmt) cc_final: -0.0863 (mtm) REVERT: C 278 LEU cc_start: 0.9234 (mt) cc_final: 0.8863 (mt) REVERT: C 348 PHE cc_start: 0.9676 (m-80) cc_final: 0.9251 (t80) REVERT: C 355 PHE cc_start: 0.9558 (m-80) cc_final: 0.9009 (m-80) REVERT: C 385 LEU cc_start: 0.9511 (tt) cc_final: 0.9217 (mt) REVERT: C 393 MET cc_start: 0.7646 (mmm) cc_final: 0.7327 (mmt) REVERT: C 410 PHE cc_start: 0.9532 (m-80) cc_final: 0.9111 (m-80) REVERT: C 428 PHE cc_start: 0.8961 (m-10) cc_final: 0.8660 (m-10) REVERT: C 607 ASP cc_start: 0.9684 (t0) cc_final: 0.9407 (t0) REVERT: C 611 ARG cc_start: 0.9351 (mtm110) cc_final: 0.9117 (mtm110) REVERT: C 621 LEU cc_start: 0.9616 (mm) cc_final: 0.9276 (mm) REVERT: C 624 ASP cc_start: 0.9039 (t0) cc_final: 0.8651 (p0) REVERT: C 701 MET cc_start: 0.9152 (ptt) cc_final: 0.8874 (ptt) REVERT: D 277 LEU cc_start: 0.9877 (tp) cc_final: 0.9590 (pp) REVERT: D 312 LEU cc_start: 0.9138 (tp) cc_final: 0.8901 (tp) REVERT: D 349 ASP cc_start: 0.8723 (t0) cc_final: 0.8320 (t0) REVERT: D 355 PHE cc_start: 0.9256 (m-80) cc_final: 0.9031 (m-80) REVERT: D 528 MET cc_start: 0.9544 (mmp) cc_final: 0.9004 (mmp) REVERT: D 664 MET cc_start: 0.8989 (mpp) cc_final: 0.8718 (mpp) REVERT: E 19 MET cc_start: 0.7911 (mmm) cc_final: 0.7600 (mmt) REVERT: E 335 ARG cc_start: 0.9439 (mtm110) cc_final: 0.9108 (ptt180) REVERT: E 349 ASP cc_start: 0.8821 (t70) cc_final: 0.8599 (t0) REVERT: E 513 PHE cc_start: 0.8886 (t80) cc_final: 0.8152 (t80) REVERT: E 611 ARG cc_start: 0.9149 (mmp80) cc_final: 0.8938 (mmm160) REVERT: E 661 LEU cc_start: 0.9667 (tp) cc_final: 0.9359 (tt) REVERT: F 334 TYR cc_start: 0.9399 (t80) cc_final: 0.9147 (t80) REVERT: F 440 MET cc_start: 0.8552 (ptt) cc_final: 0.8294 (ptt) REVERT: F 599 GLU cc_start: 0.9690 (pm20) cc_final: 0.9488 (pm20) REVERT: F 602 LYS cc_start: 0.9808 (mttt) cc_final: 0.9319 (mttt) REVERT: G 1 MET cc_start: 0.7012 (ptp) cc_final: 0.6792 (ptp) REVERT: H 1 MET cc_start: 0.8562 (mtp) cc_final: 0.8353 (ttt) REVERT: L 450 MET cc_start: -0.1425 (ptp) cc_final: -0.2276 (ptp) REVERT: L 634 ASP cc_start: 0.7261 (t70) cc_final: 0.6858 (m-30) REVERT: L 642 MET cc_start: -0.0184 (tmm) cc_final: -0.0428 (ppp) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2585 time to fit residues: 191.5646 Evaluate side-chains 374 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 475 optimal weight: 30.0000 chunk 154 optimal weight: 0.0270 chunk 239 optimal weight: 1.9990 chunk 420 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 411 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 344 optimal weight: 0.2980 chunk 454 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 overall best weight: 3.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 756 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN D 608 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.096122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.072466 restraints weight = 558370.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.073232 restraints weight = 238743.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.072716 restraints weight = 125876.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.072958 restraints weight = 84385.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.073086 restraints weight = 64655.133| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40331 Z= 0.129 Angle : 0.575 9.975 54422 Z= 0.299 Chirality : 0.041 0.238 6163 Planarity : 0.004 0.065 7056 Dihedral : 7.829 94.802 5698 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.86 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4979 helix: 1.77 (0.10), residues: 2688 sheet: -0.01 (0.18), residues: 636 loop : -0.42 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 324 TYR 0.017 0.001 TYR I 66 PHE 0.025 0.001 PHE D 610 TRP 0.020 0.001 TRP C 632 HIS 0.005 0.001 HIS H 259 Details of bonding type rmsd covalent geometry : bond 0.00277 (40331) covalent geometry : angle 0.57529 (54422) hydrogen bonds : bond 0.03305 ( 2078) hydrogen bonds : angle 4.07109 ( 6081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14491.81 seconds wall clock time: 247 minutes 59.44 seconds (14879.44 seconds total)