Starting phenix.real_space_refine on Thu Sep 18 22:34:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ily_60676/09_2025/9ily_60676.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13251 2.51 5 N 3443 2.21 5 O 3805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20595 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3441 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 2 Chain: "F" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3441 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 2 Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3441 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 2 Chain: "D" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3441 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 2 Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3390 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3441 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 2 Time building chain proxies: 5.16, per 1000 atoms: 0.25 Number of scatterers: 20595 At special positions: 0 Unit cell: (132.88, 139.04, 115.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3805 8.00 N 3443 7.00 C 13251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 489 " - pdb=" SG CYS F 491 " distance=2.03 Simple disulfide: pdb=" SG CYS D 489 " - pdb=" SG CYS D 491 " distance=2.04 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 491 " distance=2.04 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 491 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 896.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4848 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 27 sheets defined 43.0% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.630A pdb=" N ASN A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 3.765A pdb=" N ARG A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.555A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 472 through 488 removed outlier: 3.670A pdb=" N LYS A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 486 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.605A pdb=" N THR A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 513' Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 535 through 539 removed outlier: 4.165A pdb=" N GLY A 539 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 549 removed outlier: 4.947A pdb=" N ASN A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET A 547 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.685A pdb=" N GLU A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 664 through 678 removed outlier: 3.622A pdb=" N LEU A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 672 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.732A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 712 through 721 removed outlier: 4.508A pdb=" N LEU A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'F' and resid 324 through 336 Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 377 through 382 removed outlier: 4.633A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 398 Processing helix chain 'F' and resid 430 through 436 removed outlier: 4.085A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 472 through 489 removed outlier: 4.655A pdb=" N LYS F 477 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN F 478 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 521 removed outlier: 4.315A pdb=" N ARG F 514 " --> pdb=" O SER F 510 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 515 " --> pdb=" O THR F 511 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 547 Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.998A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.510A pdb=" N ILE F 659 " --> pdb=" O ASP F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 678 Processing helix chain 'F' and resid 689 through 693 removed outlier: 4.112A pdb=" N GLU F 692 " --> pdb=" O THR F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 705 Processing helix chain 'F' and resid 712 through 723 removed outlier: 4.376A pdb=" N LEU F 716 " --> pdb=" O LYS F 712 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR F 718 " --> pdb=" O ILE F 714 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 723 " --> pdb=" O ASP F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 747 removed outlier: 3.706A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 removed outlier: 5.123A pdb=" N HIS F 754 " --> pdb=" O ARG F 750 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP F 755 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.562A pdb=" N ASN E 337 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.906A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET E 399 " --> pdb=" O ASN E 395 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 400 " --> pdb=" O ILE E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 removed outlier: 3.933A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 462 removed outlier: 3.593A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 469 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 508 through 521 removed outlier: 3.883A pdb=" N LYS E 513 " --> pdb=" O LYS E 509 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 534 removed outlier: 3.973A pdb=" N LEU E 532 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 570 through 579 removed outlier: 3.893A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 619 No H-bonds generated for 'chain 'E' and resid 617 through 619' Processing helix chain 'E' and resid 656 through 660 Processing helix chain 'E' and resid 664 through 678 Processing helix chain 'E' and resid 693 through 705 removed outlier: 3.853A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 710 through 714 Processing helix chain 'E' and resid 716 through 722 Processing helix chain 'E' and resid 735 through 744 Processing helix chain 'E' and resid 752 through 762 removed outlier: 3.504A pdb=" N ASN E 761 " --> pdb=" O GLU E 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 782 No H-bonds generated for 'chain 'E' and resid 780 through 782' Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.608A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 385 through 399 Processing helix chain 'D' and resid 455 through 469 removed outlier: 3.942A pdb=" N GLU D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 through 488 removed outlier: 3.944A pdb=" N SER D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.570A pdb=" N ILE D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 547 Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.738A pdb=" N ILE D 574 " --> pdb=" O ARG D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 667 through 680 removed outlier: 3.925A pdb=" N LEU D 671 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 722 removed outlier: 3.567A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 746 removed outlier: 4.228A pdb=" N TYR D 746 " --> pdb=" O LYS D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 763 Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 430 through 437 removed outlier: 3.873A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.868A pdb=" N ALA C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 535 removed outlier: 4.239A pdb=" N VAL C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.166A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.692A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 681 removed outlier: 4.019A pdb=" N ILE C 681 " --> pdb=" O LYS C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 693 removed outlier: 3.811A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.646A pdb=" N LEU C 700 " --> pdb=" O PHE C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 717 through 724 Processing helix chain 'C' and resid 727 through 731 Processing helix chain 'C' and resid 735 through 746 removed outlier: 3.572A pdb=" N PHE C 739 " --> pdb=" O PRO C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 763 Processing helix chain 'C' and resid 780 through 782 No H-bonds generated for 'chain 'C' and resid 780 through 782' Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.547A pdb=" N ARG B 389 " --> pdb=" O CYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.558A pdb=" N LEU B 486 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 520 removed outlier: 3.826A pdb=" N ARG B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.615A pdb=" N MET B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 3.716A pdb=" N GLU B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.521A pdb=" N LEU B 700 " --> pdb=" O PHE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 723 Processing helix chain 'B' and resid 727 through 731 Processing helix chain 'B' and resid 735 through 743 Processing helix chain 'B' and resid 752 through 764 Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.682A pdb=" N MET A 426 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 604 removed outlier: 6.376A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 527 removed outlier: 6.633A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 706 through 707 Processing sheet with id=AA6, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'F' and resid 412 through 414 removed outlier: 4.006A pdb=" N MET F 426 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 601 through 604 removed outlier: 6.533A pdb=" N THR F 499 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR F 604 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE F 501 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 524 through 527 Processing sheet with id=AB1, first strand: chain 'F' and resid 706 through 708 removed outlier: 3.502A pdb=" N VAL F 707 " --> pdb=" O ILE F 777 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AB3, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AB4, first strand: chain 'E' and resid 553 through 554 removed outlier: 6.575A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR E 499 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 706 through 708 Processing sheet with id=AB6, first strand: chain 'E' and resid 727 through 728 Processing sheet with id=AB7, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AB8, first strand: chain 'D' and resid 412 through 414 Processing sheet with id=AB9, first strand: chain 'D' and resid 524 through 526 removed outlier: 3.636A pdb=" N VAL D 525 " --> pdb=" O SER D 552 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AC2, first strand: chain 'D' and resid 727 through 728 Processing sheet with id=AC3, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AC4, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AC5, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AC6, first strand: chain 'B' and resid 339 through 341 removed outlier: 4.274A pdb=" N HIS B 347 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.921A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 524 through 526 removed outlier: 3.510A pdb=" N PHE B 554 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 604 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE B 501 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 706 through 707 665 hydrogen bonds defined for protein. 1833 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: 3.50 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6524 1.35 - 1.47: 5035 1.47 - 1.60: 9327 1.60 - 1.72: 1 1.72 - 1.85: 144 Bond restraints: 21031 Sorted by residual: bond pdb=" CB PRO F 362 " pdb=" CG PRO F 362 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.57e+00 bond pdb=" CA ASN B 337 " pdb=" CB ASN B 337 " ideal model delta sigma weight residual 1.529 1.559 -0.030 1.64e-02 3.72e+03 3.42e+00 bond pdb=" CB LYS E 377 " pdb=" CG LYS E 377 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" CB LYS F 568 " pdb=" CG LYS F 568 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB ASN B 337 " pdb=" CG ASN B 337 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.02e+00 ... (remaining 21026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 28152 3.12 - 6.23: 196 6.23 - 9.35: 27 9.35 - 12.47: 13 12.47 - 15.58: 1 Bond angle restraints: 28389 Sorted by residual: angle pdb=" CA PRO F 362 " pdb=" N PRO F 362 " pdb=" CD PRO F 362 " ideal model delta sigma weight residual 112.00 100.15 11.85 1.40e+00 5.10e-01 7.16e+01 angle pdb=" CA MET F 462 " pdb=" CB MET F 462 " pdb=" CG MET F 462 " ideal model delta sigma weight residual 114.10 124.75 -10.65 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CB LYS F 568 " pdb=" CG LYS F 568 " pdb=" CD LYS F 568 " ideal model delta sigma weight residual 111.30 121.97 -10.67 2.30e+00 1.89e-01 2.15e+01 angle pdb=" N MET F 462 " pdb=" CA MET F 462 " pdb=" CB MET F 462 " ideal model delta sigma weight residual 110.28 117.27 -6.99 1.55e+00 4.16e-01 2.03e+01 angle pdb=" CA LEU C 461 " pdb=" CB LEU C 461 " pdb=" CG LEU C 461 " ideal model delta sigma weight residual 116.30 131.88 -15.58 3.50e+00 8.16e-02 1.98e+01 ... (remaining 28384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11602 17.82 - 35.64: 993 35.64 - 53.46: 166 53.46 - 71.28: 26 71.28 - 89.10: 10 Dihedral angle restraints: 12797 sinusoidal: 5335 harmonic: 7462 Sorted by residual: dihedral pdb=" CA CYS B 489 " pdb=" C CYS B 489 " pdb=" N LEU B 490 " pdb=" CA LEU B 490 " ideal model delta harmonic sigma weight residual 180.00 -143.45 -36.55 0 5.00e+00 4.00e-02 5.34e+01 dihedral pdb=" CA LEU B 490 " pdb=" C LEU B 490 " pdb=" N CYS B 491 " pdb=" CA CYS B 491 " ideal model delta harmonic sigma weight residual -180.00 -143.99 -36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CB CYS C 489 " pdb=" SG CYS C 489 " pdb=" SG CYS C 491 " pdb=" CB CYS C 491 " ideal model delta sinusoidal sigma weight residual -86.00 -141.31 55.31 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 12794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2459 0.045 - 0.091: 571 0.091 - 0.136: 167 0.136 - 0.181: 9 0.181 - 0.227: 1 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CG LEU C 515 " pdb=" CB LEU C 515 " pdb=" CD1 LEU C 515 " pdb=" CD2 LEU C 515 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASP C 424 " pdb=" N ASP C 424 " pdb=" C ASP C 424 " pdb=" CB ASP C 424 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CG LEU C 672 " pdb=" CB LEU C 672 " pdb=" CD1 LEU C 672 " pdb=" CD2 LEU C 672 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 3204 not shown) Planarity restraints: 3578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 361 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO F 362 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO F 362 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO F 362 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 463 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN E 463 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN E 463 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE E 464 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 676 " -0.016 2.00e-02 2.50e+03 2.05e-02 8.37e+00 pdb=" CG TYR A 676 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 676 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 676 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 676 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 676 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 676 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 676 " 0.002 2.00e-02 2.50e+03 ... (remaining 3575 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 870 2.72 - 3.26: 22484 3.26 - 3.81: 33305 3.81 - 4.35: 40625 4.35 - 4.90: 65338 Nonbonded interactions: 162622 Sorted by model distance: nonbonded pdb=" O ARG C 762 " pdb=" OG SER B 564 " model vdw 2.175 3.040 nonbonded pdb=" O TYR B 482 " pdb=" OG1 THR B 485 " model vdw 2.175 3.040 nonbonded pdb=" O LEU A 515 " pdb=" OG SER A 518 " model vdw 2.194 3.040 nonbonded pdb=" O ILE F 333 " pdb=" OG1 THR F 336 " model vdw 2.211 3.040 nonbonded pdb=" O ILE C 333 " pdb=" OG1 THR C 336 " model vdw 2.220 3.040 ... (remaining 162617 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 323 through 600 or resid 607 through 782)) selection = (chain 'B' and (resid 323 through 600 or resid 607 through 782)) selection = chain 'C' selection = (chain 'D' and (resid 323 through 600 or resid 607 through 782)) selection = (chain 'E' and (resid 323 through 600 or resid 607 through 782)) selection = (chain 'F' and (resid 323 through 600 or resid 607 through 782)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.146 21035 Z= 0.109 Angle : 0.663 15.583 28397 Z= 0.324 Chirality : 0.042 0.227 3207 Planarity : 0.004 0.145 3578 Dihedral : 13.304 89.099 7937 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.46 % Favored : 92.50 % Rotamer: Outliers : 0.13 % Allowed : 20.21 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 2494 helix: 0.83 (0.18), residues: 894 sheet: -0.19 (0.37), residues: 243 loop : -0.92 (0.18), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 620 TYR 0.050 0.001 TYR A 676 PHE 0.020 0.001 PHE E 766 TRP 0.008 0.001 TRP D 350 HIS 0.011 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00249 (21031) covalent geometry : angle 0.66212 (28389) SS BOND : bond 0.01491 ( 4) SS BOND : angle 1.68332 ( 8) hydrogen bonds : bond 0.17917 ( 665) hydrogen bonds : angle 5.84713 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 746 TYR cc_start: 0.9327 (t80) cc_final: 0.9044 (t80) REVERT: F 755 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: D 684 MET cc_start: 0.6065 (mmm) cc_final: 0.5733 (mmm) REVERT: C 462 MET cc_start: 0.9599 (mmm) cc_final: 0.9297 (mmm) REVERT: B 684 MET cc_start: 0.6656 (tpt) cc_final: 0.6432 (tpp) outliers start: 3 outliers final: 2 residues processed: 67 average time/residue: 0.1579 time to fit residues: 17.3899 Evaluate side-chains 65 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 755 ASP Chi-restraints excluded: chain C residue 491 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.0470 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** C 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.056592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.038035 restraints weight = 157768.774| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 5.21 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21035 Z= 0.110 Angle : 0.570 10.735 28397 Z= 0.287 Chirality : 0.041 0.189 3207 Planarity : 0.004 0.081 3578 Dihedral : 4.182 50.327 2740 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.66 % Favored : 92.30 % Rotamer: Outliers : 1.84 % Allowed : 17.91 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2494 helix: 0.86 (0.18), residues: 935 sheet: -0.26 (0.38), residues: 237 loop : -1.02 (0.19), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 389 TYR 0.030 0.001 TYR F 670 PHE 0.020 0.001 PHE E 766 TRP 0.007 0.001 TRP E 350 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00237 (21031) covalent geometry : angle 0.56886 (28389) SS BOND : bond 0.01173 ( 4) SS BOND : angle 2.52093 ( 8) hydrogen bonds : bond 0.03924 ( 665) hydrogen bonds : angle 4.71946 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8312 (ppp) cc_final: 0.7877 (ppp) REVERT: A 462 MET cc_start: 0.7718 (mpp) cc_final: 0.7483 (mpp) REVERT: A 684 MET cc_start: 0.5420 (mmm) cc_final: 0.4986 (tpt) REVERT: A 746 TYR cc_start: 0.9208 (t80) cc_final: 0.8924 (t80) REVERT: F 681 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8869 (mm) REVERT: E 458 MET cc_start: 0.8775 (ppp) cc_final: 0.8373 (ppp) REVERT: E 462 MET cc_start: 0.8165 (mpt) cc_final: 0.7878 (mpp) REVERT: E 550 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8084 (mmmt) REVERT: D 426 MET cc_start: 0.7588 (tmm) cc_final: 0.7375 (tmm) REVERT: D 458 MET cc_start: 0.9292 (tpt) cc_final: 0.9015 (mmm) REVERT: D 741 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8116 (pt0) REVERT: C 458 MET cc_start: 0.9156 (tpp) cc_final: 0.8933 (tpp) outliers start: 43 outliers final: 9 residues processed: 103 average time/residue: 0.1409 time to fit residues: 24.1415 Evaluate side-chains 71 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 550 LYS Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 491 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 141 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 193 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.0040 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.056363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.037824 restraints weight = 157514.214| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 5.24 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21035 Z= 0.105 Angle : 0.544 9.677 28397 Z= 0.273 Chirality : 0.041 0.176 3207 Planarity : 0.003 0.065 3578 Dihedral : 3.967 42.546 2735 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.82 % Rotamer: Outliers : 1.92 % Allowed : 17.56 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.18), residues: 2494 helix: 0.92 (0.18), residues: 928 sheet: -0.09 (0.38), residues: 237 loop : -0.98 (0.19), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 665 TYR 0.048 0.001 TYR F 670 PHE 0.021 0.001 PHE E 766 TRP 0.006 0.001 TRP E 350 HIS 0.008 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00229 (21031) covalent geometry : angle 0.54186 (28389) SS BOND : bond 0.01069 ( 4) SS BOND : angle 2.67585 ( 8) hydrogen bonds : bond 0.03365 ( 665) hydrogen bonds : angle 4.48679 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.5413 (mmm) cc_final: 0.5123 (tpt) REVERT: A 746 TYR cc_start: 0.9230 (t80) cc_final: 0.8943 (t80) REVERT: E 458 MET cc_start: 0.8785 (ppp) cc_final: 0.8456 (ppp) REVERT: E 462 MET cc_start: 0.8371 (mpt) cc_final: 0.8140 (mtt) REVERT: E 550 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8079 (mmmt) REVERT: D 547 MET cc_start: 0.8669 (ppp) cc_final: 0.8248 (ppp) REVERT: D 684 MET cc_start: 0.6902 (mmm) cc_final: 0.6372 (mmm) REVERT: D 741 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8221 (pt0) REVERT: C 458 MET cc_start: 0.9211 (tpp) cc_final: 0.8830 (tpp) REVERT: C 462 MET cc_start: 0.9733 (mmm) cc_final: 0.9460 (mmm) outliers start: 45 outliers final: 19 residues processed: 104 average time/residue: 0.1338 time to fit residues: 23.4511 Evaluate side-chains 78 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 609 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 550 LYS Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 11 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 153 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 541 ASN ** C 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.055462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.036865 restraints weight = 160196.652| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 5.24 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21035 Z= 0.137 Angle : 0.549 10.568 28397 Z= 0.278 Chirality : 0.041 0.185 3207 Planarity : 0.003 0.060 3578 Dihedral : 4.025 43.942 2735 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 2.22 % Allowed : 17.86 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2494 helix: 1.01 (0.18), residues: 921 sheet: -0.32 (0.37), residues: 239 loop : -0.93 (0.19), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 750 TYR 0.026 0.001 TYR F 670 PHE 0.019 0.001 PHE E 766 TRP 0.006 0.001 TRP E 350 HIS 0.008 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00302 (21031) covalent geometry : angle 0.54751 (28389) SS BOND : bond 0.01079 ( 4) SS BOND : angle 2.82925 ( 8) hydrogen bonds : bond 0.03225 ( 665) hydrogen bonds : angle 4.49283 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 58 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.5809 (mmm) cc_final: 0.5167 (tpt) REVERT: F 458 MET cc_start: 0.7973 (ppp) cc_final: 0.7679 (ppp) REVERT: E 458 MET cc_start: 0.8842 (ppp) cc_final: 0.8145 (ppp) REVERT: E 462 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7645 (tpt) REVERT: D 547 MET cc_start: 0.8825 (ppp) cc_final: 0.8285 (ppp) REVERT: D 621 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8026 (pt) REVERT: D 684 MET cc_start: 0.7158 (mmm) cc_final: 0.6503 (mmm) REVERT: D 741 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8234 (pt0) REVERT: C 458 MET cc_start: 0.9264 (tpp) cc_final: 0.8990 (tpp) REVERT: B 684 MET cc_start: 0.6676 (tpt) cc_final: 0.6452 (tpt) outliers start: 52 outliers final: 27 residues processed: 107 average time/residue: 0.1245 time to fit residues: 22.3597 Evaluate side-chains 87 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 779 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 58 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 225 optimal weight: 0.0970 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 214 optimal weight: 4.9990 chunk 189 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.056688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.038181 restraints weight = 157532.523| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 5.35 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21035 Z= 0.092 Angle : 0.538 8.102 28397 Z= 0.268 Chirality : 0.041 0.333 3207 Planarity : 0.003 0.056 3578 Dihedral : 3.899 42.692 2735 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.02 % Favored : 92.94 % Rotamer: Outliers : 2.05 % Allowed : 17.61 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2494 helix: 0.97 (0.18), residues: 934 sheet: -0.30 (0.40), residues: 212 loop : -0.88 (0.19), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.022 0.001 TYR F 670 PHE 0.019 0.001 PHE E 766 TRP 0.009 0.001 TRP D 350 HIS 0.007 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00193 (21031) covalent geometry : angle 0.53568 (28389) SS BOND : bond 0.00979 ( 4) SS BOND : angle 2.76333 ( 8) hydrogen bonds : bond 0.02586 ( 665) hydrogen bonds : angle 4.19478 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 62 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.9047 (ppp) cc_final: 0.8721 (ppp) REVERT: A 684 MET cc_start: 0.5600 (mmm) cc_final: 0.5280 (tpt) REVERT: E 458 MET cc_start: 0.8837 (ppp) cc_final: 0.8148 (ppp) REVERT: E 462 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7446 (tpp) REVERT: E 756 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8802 (mm) REVERT: D 547 MET cc_start: 0.8871 (ppp) cc_final: 0.8270 (ppp) REVERT: D 684 MET cc_start: 0.7121 (mmm) cc_final: 0.6302 (mmm) REVERT: C 458 MET cc_start: 0.9242 (tpp) cc_final: 0.8540 (tpp) REVERT: C 462 MET cc_start: 0.9678 (mmm) cc_final: 0.9421 (mmp) REVERT: B 684 MET cc_start: 0.6483 (tpt) cc_final: 0.6158 (tpt) outliers start: 48 outliers final: 27 residues processed: 109 average time/residue: 0.1301 time to fit residues: 23.9221 Evaluate side-chains 86 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 756 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 779 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 90 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 182 optimal weight: 0.3980 chunk 220 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN F 328 ASN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.054909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.036323 restraints weight = 160310.148| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.15 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21035 Z= 0.180 Angle : 0.579 7.815 28397 Z= 0.295 Chirality : 0.041 0.185 3207 Planarity : 0.004 0.053 3578 Dihedral : 4.071 44.320 2735 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.30 % Favored : 91.66 % Rotamer: Outliers : 2.09 % Allowed : 17.95 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2494 helix: 0.94 (0.18), residues: 935 sheet: -0.51 (0.38), residues: 222 loop : -0.92 (0.19), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 595 TYR 0.022 0.001 TYR F 670 PHE 0.014 0.001 PHE E 766 TRP 0.007 0.001 TRP E 350 HIS 0.010 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00391 (21031) covalent geometry : angle 0.57671 (28389) SS BOND : bond 0.01102 ( 4) SS BOND : angle 2.82688 ( 8) hydrogen bonds : bond 0.03354 ( 665) hydrogen bonds : angle 4.50696 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 56 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8698 (ppp) cc_final: 0.8213 (ppp) REVERT: A 547 MET cc_start: 0.9266 (ppp) cc_final: 0.8714 (ppp) REVERT: A 684 MET cc_start: 0.5988 (mmm) cc_final: 0.5666 (tpt) REVERT: F 547 MET cc_start: 0.8468 (ppp) cc_final: 0.8141 (ppp) REVERT: E 458 MET cc_start: 0.8750 (ppp) cc_final: 0.8037 (ppp) REVERT: E 462 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7697 (tpt) REVERT: D 547 MET cc_start: 0.8860 (ppp) cc_final: 0.8209 (ppp) REVERT: D 684 MET cc_start: 0.7734 (mmm) cc_final: 0.6796 (mmm) REVERT: C 458 MET cc_start: 0.9309 (tpp) cc_final: 0.8632 (tpp) REVERT: C 462 MET cc_start: 0.9732 (mmm) cc_final: 0.9446 (mmp) outliers start: 49 outliers final: 32 residues processed: 103 average time/residue: 0.1278 time to fit residues: 22.2073 Evaluate side-chains 88 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 777 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 133 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 114 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 GLN C 324 ASN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.055884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.037318 restraints weight = 158257.770| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 5.29 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21035 Z= 0.092 Angle : 0.546 11.185 28397 Z= 0.272 Chirality : 0.041 0.173 3207 Planarity : 0.003 0.051 3578 Dihedral : 3.961 43.668 2735 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.26 % Favored : 92.66 % Rotamer: Outliers : 2.18 % Allowed : 18.08 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.18), residues: 2494 helix: 0.98 (0.18), residues: 934 sheet: -0.40 (0.38), residues: 232 loop : -0.88 (0.19), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 551 TYR 0.021 0.001 TYR F 670 PHE 0.017 0.001 PHE E 766 TRP 0.011 0.001 TRP E 675 HIS 0.006 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00202 (21031) covalent geometry : angle 0.54409 (28389) SS BOND : bond 0.00989 ( 4) SS BOND : angle 2.75566 ( 8) hydrogen bonds : bond 0.02704 ( 665) hydrogen bonds : angle 4.22022 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 58 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8613 (ppp) cc_final: 0.8212 (ppp) REVERT: A 547 MET cc_start: 0.9272 (ppp) cc_final: 0.8992 (ppp) REVERT: A 684 MET cc_start: 0.5733 (mmm) cc_final: 0.5414 (tpt) REVERT: E 382 GLU cc_start: 0.8214 (mp0) cc_final: 0.7988 (pm20) REVERT: E 458 MET cc_start: 0.8734 (ppp) cc_final: 0.8006 (ppp) REVERT: E 462 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7539 (tpp) REVERT: D 547 MET cc_start: 0.8893 (ppp) cc_final: 0.8270 (ppp) REVERT: D 684 MET cc_start: 0.7602 (mmm) cc_final: 0.6733 (mmm) REVERT: C 458 MET cc_start: 0.9285 (tpp) cc_final: 0.8517 (tpp) REVERT: C 462 MET cc_start: 0.9705 (mmm) cc_final: 0.9463 (mmp) REVERT: C 684 MET cc_start: 0.7539 (tpp) cc_final: 0.7232 (tpt) REVERT: B 480 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: B 618 MET cc_start: 0.8488 (tpp) cc_final: 0.8144 (ttp) REVERT: B 739 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8748 (p90) outliers start: 51 outliers final: 34 residues processed: 106 average time/residue: 0.1278 time to fit residues: 22.7253 Evaluate side-chains 94 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 777 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 779 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 55 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 214 optimal weight: 0.0270 chunk 18 optimal weight: 0.4980 overall best weight: 2.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.054699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.036215 restraints weight = 158640.619| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.08 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21035 Z= 0.156 Angle : 0.576 10.013 28397 Z= 0.291 Chirality : 0.041 0.283 3207 Planarity : 0.003 0.051 3578 Dihedral : 4.093 44.579 2735 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.34 % Favored : 91.58 % Rotamer: Outliers : 2.22 % Allowed : 17.99 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2494 helix: 0.89 (0.18), residues: 941 sheet: -0.51 (0.37), residues: 230 loop : -0.95 (0.19), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.017 0.001 TYR F 670 PHE 0.017 0.001 PHE C 610 TRP 0.007 0.001 TRP E 350 HIS 0.007 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00343 (21031) covalent geometry : angle 0.57386 (28389) SS BOND : bond 0.01049 ( 4) SS BOND : angle 2.81141 ( 8) hydrogen bonds : bond 0.03223 ( 665) hydrogen bonds : angle 4.47581 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 57 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.9157 (ppp) cc_final: 0.8900 (ppp) REVERT: A 684 MET cc_start: 0.5903 (mmm) cc_final: 0.5627 (tpt) REVERT: E 458 MET cc_start: 0.8738 (ppp) cc_final: 0.8002 (ppp) REVERT: E 462 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7689 (tpt) REVERT: D 452 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.7098 (m) REVERT: D 547 MET cc_start: 0.8800 (ppp) cc_final: 0.8137 (ppp) REVERT: D 684 MET cc_start: 0.7747 (mmm) cc_final: 0.7067 (mmm) REVERT: C 458 MET cc_start: 0.9266 (tpp) cc_final: 0.8690 (tpp) REVERT: C 462 MET cc_start: 0.9707 (mmm) cc_final: 0.9445 (mmp) REVERT: B 480 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8376 (mp0) outliers start: 52 outliers final: 37 residues processed: 104 average time/residue: 0.1263 time to fit residues: 22.1443 Evaluate side-chains 95 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 777 ILE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 143 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.055354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.036844 restraints weight = 159317.311| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.17 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21035 Z= 0.100 Angle : 0.561 10.555 28397 Z= 0.278 Chirality : 0.041 0.293 3207 Planarity : 0.003 0.050 3578 Dihedral : 4.020 43.885 2735 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.18 % Rotamer: Outliers : 2.01 % Allowed : 18.42 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2494 helix: 0.96 (0.18), residues: 934 sheet: -0.55 (0.37), residues: 232 loop : -0.90 (0.19), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 551 TYR 0.019 0.001 TYR F 670 PHE 0.013 0.001 PHE E 766 TRP 0.007 0.001 TRP D 350 HIS 0.006 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00220 (21031) covalent geometry : angle 0.55953 (28389) SS BOND : bond 0.01053 ( 4) SS BOND : angle 2.82750 ( 8) hydrogen bonds : bond 0.02790 ( 665) hydrogen bonds : angle 4.29647 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 56 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.9194 (ppp) cc_final: 0.8945 (ppp) REVERT: A 684 MET cc_start: 0.5786 (mmm) cc_final: 0.5512 (tpt) REVERT: E 458 MET cc_start: 0.8687 (ppp) cc_final: 0.7969 (ppp) REVERT: E 462 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7652 (tpt) REVERT: D 452 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.7123 (m) REVERT: D 547 MET cc_start: 0.8906 (ppp) cc_final: 0.8285 (ppp) REVERT: D 684 MET cc_start: 0.7700 (mmm) cc_final: 0.7154 (mmm) REVERT: C 458 MET cc_start: 0.9267 (tpp) cc_final: 0.8677 (tpp) REVERT: C 462 MET cc_start: 0.9713 (mmm) cc_final: 0.9450 (mmp) REVERT: C 684 MET cc_start: 0.7342 (tpt) cc_final: 0.7116 (tpt) outliers start: 47 outliers final: 40 residues processed: 99 average time/residue: 0.1306 time to fit residues: 21.9092 Evaluate side-chains 97 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 777 ILE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 779 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 101 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.054853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.036307 restraints weight = 161582.092| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.20 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21035 Z= 0.133 Angle : 0.586 11.268 28397 Z= 0.290 Chirality : 0.041 0.250 3207 Planarity : 0.003 0.050 3578 Dihedral : 4.061 44.408 2735 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.18 % Favored : 91.74 % Rotamer: Outliers : 2.09 % Allowed : 18.46 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2494 helix: 0.93 (0.18), residues: 934 sheet: -0.58 (0.37), residues: 230 loop : -0.92 (0.19), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.017 0.001 TYR F 670 PHE 0.013 0.001 PHE E 766 TRP 0.006 0.001 TRP E 350 HIS 0.007 0.001 HIS C 763 Details of bonding type rmsd covalent geometry : bond 0.00296 (21031) covalent geometry : angle 0.58393 (28389) SS BOND : bond 0.01052 ( 4) SS BOND : angle 2.84294 ( 8) hydrogen bonds : bond 0.02996 ( 665) hydrogen bonds : angle 4.40151 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 56 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.9173 (ppp) cc_final: 0.8917 (ppp) REVERT: A 684 MET cc_start: 0.5830 (mmm) cc_final: 0.5582 (tpt) REVERT: E 462 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8069 (mtt) REVERT: D 452 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.7059 (m) REVERT: D 547 MET cc_start: 0.8903 (ppp) cc_final: 0.8279 (ppp) REVERT: D 684 MET cc_start: 0.7810 (mmm) cc_final: 0.7158 (mmm) REVERT: C 458 MET cc_start: 0.9269 (tpp) cc_final: 0.8672 (tpp) REVERT: C 462 MET cc_start: 0.9722 (mmm) cc_final: 0.9455 (mmp) REVERT: B 739 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.9078 (p90) outliers start: 49 outliers final: 42 residues processed: 98 average time/residue: 0.1221 time to fit residues: 20.6850 Evaluate side-chains 101 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 56 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 676 TYR Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 462 MET Chi-restraints excluded: chain F residue 481 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 760 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 623 VAL Chi-restraints excluded: chain E residue 684 MET Chi-restraints excluded: chain E residue 693 ILE Chi-restraints excluded: chain E residue 732 VAL Chi-restraints excluded: chain E residue 777 ILE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 732 VAL Chi-restraints excluded: chain D residue 741 GLN Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 555 CYS Chi-restraints excluded: chain C residue 763 HIS Chi-restraints excluded: chain C residue 779 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 436 TYR Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 779 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 95 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 213 optimal weight: 0.5980 chunk 246 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.054263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.035649 restraints weight = 161572.427| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.24 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21035 Z= 0.163 Angle : 0.605 10.510 28397 Z= 0.303 Chirality : 0.041 0.243 3207 Planarity : 0.004 0.051 3578 Dihedral : 4.287 44.695 2735 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.42 % Rotamer: Outliers : 2.01 % Allowed : 18.50 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2494 helix: 0.76 (0.17), residues: 951 sheet: -0.67 (0.36), residues: 230 loop : -0.97 (0.19), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.018 0.001 TYR F 670 PHE 0.015 0.001 PHE D 696 TRP 0.007 0.001 TRP E 350 HIS 0.007 0.001 HIS B 680 Details of bonding type rmsd covalent geometry : bond 0.00358 (21031) covalent geometry : angle 0.60272 (28389) SS BOND : bond 0.01120 ( 4) SS BOND : angle 2.87564 ( 8) hydrogen bonds : bond 0.03281 ( 665) hydrogen bonds : angle 4.58873 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.47 seconds wall clock time: 88 minutes 2.96 seconds (5282.96 seconds total)