Starting phenix.real_space_refine on Wed Feb 4 23:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwq_49890/02_2026/9nwq_49890.map" } resolution = 3.74 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= 0.031 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 84 5.16 5 C 8624 2.51 5 N 2204 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13384 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3346 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3346 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 407} Chain: "C" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3346 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 407} Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3346 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 407} Time building chain proxies: 2.38, per 1000 atoms: 0.18 Number of scatterers: 13384 At special positions: 0 Unit cell: (116.4, 124.8, 134.4, 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 84 16.00 O 2472 8.00 N 2204 7.00 C 8624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 458.8 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 52.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.799A pdb=" N TYR A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 566 through 591 removed outlier: 3.516A pdb=" N ALA A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 617 removed outlier: 3.642A pdb=" N TRP A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 612 " --> pdb=" O SER A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 658 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.600A pdb=" N MET A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.523A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 794 removed outlier: 3.934A pdb=" N VAL A 783 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.568A pdb=" N LYS A 803 " --> pdb=" O ILE A 799 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TRP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 removed outlier: 3.578A pdb=" N GLN A 821 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 824 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 856 removed outlier: 5.872A pdb=" N GLY A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET A 850 " --> pdb=" O CYS A 846 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 851 " --> pdb=" O PHE A 847 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TRP A 854 " --> pdb=" O MET A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.665A pdb=" N TYR B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.659A pdb=" N TRP B 589 " --> pdb=" O TYR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 627 through 659 removed outlier: 3.718A pdb=" N ALA B 636 " --> pdb=" O MET B 632 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 702 through 713 removed outlier: 4.332A pdb=" N SER B 706 " --> pdb=" O ASP B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 780 through 795 removed outlier: 3.527A pdb=" N SER B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 803 removed outlier: 3.813A pdb=" N ILE B 799 " --> pdb=" O GLY B 795 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 857 removed outlier: 5.732A pdb=" N GLY B 833 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 853 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP B 854 " --> pdb=" O MET B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.531A pdb=" N TYR C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 527 through 532 Processing helix chain 'C' and resid 559 through 563 removed outlier: 3.508A pdb=" N ALA C 563 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 591 removed outlier: 4.035A pdb=" N ALA C 571 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP C 589 " --> pdb=" O TYR C 585 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 Processing helix chain 'C' and resid 627 through 659 Processing helix chain 'C' and resid 667 through 674 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 703 through 713 removed outlier: 3.560A pdb=" N MET C 711 " --> pdb=" O GLN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 718 Processing helix chain 'C' and resid 724 through 734 Processing helix chain 'C' and resid 743 through 753 Processing helix chain 'C' and resid 779 through 795 removed outlier: 3.825A pdb=" N VAL C 783 " --> pdb=" O PRO C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 805 removed outlier: 3.746A pdb=" N ILE C 799 " --> pdb=" O GLY C 795 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP C 804 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 852 removed outlier: 5.383A pdb=" N GLY C 833 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 858 removed outlier: 4.227A pdb=" N ASN C 856 " --> pdb=" O THR C 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.891A pdb=" N TYR D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.771A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 removed outlier: 3.595A pdb=" N GLU D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN D 532 " --> pdb=" O PRO D 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 527 through 532' Processing helix chain 'D' and resid 558 through 562 removed outlier: 4.430A pdb=" N CYS D 561 " --> pdb=" O MET D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 591 removed outlier: 4.004A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D 585 " --> pdb=" O GLY D 581 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 591 " --> pdb=" O LEU D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 617 removed outlier: 3.782A pdb=" N TRP D 610 " --> pdb=" O TYR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 659 Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 702 through 713 removed outlier: 4.291A pdb=" N SER D 706 " --> pdb=" O ASP D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 718 Processing helix chain 'D' and resid 724 through 735 Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 779 through 795 removed outlier: 4.448A pdb=" N VAL D 783 " --> pdb=" O PRO D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 803 removed outlier: 3.675A pdb=" N LYS D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 860 removed outlier: 5.637A pdb=" N GLY D 833 " --> pdb=" O LYS D 829 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL D 834 " --> pdb=" O SER D 830 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 850 " --> pdb=" O CYS D 846 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 853 " --> pdb=" O ALA D 849 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP D 854 " --> pdb=" O MET D 850 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP D 855 " --> pdb=" O LEU D 851 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 490 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 460 removed outlier: 6.211A pdb=" N LYS A 466 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A 459 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.888A pdb=" N MET A 541 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 680 removed outlier: 6.680A pdb=" N GLY A 680 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ASP A 742 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 739 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 485 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.897A pdb=" N VAL B 456 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR B 467 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLU B 458 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.757A pdb=" N MET B 541 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 679 through 680 removed outlier: 6.614A pdb=" N GLY B 680 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 547 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 761 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 490 removed outlier: 4.851A pdb=" N SER C 522 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY C 771 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU C 524 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY C 769 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 485 through 490 removed outlier: 4.851A pdb=" N SER C 522 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY C 771 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU C 524 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY C 769 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET C 541 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 455 through 460 removed outlier: 6.976A pdb=" N LYS C 466 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN C 459 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.595A pdb=" N GLY C 680 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 485 through 490 removed outlier: 3.812A pdb=" N GLU D 487 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE D 519 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 444 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE D 521 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL D 446 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA D 523 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER D 522 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY D 771 " --> pdb=" O SER D 522 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 524 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY D 769 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 485 through 490 removed outlier: 3.812A pdb=" N GLU D 487 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE D 519 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG D 444 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE D 521 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL D 446 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ALA D 523 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER D 522 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY D 771 " --> pdb=" O SER D 522 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 524 " --> pdb=" O GLY D 769 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY D 769 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET D 541 " --> pdb=" O TYR D 770 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 455 through 460 removed outlier: 6.355A pdb=" N LYS D 466 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN D 459 " --> pdb=" O PRO D 464 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 679 through 681 removed outlier: 6.916A pdb=" N GLY D 680 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1932 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: 2.06 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4239 1.34 - 1.46: 2711 1.46 - 1.58: 6614 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 13708 Sorted by residual: bond pdb=" CA ASN A 856 " pdb=" C ASN A 856 " ideal model delta sigma weight residual 1.522 1.548 -0.027 1.72e-02 3.38e+03 2.40e+00 bond pdb=" CA ASN C 856 " pdb=" CB ASN C 856 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.75e-02 3.27e+03 1.20e+00 bond pdb=" CB PRO A 452 " pdb=" CG PRO A 452 " ideal model delta sigma weight residual 1.492 1.437 0.055 5.00e-02 4.00e+02 1.20e+00 bond pdb=" C THR C 659 " pdb=" N ARG C 660 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.35e-02 5.49e+03 9.62e-01 bond pdb=" C LEU B 652 " pdb=" O LEU B 652 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 7.97e-01 ... (remaining 13703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 18263 1.77 - 3.54: 318 3.54 - 5.31: 43 5.31 - 7.08: 5 7.08 - 8.84: 3 Bond angle restraints: 18632 Sorted by residual: angle pdb=" N ARG A 660 " pdb=" CA ARG A 660 " pdb=" C ARG A 660 " ideal model delta sigma weight residual 114.75 108.17 6.58 1.26e+00 6.30e-01 2.73e+01 angle pdb=" C SER A 816 " pdb=" N VAL A 817 " pdb=" CA VAL A 817 " ideal model delta sigma weight residual 121.97 130.81 -8.84 1.80e+00 3.09e-01 2.41e+01 angle pdb=" N ALA C 563 " pdb=" CA ALA C 563 " pdb=" C ALA C 563 " ideal model delta sigma weight residual 109.81 117.72 -7.91 2.21e+00 2.05e-01 1.28e+01 angle pdb=" CA ARG A 660 " pdb=" C ARG A 660 " pdb=" N ILE A 661 " ideal model delta sigma weight residual 119.80 115.16 4.64 1.34e+00 5.57e-01 1.20e+01 angle pdb=" C ARG C 858 " pdb=" N LYS C 859 " pdb=" CA LYS C 859 " ideal model delta sigma weight residual 120.63 125.77 -5.14 1.61e+00 3.86e-01 1.02e+01 ... (remaining 18627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 7481 17.49 - 34.97: 440 34.97 - 52.46: 75 52.46 - 69.94: 21 69.94 - 87.43: 15 Dihedral angle restraints: 8032 sinusoidal: 3140 harmonic: 4892 Sorted by residual: dihedral pdb=" CA GLU A 451 " pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual -180.00 -125.39 -54.61 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ASN A 856 " pdb=" C ASN A 856 " pdb=" N LYS A 857 " pdb=" CA LYS A 857 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PHE A 758 " pdb=" C PHE A 758 " pdb=" N TYR A 759 " pdb=" CA TYR A 759 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 8029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1291 0.031 - 0.063: 527 0.063 - 0.094: 160 0.094 - 0.125: 82 0.125 - 0.157: 4 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" C PRO A 452 " pdb=" CB PRO A 452 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA ILE B 665 " pdb=" N ILE B 665 " pdb=" C ILE B 665 " pdb=" CB ILE B 665 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL B 817 " pdb=" N VAL B 817 " pdb=" C VAL B 817 " pdb=" CB VAL B 817 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2061 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 853 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C THR B 853 " -0.064 2.00e-02 2.50e+03 pdb=" O THR B 853 " 0.024 2.00e-02 2.50e+03 pdb=" N TRP B 854 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 651 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ASN A 651 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN A 651 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 652 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " -0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 452 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.036 5.00e-02 4.00e+02 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 122 2.63 - 3.20: 12386 3.20 - 3.77: 20111 3.77 - 4.33: 28035 4.33 - 4.90: 45524 Nonbonded interactions: 106178 Sorted by model distance: nonbonded pdb=" OG1 THR D 527 " pdb=" OD1 ASP D 529 " model vdw 2.067 3.040 nonbonded pdb=" OG1 THR C 627 " pdb=" OG1 THR C 630 " model vdw 2.197 3.040 nonbonded pdb=" O PHE C 655 " pdb=" OG1 THR C 659 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR C 543 " pdb=" OD1 ASP C 742 " model vdw 2.261 3.040 nonbonded pdb=" O GLU A 451 " pdb=" N PHE A 453 " model vdw 2.281 3.120 ... (remaining 106173 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 0.055 13712 Z= 0.129 Angle : 0.587 8.845 18640 Z= 0.352 Chirality : 0.041 0.157 2064 Planarity : 0.006 0.082 2352 Dihedral : 12.496 87.427 4900 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.18 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1680 helix: -1.02 (0.15), residues: 815 sheet: -0.72 (0.47), residues: 98 loop : -0.74 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG C 781 TYR 0.024 0.003 TYR D 467 PHE 0.017 0.001 PHE C 640 TRP 0.027 0.002 TRP A 589 HIS 0.003 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00232 (13708) covalent geometry : angle 0.58751 (18632) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.41440 ( 8) hydrogen bonds : bond 0.12822 ( 655) hydrogen bonds : angle 6.63890 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 GLN cc_start: 0.7832 (mm-40) cc_final: 0.6225 (tt0) REVERT: A 632 MET cc_start: 0.7994 (tpp) cc_final: 0.7126 (tpp) REVERT: A 634 MET cc_start: 0.7744 (mmm) cc_final: 0.7400 (mmm) REVERT: A 688 TYR cc_start: 0.8148 (t80) cc_final: 0.7870 (t80) REVERT: A 705 TYR cc_start: 0.7530 (m-80) cc_final: 0.7269 (m-10) REVERT: A 709 TRP cc_start: 0.8720 (t-100) cc_final: 0.8271 (t-100) REVERT: A 797 MET cc_start: 0.7874 (tpp) cc_final: 0.7575 (tpp) REVERT: A 798 ASP cc_start: 0.8075 (m-30) cc_final: 0.7843 (t0) REVERT: B 484 PHE cc_start: 0.5937 (p90) cc_final: 0.5630 (m-10) REVERT: B 633 MET cc_start: 0.7919 (tpp) cc_final: 0.7228 (tpt) REVERT: B 679 TYR cc_start: 0.6954 (p90) cc_final: 0.6600 (p90) REVERT: B 720 ASN cc_start: 0.7265 (m-40) cc_final: 0.6889 (m-40) REVERT: B 826 LEU cc_start: 0.8342 (mt) cc_final: 0.8083 (mp) REVERT: C 484 PHE cc_start: 0.5686 (p90) cc_final: 0.5024 (m-10) REVERT: C 600 MET cc_start: 0.0176 (mtt) cc_final: -0.0480 (ttt) REVERT: C 618 GLN cc_start: 0.7725 (mt0) cc_final: 0.6307 (tt0) REVERT: C 631 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7356 (mtt180) REVERT: C 775 GLN cc_start: 0.6983 (mt0) cc_final: 0.6618 (mt0) REVERT: C 829 LYS cc_start: 0.5575 (mttt) cc_final: 0.4682 (pttm) REVERT: D 532 ASN cc_start: 0.7550 (t0) cc_final: 0.7317 (t0) REVERT: D 576 THR cc_start: 0.6850 (m) cc_final: 0.6615 (m) REVERT: D 632 MET cc_start: 0.7845 (tpt) cc_final: 0.7623 (tpp) REVERT: D 648 TYR cc_start: 0.8565 (t80) cc_final: 0.8164 (t80) REVERT: D 693 MET cc_start: 0.8369 (mmm) cc_final: 0.7789 (mmm) REVERT: D 705 TYR cc_start: 0.7135 (m-80) cc_final: 0.6932 (m-10) REVERT: D 709 TRP cc_start: 0.8590 (t-100) cc_final: 0.8088 (t-100) REVERT: D 782 ASP cc_start: 0.7658 (m-30) cc_final: 0.7254 (t0) REVERT: D 799 ILE cc_start: 0.9009 (mt) cc_final: 0.8728 (tp) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.1030 time to fit residues: 72.0956 Evaluate side-chains 275 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS B 618 GLN B 651 ASN B 674 GLN B 730 GLN B 752 ASN B 776 HIS C 468 GLN C 480 ASN C 494 HIS C 651 ASN C 720 ASN D 752 ASN D 808 ASN D 810 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.226385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.210746 restraints weight = 16658.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.206933 restraints weight = 19340.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.204265 restraints weight = 24362.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.203355 restraints weight = 25383.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.203023 restraints weight = 22446.696| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13712 Z= 0.156 Angle : 0.609 7.326 18640 Z= 0.326 Chirality : 0.044 0.235 2064 Planarity : 0.004 0.062 2352 Dihedral : 5.103 56.904 1848 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 3.31 % Allowed : 9.46 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1680 helix: 0.90 (0.18), residues: 847 sheet: -0.44 (0.46), residues: 109 loop : -0.71 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 550 TYR 0.017 0.002 TYR D 759 PHE 0.018 0.002 PHE C 758 TRP 0.014 0.001 TRP C 855 HIS 0.010 0.002 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00363 (13708) covalent geometry : angle 0.60882 (18632) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.44685 ( 8) hydrogen bonds : bond 0.04120 ( 655) hydrogen bonds : angle 4.71865 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 285 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 MET cc_start: 0.3541 (tpp) cc_final: 0.3332 (tpp) REVERT: A 632 MET cc_start: 0.7630 (tpp) cc_final: 0.7410 (tpp) REVERT: A 648 TYR cc_start: 0.8891 (t80) cc_final: 0.8647 (t80) REVERT: A 797 MET cc_start: 0.8780 (tpp) cc_final: 0.8558 (tpp) REVERT: C 450 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6853 (tp30) REVERT: C 600 MET cc_start: 0.1309 (mtt) cc_final: 0.0026 (ttt) REVERT: C 751 ILE cc_start: 0.9007 (mm) cc_final: 0.8736 (mm) REVERT: D 693 MET cc_start: 0.7313 (mmm) cc_final: 0.6714 (mmm) REVERT: D 709 TRP cc_start: 0.7413 (t-100) cc_final: 0.7059 (t-100) REVERT: D 712 ILE cc_start: 0.8116 (mm) cc_final: 0.7890 (mm) outliers start: 48 outliers final: 25 residues processed: 317 average time/residue: 0.0812 time to fit residues: 39.9120 Evaluate side-chains 252 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 776 HIS Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 101 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 148 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 802 HIS B 713 ASN B 776 HIS D 619 GLN D 651 ASN ** D 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.225045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.204137 restraints weight = 16746.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.201539 restraints weight = 25765.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.200092 restraints weight = 27796.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.199397 restraints weight = 25243.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.199143 restraints weight = 23810.187| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13712 Z= 0.128 Angle : 0.541 7.683 18640 Z= 0.289 Chirality : 0.042 0.230 2064 Planarity : 0.003 0.064 2352 Dihedral : 4.687 52.551 1848 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 3.04 % Allowed : 13.26 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1680 helix: 1.34 (0.18), residues: 846 sheet: 0.31 (0.51), residues: 91 loop : -0.70 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 516 TYR 0.015 0.001 TYR D 759 PHE 0.027 0.001 PHE D 655 TRP 0.016 0.001 TRP A 709 HIS 0.010 0.001 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00290 (13708) covalent geometry : angle 0.54076 (18632) SS BOND : bond 0.00208 ( 4) SS BOND : angle 1.44031 ( 8) hydrogen bonds : bond 0.03612 ( 655) hydrogen bonds : angle 4.47883 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 MET cc_start: 0.7604 (tpp) cc_final: 0.7356 (tpp) REVERT: A 704 MET cc_start: 0.6067 (ptm) cc_final: 0.5790 (ptm) REVERT: A 797 MET cc_start: 0.8832 (tpp) cc_final: 0.8500 (tpp) REVERT: A 802 HIS cc_start: 0.7207 (t70) cc_final: 0.7004 (t-90) REVERT: B 669 GLN cc_start: 0.6369 (OUTLIER) cc_final: 0.5222 (mm110) REVERT: B 776 HIS cc_start: 0.7298 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: C 597 MET cc_start: 0.4565 (mpp) cc_final: 0.3651 (tpp) REVERT: C 600 MET cc_start: 0.1588 (mtt) cc_final: 0.0187 (ttt) REVERT: C 828 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 693 MET cc_start: 0.7243 (mmm) cc_final: 0.6739 (mmm) REVERT: D 709 TRP cc_start: 0.7459 (t-100) cc_final: 0.7228 (t-100) outliers start: 44 outliers final: 21 residues processed: 264 average time/residue: 0.0893 time to fit residues: 37.1473 Evaluate side-chains 232 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 669 GLN Chi-restraints excluded: chain B residue 674 GLN Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain B residue 776 HIS Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 HIS B 651 ASN B 674 GLN B 713 ASN C 752 ASN ** C 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 720 ASN D 808 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.216538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.200797 restraints weight = 16648.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.199193 restraints weight = 20889.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.197363 restraints weight = 20003.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.196170 restraints weight = 22147.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.194708 restraints weight = 23501.000| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13712 Z= 0.234 Angle : 0.644 10.091 18640 Z= 0.341 Chirality : 0.046 0.262 2064 Planarity : 0.004 0.070 2352 Dihedral : 4.941 50.517 1848 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 4.35 % Allowed : 13.47 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1680 helix: 1.13 (0.18), residues: 830 sheet: 0.48 (0.52), residues: 95 loop : -0.66 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 768 TYR 0.023 0.002 TYR D 540 PHE 0.021 0.002 PHE D 655 TRP 0.018 0.002 TRP D 589 HIS 0.023 0.002 HIS B 776 Details of bonding type rmsd covalent geometry : bond 0.00561 (13708) covalent geometry : angle 0.64323 (18632) SS BOND : bond 0.00218 ( 4) SS BOND : angle 1.12925 ( 8) hydrogen bonds : bond 0.04534 ( 655) hydrogen bonds : angle 4.82330 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 LEU cc_start: 0.7882 (mt) cc_final: 0.7639 (tp) REVERT: A 597 MET cc_start: 0.2092 (mmp) cc_final: 0.1836 (mmp) REVERT: A 632 MET cc_start: 0.7674 (tpp) cc_final: 0.7443 (tpp) REVERT: A 759 TYR cc_start: 0.6580 (p90) cc_final: 0.6359 (p90) REVERT: A 763 ASN cc_start: 0.8168 (p0) cc_final: 0.7710 (p0) REVERT: A 797 MET cc_start: 0.8783 (tpp) cc_final: 0.8568 (tpp) REVERT: B 634 MET cc_start: 0.8774 (mmm) cc_final: 0.8422 (mmm) REVERT: B 753 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: B 848 ILE cc_start: 0.7849 (mm) cc_final: 0.7303 (mt) REVERT: C 597 MET cc_start: 0.4222 (mpp) cc_final: 0.3286 (tpp) REVERT: C 600 MET cc_start: 0.1589 (mtt) cc_final: 0.0115 (ttt) REVERT: C 609 MET cc_start: 0.7984 (tpp) cc_final: 0.7759 (tpp) REVERT: C 753 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: C 797 MET cc_start: 0.8980 (tpp) cc_final: 0.8669 (mmt) REVERT: C 848 ILE cc_start: 0.7896 (mm) cc_final: 0.7464 (mt) REVERT: D 709 TRP cc_start: 0.7351 (t-100) cc_final: 0.7101 (t-100) outliers start: 63 outliers final: 37 residues processed: 270 average time/residue: 0.0899 time to fit residues: 38.4320 Evaluate side-chains 247 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 589 TRP Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 753 ASP Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 655 PHE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 802 HIS ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN ** C 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.220408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.203948 restraints weight = 16678.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.201584 restraints weight = 24317.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.200262 restraints weight = 25279.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.199441 restraints weight = 23055.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.198468 restraints weight = 22579.217| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13712 Z= 0.134 Angle : 0.550 9.062 18640 Z= 0.287 Chirality : 0.042 0.240 2064 Planarity : 0.003 0.067 2352 Dihedral : 4.465 43.580 1848 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 3.31 % Allowed : 15.26 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1680 helix: 1.52 (0.18), residues: 832 sheet: 0.60 (0.51), residues: 100 loop : -0.60 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 701 TYR 0.014 0.001 TYR C 679 PHE 0.027 0.001 PHE D 655 TRP 0.018 0.001 TRP C 709 HIS 0.011 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00316 (13708) covalent geometry : angle 0.54964 (18632) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.57874 ( 8) hydrogen bonds : bond 0.03496 ( 655) hydrogen bonds : angle 4.42380 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 230 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 632 MET cc_start: 0.7215 (tpp) cc_final: 0.6925 (tpp) REVERT: A 763 ASN cc_start: 0.7806 (p0) cc_final: 0.7100 (p0) REVERT: A 797 MET cc_start: 0.8804 (tpp) cc_final: 0.8493 (tpp) REVERT: B 797 MET cc_start: 0.8820 (tpp) cc_final: 0.8510 (mmt) REVERT: C 450 GLU cc_start: 0.7201 (tp30) cc_final: 0.6173 (tt0) REVERT: C 597 MET cc_start: 0.4025 (mpp) cc_final: 0.3127 (tpp) REVERT: C 600 MET cc_start: 0.1434 (mtt) cc_final: -0.0436 (ttm) REVERT: C 797 MET cc_start: 0.9033 (tpp) cc_final: 0.8635 (mmt) REVERT: C 848 ILE cc_start: 0.7767 (mm) cc_final: 0.7217 (mt) REVERT: D 632 MET cc_start: 0.6850 (tpp) cc_final: 0.6646 (ttm) REVERT: D 709 TRP cc_start: 0.7363 (t-100) cc_final: 0.7083 (t-100) outliers start: 48 outliers final: 35 residues processed: 262 average time/residue: 0.0916 time to fit residues: 37.9580 Evaluate side-chains 243 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 143 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 707 GLN C 669 GLN C 776 HIS C 786 GLN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.220677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.202059 restraints weight = 16592.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.198928 restraints weight = 22277.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.196881 restraints weight = 25227.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.196424 restraints weight = 24675.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.195767 restraints weight = 21878.944| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13712 Z= 0.127 Angle : 0.551 9.569 18640 Z= 0.285 Chirality : 0.042 0.247 2064 Planarity : 0.003 0.067 2352 Dihedral : 4.301 40.638 1848 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 3.94 % Allowed : 14.99 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1680 helix: 1.61 (0.18), residues: 835 sheet: 0.72 (0.53), residues: 94 loop : -0.60 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 701 TYR 0.017 0.001 TYR B 688 PHE 0.023 0.001 PHE D 655 TRP 0.015 0.001 TRP C 709 HIS 0.006 0.001 HIS C 776 Details of bonding type rmsd covalent geometry : bond 0.00297 (13708) covalent geometry : angle 0.55091 (18632) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.53301 ( 8) hydrogen bonds : bond 0.03465 ( 655) hydrogen bonds : angle 4.37931 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 632 MET cc_start: 0.7249 (tpp) cc_final: 0.6977 (tpp) REVERT: A 763 ASN cc_start: 0.7865 (p0) cc_final: 0.7177 (p0) REVERT: B 450 GLU cc_start: 0.7361 (tp30) cc_final: 0.7159 (tp30) REVERT: B 632 MET cc_start: 0.8359 (tpt) cc_final: 0.8083 (tpp) REVERT: B 797 MET cc_start: 0.8767 (tpp) cc_final: 0.8461 (mmt) REVERT: C 450 GLU cc_start: 0.7342 (tp30) cc_final: 0.6208 (tt0) REVERT: C 562 LEU cc_start: 0.8530 (mt) cc_final: 0.8214 (mt) REVERT: C 597 MET cc_start: 0.4275 (mpp) cc_final: 0.3351 (tpp) REVERT: C 600 MET cc_start: 0.1366 (mtt) cc_final: -0.0437 (ttt) REVERT: C 669 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6314 (tp40) REVERT: C 753 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7066 (m-30) REVERT: C 797 MET cc_start: 0.9015 (tpp) cc_final: 0.8639 (mmt) REVERT: C 848 ILE cc_start: 0.7669 (mm) cc_final: 0.7110 (mt) REVERT: D 709 TRP cc_start: 0.7415 (t-100) cc_final: 0.7062 (t-100) REVERT: D 850 MET cc_start: 0.6096 (ttt) cc_final: 0.5800 (ttm) outliers start: 57 outliers final: 36 residues processed: 256 average time/residue: 0.0944 time to fit residues: 38.0850 Evaluate side-chains 250 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 753 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 1 optimal weight: 0.1980 chunk 155 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 775 GLN A 802 HIS C 707 GLN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.220841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.201044 restraints weight = 16658.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.198332 restraints weight = 24723.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.197357 restraints weight = 25483.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.196627 restraints weight = 23264.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.195869 restraints weight = 21876.680| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13712 Z= 0.123 Angle : 0.557 10.884 18640 Z= 0.288 Chirality : 0.042 0.260 2064 Planarity : 0.003 0.066 2352 Dihedral : 4.198 38.939 1848 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 3.25 % Allowed : 16.09 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1680 helix: 1.66 (0.18), residues: 840 sheet: 0.74 (0.53), residues: 94 loop : -0.67 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 710 TYR 0.016 0.001 TYR C 705 PHE 0.020 0.001 PHE D 655 TRP 0.024 0.001 TRP C 709 HIS 0.011 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00286 (13708) covalent geometry : angle 0.55753 (18632) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.37081 ( 8) hydrogen bonds : bond 0.03359 ( 655) hydrogen bonds : angle 4.32102 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 632 MET cc_start: 0.7155 (tpp) cc_final: 0.6864 (tpp) REVERT: A 763 ASN cc_start: 0.7722 (p0) cc_final: 0.7011 (p0) REVERT: B 797 MET cc_start: 0.8753 (tpp) cc_final: 0.8423 (mmt) REVERT: B 834 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8239 (t) REVERT: B 848 ILE cc_start: 0.7636 (mm) cc_final: 0.7244 (mp) REVERT: C 450 GLU cc_start: 0.7320 (tp30) cc_final: 0.6257 (tt0) REVERT: C 455 MET cc_start: 0.6053 (mtm) cc_final: 0.5812 (mtm) REVERT: C 597 MET cc_start: 0.4005 (mpp) cc_final: 0.3094 (tpp) REVERT: C 600 MET cc_start: 0.1107 (mtt) cc_final: -0.0511 (ttt) REVERT: C 797 MET cc_start: 0.9017 (tpp) cc_final: 0.8629 (mmt) REVERT: C 848 ILE cc_start: 0.7662 (mm) cc_final: 0.7108 (mt) REVERT: D 597 MET cc_start: 0.1600 (mmt) cc_final: 0.1201 (mmp) REVERT: D 709 TRP cc_start: 0.7472 (t-100) cc_final: 0.7131 (t-100) REVERT: D 850 MET cc_start: 0.6082 (ttt) cc_final: 0.5803 (ttm) outliers start: 47 outliers final: 32 residues processed: 252 average time/residue: 0.0920 time to fit residues: 36.8253 Evaluate side-chains 241 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 707 GLN C 713 ASN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.218232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.198338 restraints weight = 16551.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.196791 restraints weight = 26868.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.195643 restraints weight = 24596.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.194491 restraints weight = 23045.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.193203 restraints weight = 24830.318| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13712 Z= 0.165 Angle : 0.590 10.850 18640 Z= 0.308 Chirality : 0.043 0.259 2064 Planarity : 0.003 0.069 2352 Dihedral : 4.314 38.706 1848 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Rotamer: Outliers : 3.25 % Allowed : 15.95 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1680 helix: 1.53 (0.18), residues: 836 sheet: 0.72 (0.54), residues: 94 loop : -0.70 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 701 TYR 0.016 0.002 TYR B 540 PHE 0.018 0.001 PHE D 655 TRP 0.028 0.001 TRP C 709 HIS 0.003 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00395 (13708) covalent geometry : angle 0.58979 (18632) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.40946 ( 8) hydrogen bonds : bond 0.03788 ( 655) hydrogen bonds : angle 4.46411 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6975 (mt) REVERT: A 632 MET cc_start: 0.7262 (tpp) cc_final: 0.6976 (tpp) REVERT: A 763 ASN cc_start: 0.7916 (p0) cc_final: 0.7503 (p0) REVERT: B 597 MET cc_start: 0.4323 (ttm) cc_final: 0.4063 (ttm) REVERT: B 797 MET cc_start: 0.8763 (tpp) cc_final: 0.8451 (mmt) REVERT: B 834 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8292 (t) REVERT: B 848 ILE cc_start: 0.7949 (mm) cc_final: 0.7425 (mp) REVERT: C 450 GLU cc_start: 0.7346 (tp30) cc_final: 0.6216 (tt0) REVERT: C 597 MET cc_start: 0.3729 (mpp) cc_final: 0.2860 (tpp) REVERT: C 600 MET cc_start: 0.0989 (mtt) cc_final: -0.0638 (ttt) REVERT: C 797 MET cc_start: 0.9001 (tpp) cc_final: 0.8646 (mmt) REVERT: D 597 MET cc_start: 0.2030 (mmt) cc_final: 0.1678 (mmp) REVERT: D 609 MET cc_start: 0.7746 (mmm) cc_final: 0.7115 (tmm) REVERT: D 709 TRP cc_start: 0.7371 (t-100) cc_final: 0.7082 (t-100) REVERT: D 850 MET cc_start: 0.6019 (ttt) cc_final: 0.5779 (ttm) outliers start: 47 outliers final: 39 residues processed: 244 average time/residue: 0.0945 time to fit residues: 36.6189 Evaluate side-chains 247 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 808 ASN Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.227646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197314 restraints weight = 17538.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.192533 restraints weight = 26570.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.189477 restraints weight = 25698.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.190161 restraints weight = 24668.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.189683 restraints weight = 18997.750| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13712 Z= 0.170 Angle : 0.594 9.439 18640 Z= 0.309 Chirality : 0.043 0.264 2064 Planarity : 0.003 0.067 2352 Dihedral : 4.370 38.223 1848 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 3.66 % Allowed : 16.09 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1680 helix: 1.51 (0.18), residues: 837 sheet: 0.79 (0.54), residues: 94 loop : -0.78 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 701 TYR 0.024 0.002 TYR C 481 PHE 0.018 0.001 PHE D 655 TRP 0.025 0.001 TRP C 709 HIS 0.003 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00408 (13708) covalent geometry : angle 0.59377 (18632) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.35479 ( 8) hydrogen bonds : bond 0.03818 ( 655) hydrogen bonds : angle 4.49498 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7091 (mt) REVERT: A 632 MET cc_start: 0.7342 (tpp) cc_final: 0.7043 (tpp) REVERT: A 802 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.7170 (t-90) REVERT: B 597 MET cc_start: 0.4404 (ttm) cc_final: 0.4047 (ttm) REVERT: B 797 MET cc_start: 0.8763 (tpp) cc_final: 0.8430 (mmt) REVERT: B 834 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8225 (t) REVERT: B 848 ILE cc_start: 0.7823 (mm) cc_final: 0.7395 (mp) REVERT: C 450 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: C 597 MET cc_start: 0.4535 (mpp) cc_final: 0.3572 (tpp) REVERT: C 600 MET cc_start: 0.0982 (mtt) cc_final: -0.0189 (ttm) REVERT: C 797 MET cc_start: 0.8824 (tpp) cc_final: 0.8440 (mmt) REVERT: D 573 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7222 (mt) REVERT: D 597 MET cc_start: 0.1811 (mmt) cc_final: 0.1454 (mmp) REVERT: D 609 MET cc_start: 0.7914 (mmm) cc_final: 0.7212 (tmm) REVERT: D 709 TRP cc_start: 0.7913 (t-100) cc_final: 0.7458 (t-100) REVERT: D 850 MET cc_start: 0.6505 (ttt) cc_final: 0.6149 (ttm) outliers start: 53 outliers final: 41 residues processed: 242 average time/residue: 0.0899 time to fit residues: 34.7936 Evaluate side-chains 251 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 802 HIS Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 MET Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 808 ASN Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 HIS C 485 ASN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.228411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196685 restraints weight = 17491.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.195566 restraints weight = 24162.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.193959 restraints weight = 22659.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.189991 restraints weight = 22951.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.189062 restraints weight = 26744.738| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13712 Z= 0.149 Angle : 0.590 9.572 18640 Z= 0.306 Chirality : 0.043 0.276 2064 Planarity : 0.003 0.067 2352 Dihedral : 4.293 37.833 1848 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % Rotamer: Outliers : 3.31 % Allowed : 16.16 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1680 helix: 1.59 (0.18), residues: 834 sheet: 0.88 (0.54), residues: 94 loop : -0.77 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 701 TYR 0.031 0.002 TYR D 585 PHE 0.017 0.001 PHE D 655 TRP 0.028 0.001 TRP C 709 HIS 0.006 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00354 (13708) covalent geometry : angle 0.58979 (18632) SS BOND : bond 0.00322 ( 4) SS BOND : angle 1.24911 ( 8) hydrogen bonds : bond 0.03653 ( 655) hydrogen bonds : angle 4.43953 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6942 (mt) REVERT: A 632 MET cc_start: 0.7191 (tpp) cc_final: 0.6957 (tpp) REVERT: A 763 ASN cc_start: 0.7579 (p0) cc_final: 0.7187 (p0) REVERT: B 597 MET cc_start: 0.4705 (ttm) cc_final: 0.4480 (ttm) REVERT: B 797 MET cc_start: 0.8751 (tpp) cc_final: 0.8411 (mmt) REVERT: B 834 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (t) REVERT: C 450 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: C 597 MET cc_start: 0.4368 (mpp) cc_final: 0.3422 (tpp) REVERT: C 600 MET cc_start: 0.0944 (mtt) cc_final: -0.0229 (ttt) REVERT: C 797 MET cc_start: 0.8935 (tpp) cc_final: 0.8535 (mmt) REVERT: D 573 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7046 (mt) REVERT: D 597 MET cc_start: 0.1478 (mmt) cc_final: 0.1082 (mmp) REVERT: D 609 MET cc_start: 0.7981 (mmm) cc_final: 0.7484 (mmm) REVERT: D 709 TRP cc_start: 0.7771 (t-100) cc_final: 0.7354 (t-100) REVERT: D 850 MET cc_start: 0.6335 (ttt) cc_final: 0.6020 (ttm) outliers start: 48 outliers final: 37 residues processed: 245 average time/residue: 0.0945 time to fit residues: 36.4908 Evaluate side-chains 251 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 655 PHE Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain C residue 591 ASN Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 676 GLU Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 487 GLU Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 521 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 600 MET Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 784 PHE Chi-restraints excluded: chain D residue 834 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 161 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 674 GLN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.224402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.193709 restraints weight = 17135.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.188552 restraints weight = 22978.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.185880 restraints weight = 24588.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.184978 restraints weight = 21111.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.183463 restraints weight = 21006.553| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13712 Z= 0.119 Angle : 0.569 10.122 18640 Z= 0.291 Chirality : 0.042 0.254 2064 Planarity : 0.003 0.064 2352 Dihedral : 4.104 36.733 1848 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 2.76 % Allowed : 17.20 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1680 helix: 1.72 (0.18), residues: 838 sheet: 1.00 (0.53), residues: 94 loop : -0.72 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 701 TYR 0.019 0.001 TYR C 481 PHE 0.013 0.001 PHE D 655 TRP 0.029 0.001 TRP C 709 HIS 0.002 0.000 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00279 (13708) covalent geometry : angle 0.56893 (18632) SS BOND : bond 0.00031 ( 4) SS BOND : angle 0.88448 ( 8) hydrogen bonds : bond 0.03260 ( 655) hydrogen bonds : angle 4.29337 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.80 seconds wall clock time: 36 minutes 47.83 seconds (2207.83 seconds total)