Starting phenix.real_space_refine on Sun May 3 12:13:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrh_61755/05_2026/9jrh_61755.map" } resolution = 4.0 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= 0.080 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 59 5.16 5 C 8251 2.51 5 N 2143 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3215 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 1 Chain: "B" Number of atoms: 3221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3221 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 12, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3208 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3153 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 12, 'TRANS': 391} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.25 Number of scatterers: 12825 At special positions: 0 Unit cell: (116.16, 120, 121.92, 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 59 16.00 O 2372 8.00 N 2143 7.00 C 8251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 471.0 milliseconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DSN A 901 " pdb=" CB DSN B 901 " pdb=" CB DSN C 901 " pdb=" CB DSN D 901 " Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 14 sheets defined 45.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 565 through 587 Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.532A pdb=" N GLY A 614 " --> pdb=" O TRP A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 645 removed outlier: 3.518A pdb=" N ARG A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 4.260A pdb=" N ARG A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 removed outlier: 3.879A pdb=" N GLN A 674 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.514A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 712 Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 724 through 735 removed outlier: 4.197A pdb=" N GLY A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.906A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 removed outlier: 4.358A pdb=" N PHE A 784 " --> pdb=" O TYR A 780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 785' Processing helix chain 'A' and resid 795 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 812 through 817 Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.815A pdb=" N ALA A 832 " --> pdb=" O HIS A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.568A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 850 " --> pdb=" O CYS A 846 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 853 " --> pdb=" O ALA A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 476 removed outlier: 4.009A pdb=" N VAL B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 554 through 559 removed outlier: 4.013A pdb=" N PHE B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.585A pdb=" N ALA B 570 " --> pdb=" O TRP B 566 " (cutoff:3.500A) Proline residue: B 574 - end of helix Processing helix chain 'B' and resid 605 through 615 removed outlier: 4.345A pdb=" N TRP B 610 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR B 613 " --> pdb=" O ILE B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 634 removed outlier: 4.200A pdb=" N ARG B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 645 removed outlier: 4.178A pdb=" N LEU B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.762A pdb=" N ALA B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 removed outlier: 3.933A pdb=" N ARG B 666 " --> pdb=" O ASN B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.670A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.698A pdb=" N GLU B 707 " --> pdb=" O THR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 732 Processing helix chain 'B' and resid 743 through 753 removed outlier: 4.052A pdb=" N TYR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 794 removed outlier: 4.459A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 790 " --> pdb=" O GLN B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.703A pdb=" N LEU B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 827 through 831 Processing helix chain 'B' and resid 834 through 851 removed outlier: 3.541A pdb=" N LEU B 847 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 857 removed outlier: 4.067A pdb=" N TRP B 855 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.794A pdb=" N GLU C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 587 removed outlier: 3.591A pdb=" N ALA C 570 " --> pdb=" O TRP C 566 " (cutoff:3.500A) Proline residue: C 574 - end of helix removed outlier: 3.575A pdb=" N GLN C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 610 through 615 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 636 through 659 removed outlier: 4.106A pdb=" N LEU C 642 " --> pdb=" O TRP C 638 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 649 " --> pdb=" O CYS C 645 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 654 " --> pdb=" O ALA C 650 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 702 through 713 removed outlier: 4.445A pdb=" N ARG C 710 " --> pdb=" O ALA C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 733 removed outlier: 3.793A pdb=" N GLY C 728 " --> pdb=" O ASN C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 753 removed outlier: 5.824A pdb=" N TYR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 804 removed outlier: 3.587A pdb=" N LYS C 803 " --> pdb=" O LEU C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 850 Processing helix chain 'C' and resid 850 through 856 removed outlier: 4.400A pdb=" N TRP C 854 " --> pdb=" O ALA C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 476 Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.138A pdb=" N SER D 528 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 586 Proline residue: D 574 - end of helix removed outlier: 3.718A pdb=" N LEU D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 615 removed outlier: 4.962A pdb=" N TRP D 610 " --> pdb=" O HIS D 606 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR D 613 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 634 Processing helix chain 'D' and resid 634 through 645 removed outlier: 3.874A pdb=" N TRP D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE D 640 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 659 removed outlier: 3.651A pdb=" N ALA D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.652A pdb=" N LEU D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 703 through 714 removed outlier: 3.583A pdb=" N GLU D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 722 removed outlier: 3.548A pdb=" N CYS D 721 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D 722 " --> pdb=" O ASP D 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 718 through 722' Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.592A pdb=" N ARG D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 747 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.747A pdb=" N LEU D 751 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 793 removed outlier: 3.557A pdb=" N LEU D 783 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU D 790 " --> pdb=" O GLN D 786 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 801 removed outlier: 4.191A pdb=" N VAL D 799 " --> pdb=" O GLY D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 804 No H-bonds generated for 'chain 'D' and resid 802 through 804' Processing helix chain 'D' and resid 812 through 818 removed outlier: 4.424A pdb=" N HIS D 816 " --> pdb=" O LEU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 830 Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.245A pdb=" N ILE D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 532 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 Processing sheet with id=AA3, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AA4, first strand: chain 'B' and resid 441 through 443 removed outlier: 5.715A pdb=" N VAL B 441 " --> pdb=" O TYR B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 521 through 522 removed outlier: 3.682A pdb=" N GLY B 769 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.838A pdb=" N ASP B 531 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 679 through 680 removed outlier: 6.818A pdb=" N GLY B 680 " --> pdb=" O LEU B 740 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 432 through 435 removed outlier: 7.274A pdb=" N ILE C 484 " --> pdb=" O ARG C 433 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN C 435 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'C' and resid 520 through 521 removed outlier: 4.118A pdb=" N ILE C 520 " --> pdb=" O GLY C 771 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 739 through 742 Processing sheet with id=AB3, first strand: chain 'D' and resid 441 through 442 removed outlier: 4.143A pdb=" N ILE D 517 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N SER D 518 " --> pdb=" O ALA D 773 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ALA D 773 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE D 520 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY D 769 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET D 537 " --> pdb=" O TYR D 770 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 542 through 546 removed outlier: 4.059A pdb=" N GLY D 762 " --> pdb=" O ILE D 543 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE D 545 " --> pdb=" O VAL D 760 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL D 760 " --> pdb=" O ILE D 545 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 678 through 679 removed outlier: 6.036A pdb=" N SER D 678 " --> pdb=" O ALA D 738 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 408 hydrogen bonds defined for protein. 1155 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: 1.63 Time building geometry restraints manager: 1.17 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: 4075 1.34 - 1.46: 3100 1.46 - 1.58: 5843 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 13108 Sorted by residual: bond pdb=" C TRP C 805 " pdb=" O TRP C 805 " ideal model delta sigma weight residual 1.235 1.226 0.009 4.70e-03 4.53e+04 3.79e+00 bond pdb=" CB ARG C 710 " pdb=" CG ARG C 710 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CA ILE C 522 " pdb=" CB ILE C 522 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.31e-02 5.83e+03 1.95e+00 bond pdb=" C ALA A 559 " pdb=" N PRO A 560 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.91e+00 bond pdb=" C ILE C 573 " pdb=" N PRO C 574 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.84e+00 ... (remaining 13103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 17545 2.83 - 5.65: 203 5.65 - 8.48: 28 8.48 - 11.30: 4 11.30 - 14.13: 2 Bond angle restraints: 17782 Sorted by residual: angle pdb=" N ARG B 660 " pdb=" CA ARG B 660 " pdb=" C ARG B 660 " ideal model delta sigma weight residual 114.62 106.91 7.71 1.14e+00 7.69e-01 4.58e+01 angle pdb=" CA LEU C 471 " pdb=" C LEU C 471 " pdb=" O LEU C 471 " ideal model delta sigma weight residual 121.02 116.04 4.98 9.00e-01 1.23e+00 3.07e+01 angle pdb=" N LEU C 471 " pdb=" CA LEU C 471 " pdb=" C LEU C 471 " ideal model delta sigma weight residual 110.41 116.26 -5.85 1.18e+00 7.18e-01 2.46e+01 angle pdb=" C GLN A 701 " pdb=" CA GLN A 701 " pdb=" CB GLN A 701 " ideal model delta sigma weight residual 117.23 110.58 6.65 1.36e+00 5.41e-01 2.39e+01 angle pdb=" CA LEU C 471 " pdb=" C LEU C 471 " pdb=" N ASP C 472 " ideal model delta sigma weight residual 116.77 122.69 -5.92 1.21e+00 6.83e-01 2.39e+01 ... (remaining 17777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6776 17.95 - 35.90: 714 35.90 - 53.85: 167 53.85 - 71.80: 25 71.80 - 89.75: 12 Dihedral angle restraints: 7694 sinusoidal: 2967 harmonic: 4727 Sorted by residual: dihedral pdb=" CA ILE C 788 " pdb=" C ILE C 788 " pdb=" N LEU C 789 " pdb=" CA LEU C 789 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ALA A 559 " pdb=" C ALA A 559 " pdb=" N PRO A 560 " pdb=" CA PRO A 560 " ideal model delta harmonic sigma weight residual -180.00 -155.09 -24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ALA D 559 " pdb=" C ALA D 559 " pdb=" N PRO D 560 " pdb=" CA PRO D 560 " ideal model delta harmonic sigma weight residual 180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 7691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1195 0.032 - 0.064: 542 0.064 - 0.097: 201 0.097 - 0.129: 67 0.129 - 0.161: 13 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA PRO C 448 " pdb=" N PRO C 448 " pdb=" C PRO C 448 " pdb=" CB PRO C 448 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA PHE C 480 " pdb=" N PHE C 480 " pdb=" C PHE C 480 " pdb=" CB PHE C 480 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CG LEU C 557 " pdb=" CB LEU C 557 " pdb=" CD1 LEU C 557 " pdb=" CD2 LEU C 557 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2015 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 559 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO C 560 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 709 " 0.020 2.00e-02 2.50e+03 1.90e-02 9.04e+00 pdb=" CG TRP A 709 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 709 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 709 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 709 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 709 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 709 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 709 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 709 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 638 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C TRP D 638 " -0.033 2.00e-02 2.50e+03 pdb=" O TRP D 638 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU D 639 " 0.011 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 264 2.66 - 3.22: 13270 3.22 - 3.78: 19399 3.78 - 4.34: 26051 4.34 - 4.90: 40344 Nonbonded interactions: 99328 Sorted by model distance: nonbonded pdb=" O ARG D 666 " pdb=" NH1 ARG D 666 " model vdw 2.102 3.120 nonbonded pdb=" O TYR C 780 " pdb=" NH1 ARG C 781 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR D 485 " pdb=" OE2 GLU D 507 " model vdw 2.195 3.040 nonbonded pdb=" O PRO C 664 " pdb=" N ARG C 666 " model vdw 2.217 3.120 nonbonded pdb=" O PHE C 616 " pdb=" OG1 THR C 641 " model vdw 2.219 3.040 ... (remaining 99323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 433 through 484 or (resid 485 and (name N or name CA or na \ me C or name O or name CB )) or resid 486 through 852 or resid 901)) selection = (chain 'B' and (resid 433 through 484 or (resid 485 and (name N or name CA or na \ me C or name O or name CB )) or resid 486 through 852 or resid 901)) selection = (chain 'C' and (resid 433 through 852 or resid 901)) selection = (chain 'D' and (resid 433 through 484 or (resid 485 and (name N or name CA or na \ me C or name O or name CB )) or resid 486 through 901)) } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.550 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 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 : 0.003 0.043 13108 Z= 0.162 Angle : 0.798 14.128 17782 Z= 0.451 Chirality : 0.044 0.161 2018 Planarity : 0.004 0.084 2230 Dihedral : 15.806 89.751 4656 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.37 % Favored : 90.32 % Rotamer: Outliers : 3.27 % Allowed : 19.01 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.20), residues: 1622 helix: -1.48 (0.20), residues: 597 sheet: -1.13 (0.81), residues: 56 loop : -1.83 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 781 TYR 0.023 0.001 TYR C 688 PHE 0.028 0.002 PHE C 480 TRP 0.052 0.002 TRP A 709 HIS 0.006 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00300 (13108) covalent geometry : angle 0.79837 (17782) hydrogen bonds : bond 0.16049 ( 408) hydrogen bonds : angle 7.19133 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 PHE cc_start: 0.6601 (m-80) cc_final: 0.6218 (m-10) REVERT: A 585 ARG cc_start: 0.5846 (mmp-170) cc_final: 0.4738 (ttm170) REVERT: B 551 LYS cc_start: 0.5256 (OUTLIER) cc_final: 0.3417 (ttpt) REVERT: B 638 TRP cc_start: 0.6563 (m-10) cc_final: 0.6107 (m-90) REVERT: B 724 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7310 (p0) REVERT: C 553 SER cc_start: 0.7632 (m) cc_final: 0.7184 (p) REVERT: D 630 MET cc_start: 0.8003 (mmp) cc_final: 0.7424 (mmm) REVERT: D 812 ASP cc_start: 0.7073 (t0) cc_final: 0.6759 (t0) outliers start: 45 outliers final: 39 residues processed: 192 average time/residue: 0.0992 time to fit residues: 28.7829 Evaluate side-chains 198 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 637 TRP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 755 ASP Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 GLN D 486 GLN D 763 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.214958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.181885 restraints weight = 18989.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.180565 restraints weight = 23203.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.176825 restraints weight = 18714.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.174030 restraints weight = 22692.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173221 restraints weight = 20386.902| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13108 Z= 0.156 Angle : 0.689 12.332 17782 Z= 0.361 Chirality : 0.045 0.177 2018 Planarity : 0.004 0.077 2230 Dihedral : 8.310 88.951 1836 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.37 % Favored : 90.32 % Rotamer: Outliers : 5.22 % Allowed : 17.34 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1622 helix: -1.12 (0.20), residues: 598 sheet: -1.08 (0.80), residues: 56 loop : -1.80 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 781 TYR 0.025 0.002 TYR C 688 PHE 0.019 0.002 PHE D 655 TRP 0.025 0.001 TRP B 804 HIS 0.005 0.001 HIS C 829 Details of bonding type rmsd covalent geometry : bond 0.00346 (13108) covalent geometry : angle 0.68885 (17782) hydrogen bonds : bond 0.04634 ( 408) hydrogen bonds : angle 5.85910 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8403 (pt) cc_final: 0.8052 (mp) REVERT: A 555 PHE cc_start: 0.6700 (m-80) cc_final: 0.6240 (m-10) REVERT: A 585 ARG cc_start: 0.5824 (mmp-170) cc_final: 0.4783 (ttm170) REVERT: A 826 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6197 (mt) REVERT: B 551 LYS cc_start: 0.5253 (OUTLIER) cc_final: 0.3476 (ttpt) REVERT: B 724 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7630 (p0) REVERT: B 826 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6854 (mt) REVERT: C 553 SER cc_start: 0.7467 (m) cc_final: 0.7123 (p) REVERT: C 630 MET cc_start: 0.8324 (tmm) cc_final: 0.7935 (tmm) REVERT: D 468 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7015 (pt) REVERT: D 630 MET cc_start: 0.7880 (mmp) cc_final: 0.7543 (mmm) REVERT: D 636 SER cc_start: 0.8593 (t) cc_final: 0.8329 (t) REVERT: D 812 ASP cc_start: 0.6863 (t0) cc_final: 0.6460 (t0) outliers start: 72 outliers final: 47 residues processed: 223 average time/residue: 0.0917 time to fit residues: 31.0238 Evaluate side-chains 206 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 637 TRP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 828 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 103 optimal weight: 0.0770 chunk 157 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 ASN ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.208226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.175083 restraints weight = 20097.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.174114 restraints weight = 26345.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.172487 restraints weight = 20225.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.170769 restraints weight = 20501.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.170476 restraints weight = 20104.188| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 13108 Z= 0.263 Angle : 0.768 13.082 17782 Z= 0.402 Chirality : 0.048 0.227 2018 Planarity : 0.005 0.097 2230 Dihedral : 8.170 85.405 1806 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.73 % Favored : 88.96 % Rotamer: Outliers : 7.11 % Allowed : 17.27 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.20), residues: 1622 helix: -1.37 (0.20), residues: 601 sheet: -1.28 (0.77), residues: 58 loop : -1.91 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 666 TYR 0.025 0.002 TYR C 688 PHE 0.036 0.003 PHE D 655 TRP 0.039 0.002 TRP A 709 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00619 (13108) covalent geometry : angle 0.76790 (17782) hydrogen bonds : bond 0.05262 ( 408) hydrogen bonds : angle 6.14154 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 158 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8512 (pt) cc_final: 0.8203 (mp) REVERT: A 585 ARG cc_start: 0.6012 (mmp-170) cc_final: 0.4829 (ttm170) REVERT: A 826 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6241 (mt) REVERT: B 551 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.3551 (ttpt) REVERT: B 585 ARG cc_start: 0.5703 (mmp-170) cc_final: 0.4250 (ttp-170) REVERT: B 638 TRP cc_start: 0.6840 (m-10) cc_final: 0.6215 (m-90) REVERT: B 724 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7861 (p0) REVERT: B 826 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6971 (mt) REVERT: C 482 TYR cc_start: 0.3805 (m-10) cc_final: 0.3283 (m-10) REVERT: C 553 SER cc_start: 0.7583 (m) cc_final: 0.7184 (p) REVERT: C 630 MET cc_start: 0.8398 (tmm) cc_final: 0.8158 (tmm) REVERT: C 688 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7866 (t80) REVERT: C 802 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6721 (mp10) REVERT: D 468 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6972 (pt) REVERT: D 812 ASP cc_start: 0.7021 (t0) cc_final: 0.6617 (t0) outliers start: 98 outliers final: 72 residues processed: 236 average time/residue: 0.0903 time to fit residues: 32.9626 Evaluate side-chains 234 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 155 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 637 TRP Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 688 TYR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 144 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 119 optimal weight: 0.0370 chunk 69 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178458 restraints weight = 19943.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.175554 restraints weight = 23876.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.171550 restraints weight = 24899.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.170945 restraints weight = 23421.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.169826 restraints weight = 21966.925| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13108 Z= 0.129 Angle : 0.655 12.958 17782 Z= 0.340 Chirality : 0.043 0.162 2018 Planarity : 0.004 0.069 2230 Dihedral : 7.594 82.460 1806 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.25 % Favored : 90.44 % Rotamer: Outliers : 5.08 % Allowed : 20.61 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.21), residues: 1622 helix: -1.03 (0.20), residues: 596 sheet: -1.36 (0.75), residues: 58 loop : -1.80 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 666 TYR 0.025 0.001 TYR C 688 PHE 0.016 0.002 PHE D 466 TRP 0.067 0.002 TRP A 709 HIS 0.003 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00278 (13108) covalent geometry : angle 0.65548 (17782) hydrogen bonds : bond 0.04030 ( 408) hydrogen bonds : angle 5.48976 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 555 PHE cc_start: 0.6462 (m-80) cc_final: 0.6077 (m-10) REVERT: A 585 ARG cc_start: 0.5838 (mmp-170) cc_final: 0.4660 (ttm170) REVERT: A 826 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6077 (mt) REVERT: B 478 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 551 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.3548 (ttpt) REVERT: B 724 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7904 (p0) REVERT: C 482 TYR cc_start: 0.3829 (m-10) cc_final: 0.3488 (m-10) REVERT: C 537 MET cc_start: 0.7789 (tpp) cc_final: 0.7416 (tpp) REVERT: C 553 SER cc_start: 0.7514 (m) cc_final: 0.7099 (p) REVERT: C 630 MET cc_start: 0.8353 (tmm) cc_final: 0.8064 (tmm) REVERT: C 734 LYS cc_start: 0.5769 (ptpp) cc_final: 0.5430 (ptpp) REVERT: C 802 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: D 468 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6985 (pt) REVERT: D 617 VAL cc_start: 0.6080 (OUTLIER) cc_final: 0.5258 (p) REVERT: D 630 MET cc_start: 0.8060 (mmp) cc_final: 0.7589 (mmm) REVERT: D 812 ASP cc_start: 0.7046 (t0) cc_final: 0.6660 (t0) outliers start: 70 outliers final: 51 residues processed: 212 average time/residue: 0.0890 time to fit residues: 29.1500 Evaluate side-chains 208 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 637 TRP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 66 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 41 optimal weight: 40.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.212089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.179675 restraints weight = 20089.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.175277 restraints weight = 23146.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.173300 restraints weight = 21272.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.172527 restraints weight = 21417.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.170730 restraints weight = 20942.325| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13108 Z= 0.152 Angle : 0.662 13.321 17782 Z= 0.344 Chirality : 0.044 0.191 2018 Planarity : 0.004 0.074 2230 Dihedral : 7.427 81.738 1801 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.49 % Favored : 90.26 % Rotamer: Outliers : 6.02 % Allowed : 20.61 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.21), residues: 1622 helix: -0.96 (0.20), residues: 601 sheet: -1.40 (0.74), residues: 58 loop : -1.84 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 666 TYR 0.034 0.001 TYR C 688 PHE 0.020 0.002 PHE D 655 TRP 0.053 0.001 TRP A 709 HIS 0.003 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00346 (13108) covalent geometry : angle 0.66200 (17782) hydrogen bonds : bond 0.04087 ( 408) hydrogen bonds : angle 5.48313 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 158 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 555 PHE cc_start: 0.6481 (m-80) cc_final: 0.6020 (m-10) REVERT: A 585 ARG cc_start: 0.5897 (mmp-170) cc_final: 0.4714 (ttm170) REVERT: A 826 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6131 (mt) REVERT: B 478 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7680 (tt) REVERT: B 508 LEU cc_start: 0.7362 (tp) cc_final: 0.7067 (tp) REVERT: B 551 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.3575 (ttpt) REVERT: B 724 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.8006 (p0) REVERT: B 826 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6849 (mt) REVERT: C 482 TYR cc_start: 0.3837 (m-10) cc_final: 0.3495 (m-10) REVERT: C 537 MET cc_start: 0.7913 (tpp) cc_final: 0.7623 (tpp) REVERT: C 553 SER cc_start: 0.7516 (m) cc_final: 0.7074 (p) REVERT: C 630 MET cc_start: 0.8388 (tmm) cc_final: 0.8105 (tmm) REVERT: C 658 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8567 (t) REVERT: C 802 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: D 468 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7020 (pt) REVERT: D 617 VAL cc_start: 0.6229 (OUTLIER) cc_final: 0.5392 (p) REVERT: D 630 MET cc_start: 0.8113 (mmp) cc_final: 0.7609 (mmm) REVERT: D 812 ASP cc_start: 0.7097 (t0) cc_final: 0.6724 (t0) outliers start: 83 outliers final: 64 residues processed: 220 average time/residue: 0.0906 time to fit residues: 30.9580 Evaluate side-chains 227 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 724 ASN ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.210047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.177542 restraints weight = 19897.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174686 restraints weight = 23325.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.172021 restraints weight = 17785.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.170262 restraints weight = 18898.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168547 restraints weight = 20037.298| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13108 Z= 0.198 Angle : 0.696 12.661 17782 Z= 0.362 Chirality : 0.045 0.203 2018 Planarity : 0.004 0.078 2230 Dihedral : 7.449 78.925 1799 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.99 % Favored : 89.77 % Rotamer: Outliers : 6.68 % Allowed : 19.96 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.21), residues: 1622 helix: -1.08 (0.20), residues: 603 sheet: -1.40 (0.74), residues: 58 loop : -1.88 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 666 TYR 0.029 0.002 TYR C 688 PHE 0.029 0.002 PHE D 655 TRP 0.051 0.002 TRP A 709 HIS 0.003 0.001 HIS C 829 Details of bonding type rmsd covalent geometry : bond 0.00464 (13108) covalent geometry : angle 0.69600 (17782) hydrogen bonds : bond 0.04438 ( 408) hydrogen bonds : angle 5.61736 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 152 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 ARG cc_start: 0.6019 (mmp-170) cc_final: 0.4788 (ttm170) REVERT: A 826 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6215 (mt) REVERT: B 478 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7590 (tt) REVERT: B 551 LYS cc_start: 0.5232 (OUTLIER) cc_final: 0.3468 (ttpt) REVERT: B 585 ARG cc_start: 0.5637 (mmp-170) cc_final: 0.4202 (ttp-170) REVERT: B 826 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6797 (mt) REVERT: C 537 MET cc_start: 0.7943 (tpp) cc_final: 0.7615 (tpp) REVERT: C 553 SER cc_start: 0.7689 (m) cc_final: 0.7286 (p) REVERT: C 630 MET cc_start: 0.8403 (tmm) cc_final: 0.8052 (tmm) REVERT: C 658 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (t) REVERT: C 802 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6701 (mp10) REVERT: D 468 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7117 (pt) REVERT: D 630 MET cc_start: 0.8189 (mmp) cc_final: 0.7686 (mmm) REVERT: D 812 ASP cc_start: 0.7046 (t0) cc_final: 0.6673 (t0) outliers start: 92 outliers final: 72 residues processed: 225 average time/residue: 0.0900 time to fit residues: 31.5180 Evaluate side-chains 226 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 147 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 563 PHE Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 532 PHE Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 804 TRP Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 840 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 103 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 77 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.214774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.180333 restraints weight = 19793.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.180032 restraints weight = 23245.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177099 restraints weight = 21910.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176500 restraints weight = 21393.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.174701 restraints weight = 20125.994| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13108 Z= 0.119 Angle : 0.646 13.423 17782 Z= 0.334 Chirality : 0.043 0.160 2018 Planarity : 0.004 0.065 2230 Dihedral : 6.945 77.293 1798 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.56 % Favored : 90.20 % Rotamer: Outliers : 4.57 % Allowed : 22.13 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1622 helix: -0.72 (0.21), residues: 595 sheet: -1.36 (0.76), residues: 56 loop : -1.84 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 710 TYR 0.027 0.001 TYR C 688 PHE 0.012 0.001 PHE B 668 TRP 0.048 0.001 TRP A 709 HIS 0.006 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00254 (13108) covalent geometry : angle 0.64581 (17782) hydrogen bonds : bond 0.03511 ( 408) hydrogen bonds : angle 5.19829 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 0.422 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: A 585 ARG cc_start: 0.5820 (mmp-170) cc_final: 0.4661 (ttm170) REVERT: B 478 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7662 (tt) REVERT: C 537 MET cc_start: 0.7839 (tpp) cc_final: 0.7477 (tpp) REVERT: C 553 SER cc_start: 0.7103 (m) cc_final: 0.6667 (p) REVERT: C 630 MET cc_start: 0.8415 (tmm) cc_final: 0.8076 (tmm) REVERT: C 658 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8380 (t) REVERT: C 802 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6654 (mp10) REVERT: D 468 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7098 (pt) REVERT: D 812 ASP cc_start: 0.7157 (t0) cc_final: 0.6744 (t0) outliers start: 63 outliers final: 50 residues processed: 208 average time/residue: 0.0900 time to fit residues: 28.9558 Evaluate side-chains 219 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 637 TRP Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 805 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.209053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174484 restraints weight = 19724.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.172908 restraints weight = 24324.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.170363 restraints weight = 24019.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.169870 restraints weight = 20400.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.167956 restraints weight = 20412.564| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13108 Z= 0.238 Angle : 0.732 12.921 17782 Z= 0.380 Chirality : 0.047 0.217 2018 Planarity : 0.005 0.090 2230 Dihedral : 7.286 76.297 1794 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.91 % Favored : 88.84 % Rotamer: Outliers : 5.66 % Allowed : 20.90 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.20), residues: 1622 helix: -1.06 (0.20), residues: 600 sheet: -1.46 (0.74), residues: 58 loop : -1.93 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 710 TYR 0.024 0.002 TYR C 688 PHE 0.036 0.003 PHE D 655 TRP 0.052 0.002 TRP A 709 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00564 (13108) covalent geometry : angle 0.73242 (17782) hydrogen bonds : bond 0.04620 ( 408) hydrogen bonds : angle 5.65995 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 149 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 PHE cc_start: 0.6444 (m-80) cc_final: 0.6233 (m-10) REVERT: A 585 ARG cc_start: 0.5996 (mmp-170) cc_final: 0.4751 (ttm170) REVERT: A 826 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6425 (mt) REVERT: B 478 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7654 (tt) REVERT: B 551 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.3529 (ttpt) REVERT: B 585 ARG cc_start: 0.5587 (mmp-170) cc_final: 0.4164 (ttp-170) REVERT: B 638 TRP cc_start: 0.6879 (m-10) cc_final: 0.6318 (m-10) REVERT: B 826 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7059 (mp) REVERT: C 553 SER cc_start: 0.7616 (m) cc_final: 0.7180 (p) REVERT: C 630 MET cc_start: 0.8511 (tmm) cc_final: 0.8168 (tmm) REVERT: C 658 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (t) REVERT: C 802 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: D 468 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7331 (pt) REVERT: D 712 ILE cc_start: 0.5963 (OUTLIER) cc_final: 0.5748 (mt) REVERT: D 812 ASP cc_start: 0.7298 (t0) cc_final: 0.6833 (t0) outliers start: 78 outliers final: 65 residues processed: 215 average time/residue: 0.0939 time to fit residues: 30.9453 Evaluate side-chains 216 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 804 TRP Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 840 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.209114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.172992 restraints weight = 19856.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.172590 restraints weight = 24802.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.169809 restraints weight = 26390.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169693 restraints weight = 23533.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.167675 restraints weight = 20816.284| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13108 Z= 0.223 Angle : 0.728 13.236 17782 Z= 0.375 Chirality : 0.046 0.199 2018 Planarity : 0.005 0.075 2230 Dihedral : 7.302 70.812 1794 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.36 % Favored : 89.40 % Rotamer: Outliers : 5.66 % Allowed : 21.12 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.20), residues: 1622 helix: -1.10 (0.20), residues: 595 sheet: -1.44 (0.75), residues: 58 loop : -1.92 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 631 TYR 0.024 0.002 TYR C 688 PHE 0.031 0.002 PHE D 655 TRP 0.052 0.002 TRP A 709 HIS 0.003 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00523 (13108) covalent geometry : angle 0.72763 (17782) hydrogen bonds : bond 0.04480 ( 408) hydrogen bonds : angle 5.68634 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 151 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 ARG cc_start: 0.6049 (mmp-170) cc_final: 0.4783 (ttm170) REVERT: A 826 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6454 (mt) REVERT: B 478 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 551 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.3581 (ttpt) REVERT: B 585 ARG cc_start: 0.5617 (mmp-170) cc_final: 0.4217 (ttp-170) REVERT: B 826 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6482 (mt) REVERT: C 553 SER cc_start: 0.7699 (m) cc_final: 0.7221 (p) REVERT: C 630 MET cc_start: 0.8536 (tmm) cc_final: 0.8148 (tmm) REVERT: C 658 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8614 (t) REVERT: C 802 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: D 468 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7271 (pt) REVERT: D 712 ILE cc_start: 0.5780 (OUTLIER) cc_final: 0.5419 (mt) REVERT: D 812 ASP cc_start: 0.7322 (t0) cc_final: 0.6869 (t0) outliers start: 78 outliers final: 63 residues processed: 218 average time/residue: 0.0947 time to fit residues: 31.7145 Evaluate side-chains 216 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 145 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 TYR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 578 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 804 TRP Chi-restraints excluded: chain D residue 805 TRP Chi-restraints excluded: chain D residue 840 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN ** C 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.213451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178159 restraints weight = 19790.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.174978 restraints weight = 25173.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.173897 restraints weight = 23855.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173189 restraints weight = 21099.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.172049 restraints weight = 20659.498| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13108 Z= 0.125 Angle : 0.670 11.955 17782 Z= 0.343 Chirality : 0.043 0.160 2018 Planarity : 0.004 0.068 2230 Dihedral : 6.911 69.077 1794 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.99 % Favored : 89.77 % Rotamer: Outliers : 4.06 % Allowed : 23.15 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.21), residues: 1622 helix: -0.80 (0.21), residues: 595 sheet: -1.48 (0.74), residues: 58 loop : -1.82 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 660 TYR 0.024 0.001 TYR C 688 PHE 0.023 0.002 PHE C 449 TRP 0.049 0.002 TRP A 709 HIS 0.004 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00273 (13108) covalent geometry : angle 0.66989 (17782) hydrogen bonds : bond 0.03607 ( 408) hydrogen bonds : angle 5.24896 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ILE cc_start: 0.6140 (mm) cc_final: 0.5785 (mt) REVERT: A 585 ARG cc_start: 0.5958 (mmp-170) cc_final: 0.4689 (ttm170) REVERT: A 826 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6216 (mt) REVERT: B 478 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7534 (tt) REVERT: B 551 LYS cc_start: 0.5384 (OUTLIER) cc_final: 0.3569 (ttpt) REVERT: C 553 SER cc_start: 0.7320 (m) cc_final: 0.6844 (p) REVERT: C 630 MET cc_start: 0.8472 (tmm) cc_final: 0.8090 (tmm) REVERT: C 658 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8427 (t) REVERT: C 802 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6432 (mp10) REVERT: D 468 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7259 (pt) REVERT: D 666 ARG cc_start: 0.6421 (tpt90) cc_final: 0.6020 (tpt90) REVERT: D 712 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5333 (mt) REVERT: D 812 ASP cc_start: 0.7155 (t0) cc_final: 0.6752 (t0) outliers start: 56 outliers final: 45 residues processed: 200 average time/residue: 0.0941 time to fit residues: 28.7438 Evaluate side-chains 206 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 709 TRP Chi-restraints excluded: chain A residue 780 TYR Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 551 LYS Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 724 ASN Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 802 GLN Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain D residue 518 SER Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 651 ASN Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 674 GLN Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 712 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 780 TYR Chi-restraints excluded: chain D residue 804 TRP Chi-restraints excluded: chain D residue 805 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.211715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178894 restraints weight = 19676.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.173890 restraints weight = 22424.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.171521 restraints weight = 21685.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.170765 restraints weight = 19080.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.169203 restraints weight = 20464.488| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13108 Z= 0.163 Angle : 0.691 11.744 17782 Z= 0.355 Chirality : 0.044 0.193 2018 Planarity : 0.004 0.079 2230 Dihedral : 6.796 68.313 1791 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.48 % Favored : 89.27 % Rotamer: Outliers : 4.21 % Allowed : 23.37 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.21), residues: 1622 helix: -0.86 (0.21), residues: 597 sheet: -1.46 (0.74), residues: 58 loop : -1.87 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 631 TYR 0.023 0.001 TYR C 688 PHE 0.032 0.002 PHE B 466 TRP 0.050 0.002 TRP A 709 HIS 0.003 0.001 HIS B 829 Details of bonding type rmsd covalent geometry : bond 0.00376 (13108) covalent geometry : angle 0.69142 (17782) hydrogen bonds : bond 0.03981 ( 408) hydrogen bonds : angle 5.31647 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.71 seconds wall clock time: 34 minutes 40.45 seconds (2080.45 seconds total)