Starting phenix.real_space_refine on Sun Aug 24 20:45:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pba_17582/08_2025/8pba_17582.map" } resolution = 2.64 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 7410 2.51 5 N 2004 2.21 5 O 2146 1.98 5 H 11332 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11482 Classifications: {'peptide': 722} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688} Chain breaks: 2 Chain: "B" Number of atoms: 11482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11482 Classifications: {'peptide': 722} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688} Chain breaks: 2 Time building chain proxies: 3.16, per 1000 atoms: 0.14 Number of scatterers: 22964 At special positions: 0 Unit cell: (97.175, 149.565, 104.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2146 8.00 N 2004 7.00 C 7410 6.00 H 11332 1.00 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: 1.73 Conformation dependent library (CDL) restraints added in 476.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 23.1% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 60 removed outlier: 3.547A pdb=" N THR A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.630A pdb=" N TYR A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.897A pdb=" N GLN A 716 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 753 through 769 Processing helix chain 'A' and resid 784 through 797 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.800A pdb=" N ARG A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 839 through 846 removed outlier: 4.668A pdb=" N GLU A 844 " --> pdb=" O GLY A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 880 removed outlier: 3.978A pdb=" N LEU A 869 " --> pdb=" O HIS A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 917 Processing helix chain 'B' and resid 44 through 60 removed outlier: 3.537A pdb=" N THR B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.579A pdb=" N TYR B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.894A pdb=" N GLN B 716 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 753 through 769 Processing helix chain 'B' and resid 784 through 797 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.804A pdb=" N ARG B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 837 Processing helix chain 'B' and resid 839 through 846 removed outlier: 4.668A pdb=" N GLU B 844 " --> pdb=" O GLY B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 880 removed outlier: 3.978A pdb=" N LEU B 869 " --> pdb=" O HIS B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 917 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.764A pdb=" N GLU A 36 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 730 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.764A pdb=" N GLU A 36 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N LYS A 691 " --> pdb=" O MET A 773 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N MET A 775 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N TYR A 693 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 777 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP A 783 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 803 " --> pdb=" O SER A 776 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 778 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE A 805 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 780 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY A 807 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY A 782 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 80 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 100 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 119 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 116 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 648 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 118 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR A 641 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 631 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A 643 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 629 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 625 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N VAL A 649 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 14.695A pdb=" N ALA A 623 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER A 618 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 615 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 80 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 100 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 119 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 116 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 648 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 118 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR A 641 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 631 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A 643 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 629 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 625 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N VAL A 649 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 14.695A pdb=" N ALA A 623 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER A 618 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 605 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.746A pdb=" N VAL A 276 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 287 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 398 removed outlier: 6.558A pdb=" N GLN A 408 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 396 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP A 406 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE A 398 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A 404 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLN A 416 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 421 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 475 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 492 through 493 removed outlier: 6.716A pdb=" N SER A 522 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 534 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU A 524 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.626A pdb=" N GLU A 567 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU A 572 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.761A pdb=" N GLU B 36 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 730 " --> pdb=" O TYR B 698 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.761A pdb=" N GLU B 36 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LYS B 691 " --> pdb=" O MET B 773 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N MET B 775 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N TYR B 693 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 777 " --> pdb=" O TYR B 693 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP B 783 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA B 803 " --> pdb=" O SER B 776 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 778 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE B 805 " --> pdb=" O VAL B 778 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 780 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY B 807 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY B 782 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N ALA B 75 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 100 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 119 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 641 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 631 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR B 643 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 629 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 625 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL B 649 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 14.715A pdb=" N ALA B 623 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 618 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR B 615 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N ALA B 75 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 100 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 119 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 641 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 631 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR B 643 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 629 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 625 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL B 649 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 14.715A pdb=" N ALA B 623 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 618 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 605 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 260 removed outlier: 6.744A pdb=" N VAL B 276 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 287 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC1, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC3, first strand: chain 'B' and resid 390 through 398 removed outlier: 6.558A pdb=" N GLN B 408 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 396 " --> pdb=" O TRP B 406 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP B 406 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE B 398 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 404 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 416 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 421 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 475 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 493 removed outlier: 6.716A pdb=" N SER B 522 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 534 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU B 524 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 554 removed outlier: 4.626A pdb=" N GLU B 567 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU B 572 " --> pdb=" O GLU B 567 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1359 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: 6.90 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 11308 1.12 - 1.29: 1914 1.29 - 1.46: 5045 1.46 - 1.64: 4879 1.64 - 1.81: 120 Bond restraints: 23266 Sorted by residual: bond pdb=" CD2 PHE B 399 " pdb=" HD2 PHE B 399 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" CD2 PHE A 399 " pdb=" HD2 PHE A 399 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" NE2 HIS B 286 " pdb=" HE2 HIS B 286 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CD1 PHE A 712 " pdb=" HD1 PHE A 712 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" CD2 PHE B 742 " pdb=" HD2 PHE B 742 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 23261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 37743 2.73 - 5.46: 2971 5.46 - 8.19: 1168 8.19 - 10.93: 0 10.93 - 13.66: 24 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ASP A 343 " pdb=" N PRO A 344 " pdb=" CA PRO A 344 " ideal model delta sigma weight residual 119.66 125.32 -5.66 7.30e-01 1.88e+00 6.00e+01 angle pdb=" C CYS A 387 " pdb=" N PRO A 388 " pdb=" CA PRO A 388 " ideal model delta sigma weight residual 119.56 127.39 -7.83 1.02e+00 9.61e-01 5.89e+01 angle pdb=" C CYS B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta sigma weight residual 119.56 127.36 -7.80 1.02e+00 9.61e-01 5.86e+01 angle pdb=" C HIS A 797 " pdb=" N PRO A 798 " pdb=" CA PRO A 798 " ideal model delta sigma weight residual 119.56 126.76 -7.20 1.01e+00 9.80e-01 5.08e+01 angle pdb=" C HIS B 797 " pdb=" N PRO B 798 " pdb=" CA PRO B 798 " ideal model delta sigma weight residual 119.56 126.72 -7.16 1.01e+00 9.80e-01 5.03e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 10336 17.10 - 34.20: 494 34.20 - 51.29: 119 51.29 - 68.39: 59 68.39 - 85.49: 12 Dihedral angle restraints: 11020 sinusoidal: 5888 harmonic: 5132 Sorted by residual: dihedral pdb=" CA TYR A 392 " pdb=" C TYR A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR B 392 " pdb=" C TYR B 392 " pdb=" N ILE B 393 " pdb=" CA ILE B 393 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 429 " pdb=" C LEU A 429 " pdb=" N PRO A 430 " pdb=" CA PRO A 430 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 11017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1092 0.062 - 0.124: 483 0.124 - 0.186: 111 0.186 - 0.248: 18 0.248 - 0.310: 6 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA TYR A 580 " pdb=" N TYR A 580 " pdb=" C TYR A 580 " pdb=" CB TYR A 580 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA PHE B 67 " pdb=" N PHE B 67 " pdb=" C PHE B 67 " pdb=" CB PHE B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR B 580 " pdb=" N TYR B 580 " pdb=" C TYR B 580 " pdb=" CB TYR B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1707 not shown) Planarity restraints: 3458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 910 " 0.107 2.00e-02 2.50e+03 4.27e-02 5.48e+01 pdb=" CG TYR B 910 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 910 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 910 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 910 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 910 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 910 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 910 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR B 910 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR B 910 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR B 910 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 910 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 910 " -0.106 2.00e-02 2.50e+03 4.26e-02 5.46e+01 pdb=" CG TYR A 910 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 910 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 910 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 910 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 910 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 910 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 910 " -0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 910 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 910 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR A 910 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 910 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 316 " 0.112 2.00e-02 2.50e+03 3.57e-02 5.10e+01 pdb=" CG TRP A 316 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 316 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 316 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 316 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP A 316 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 316 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 316 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 316 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 316 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP A 316 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 316 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 316 " -0.030 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 316 " 0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 316 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 316 " 0.024 2.00e-02 2.50e+03 ... (remaining 3455 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 403 1.94 - 2.61: 26083 2.61 - 3.27: 70176 3.27 - 3.94: 94733 3.94 - 4.60: 144903 Nonbonded interactions: 336298 Sorted by model distance: nonbonded pdb=" HG1 THR B 91 " pdb=" H ASN B 92 " model vdw 1.281 2.100 nonbonded pdb=" HG1 THR A 91 " pdb=" H ASN A 92 " model vdw 1.283 2.100 nonbonded pdb=" HG1 THR A 673 " pdb=" H LEU A 675 " model vdw 1.293 2.100 nonbonded pdb=" HH TYR A 903 " pdb="HH11 ARG A 907 " model vdw 1.443 2.100 nonbonded pdb=" HH TYR B 903 " pdb="HH11 ARG B 907 " model vdw 1.447 2.100 ... (remaining 336293 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 20.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.017 0.117 11934 Z= 0.893 Angle : 1.313 7.827 16154 Z= 0.901 Chirality : 0.071 0.310 1710 Planarity : 0.011 0.056 2084 Dihedral : 11.775 85.487 4402 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.32 % Allowed : 2.31 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.22), residues: 1432 helix: -1.95 (0.26), residues: 270 sheet: 1.43 (0.25), residues: 428 loop : 1.41 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 74 TYR 0.097 0.015 TYR B 910 PHE 0.069 0.010 PHE A 40 TRP 0.076 0.015 TRP A 316 HIS 0.013 0.003 HIS B 865 Details of bonding type rmsd covalent geometry : bond 0.01679 (11934) covalent geometry : angle 1.31330 (16154) hydrogen bonds : bond 0.17504 ( 430) hydrogen bonds : angle 7.94680 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.8212 (mmm) cc_final: 0.7928 (mmt) REVERT: B 616 MET cc_start: 0.8121 (mmm) cc_final: 0.7821 (mmt) outliers start: 4 outliers final: 0 residues processed: 195 average time/residue: 1.4416 time to fit residues: 301.0492 Evaluate side-chains 108 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.083446 restraints weight = 83692.209| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.45 r_work: 0.3417 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11934 Z= 0.144 Angle : 0.606 7.658 16154 Z= 0.334 Chirality : 0.047 0.183 1710 Planarity : 0.005 0.067 2084 Dihedral : 5.596 25.175 1594 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.59 % Allowed : 9.24 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.22), residues: 1432 helix: -0.13 (0.31), residues: 252 sheet: 0.55 (0.24), residues: 454 loop : 1.02 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 814 TYR 0.016 0.002 TYR A 628 PHE 0.024 0.002 PHE B 772 TRP 0.015 0.001 TRP B 55 HIS 0.004 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00312 (11934) covalent geometry : angle 0.60600 (16154) hydrogen bonds : bond 0.05114 ( 430) hydrogen bonds : angle 5.45048 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8390 (mm) REVERT: A 114 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8486 (tpp80) REVERT: A 424 TYR cc_start: 0.7923 (t80) cc_final: 0.7685 (t80) REVERT: B 35 ASN cc_start: 0.6308 (m-40) cc_final: 0.5946 (m110) REVERT: B 105 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8881 (tm) REVERT: B 268 LEU cc_start: 0.8144 (mp) cc_final: 0.7932 (mm) REVERT: B 593 ILE cc_start: 0.8575 (mt) cc_final: 0.8349 (tp) outliers start: 20 outliers final: 6 residues processed: 146 average time/residue: 1.6134 time to fit residues: 252.6134 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 890 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.095012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079318 restraints weight = 83614.218| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.44 r_work: 0.3351 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11934 Z= 0.241 Angle : 0.592 5.106 16154 Z= 0.327 Chirality : 0.046 0.177 1710 Planarity : 0.004 0.038 2084 Dihedral : 5.438 24.080 1594 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.51 % Allowed : 11.31 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1432 helix: -0.14 (0.32), residues: 262 sheet: 0.05 (0.24), residues: 452 loop : 0.56 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 907 TYR 0.014 0.002 TYR A 628 PHE 0.018 0.002 PHE B 772 TRP 0.011 0.002 TRP B 55 HIS 0.004 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00529 (11934) covalent geometry : angle 0.59249 (16154) hydrogen bonds : bond 0.04932 ( 430) hydrogen bonds : angle 5.06941 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 73 MET cc_start: 0.8319 (ppp) cc_final: 0.8109 (ppp) REVERT: A 117 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 60 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8322 (mtm180) REVERT: B 62 MET cc_start: 0.8368 (mtp) cc_final: 0.8147 (mtm) REVERT: B 105 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8895 (tm) outliers start: 19 outliers final: 8 residues processed: 136 average time/residue: 1.4581 time to fit residues: 212.6613 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.094675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.079087 restraints weight = 83982.450| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.41 r_work: 0.3335 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11934 Z= 0.183 Angle : 0.547 4.726 16154 Z= 0.297 Chirality : 0.045 0.204 1710 Planarity : 0.004 0.043 2084 Dihedral : 5.310 25.791 1594 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.59 % Allowed : 12.26 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.22), residues: 1432 helix: -0.11 (0.31), residues: 268 sheet: -0.17 (0.23), residues: 438 loop : 0.32 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 907 TYR 0.012 0.002 TYR A 628 PHE 0.016 0.002 PHE B 772 TRP 0.012 0.002 TRP B 55 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00407 (11934) covalent geometry : angle 0.54676 (16154) hydrogen bonds : bond 0.04311 ( 430) hydrogen bonds : angle 4.82046 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8400 (mm) REVERT: A 117 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 62 MET cc_start: 0.8419 (mtp) cc_final: 0.8159 (mtm) REVERT: B 105 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9003 (tm) outliers start: 20 outliers final: 9 residues processed: 126 average time/residue: 1.4358 time to fit residues: 193.7524 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 857 HIS B 408 GLN B 857 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.094623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078919 restraints weight = 83295.148| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.46 r_work: 0.3348 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11934 Z= 0.166 Angle : 0.529 4.765 16154 Z= 0.285 Chirality : 0.044 0.179 1710 Planarity : 0.004 0.070 2084 Dihedral : 5.140 24.948 1594 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.43 % Allowed : 12.90 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.22), residues: 1432 helix: 0.05 (0.32), residues: 268 sheet: -0.36 (0.23), residues: 450 loop : 0.27 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 287 TYR 0.011 0.002 TYR A 628 PHE 0.015 0.001 PHE B 772 TRP 0.011 0.002 TRP B 55 HIS 0.007 0.001 HIS B 610 Details of bonding type rmsd covalent geometry : bond 0.00372 (11934) covalent geometry : angle 0.52922 (16154) hydrogen bonds : bond 0.04052 ( 430) hydrogen bonds : angle 4.67731 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.696 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 48 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 117 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 62 MET cc_start: 0.8487 (mtp) cc_final: 0.8217 (mtm) outliers start: 18 outliers final: 7 residues processed: 119 average time/residue: 1.6982 time to fit residues: 217.2302 Evaluate side-chains 110 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 HIS B 797 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.077758 restraints weight = 84427.768| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.47 r_work: 0.3322 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11934 Z= 0.204 Angle : 0.550 4.479 16154 Z= 0.296 Chirality : 0.045 0.184 1710 Planarity : 0.004 0.047 2084 Dihedral : 5.188 24.810 1594 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.99 % Allowed : 12.26 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1432 helix: 0.20 (0.32), residues: 256 sheet: -0.43 (0.23), residues: 440 loop : 0.06 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 907 TYR 0.012 0.002 TYR A 628 PHE 0.014 0.002 PHE A 116 TRP 0.011 0.002 TRP B 55 HIS 0.004 0.001 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.00457 (11934) covalent geometry : angle 0.54972 (16154) hydrogen bonds : bond 0.04183 ( 430) hydrogen bonds : angle 4.70753 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.646 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 36 GLU cc_start: 0.8213 (tt0) cc_final: 0.7983 (tt0) REVERT: A 48 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 114 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8526 (tpp80) REVERT: A 117 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 62 MET cc_start: 0.8476 (mtp) cc_final: 0.8198 (mtm) REVERT: B 105 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9060 (tm) outliers start: 25 outliers final: 10 residues processed: 124 average time/residue: 1.6327 time to fit residues: 217.3392 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.093452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.077861 restraints weight = 84256.849| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.41 r_work: 0.3311 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11934 Z= 0.188 Angle : 0.543 5.217 16154 Z= 0.292 Chirality : 0.044 0.180 1710 Planarity : 0.004 0.046 2084 Dihedral : 5.152 24.541 1594 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 12.98 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.22), residues: 1432 helix: 0.23 (0.32), residues: 256 sheet: -0.55 (0.24), residues: 424 loop : 0.03 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 907 TYR 0.011 0.002 TYR A 628 PHE 0.015 0.002 PHE B 772 TRP 0.011 0.002 TRP B 55 HIS 0.003 0.001 HIS B 610 Details of bonding type rmsd covalent geometry : bond 0.00422 (11934) covalent geometry : angle 0.54284 (16154) hydrogen bonds : bond 0.04050 ( 430) hydrogen bonds : angle 4.66342 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.661 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 36 GLU cc_start: 0.8214 (tt0) cc_final: 0.7934 (tt0) REVERT: A 114 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8541 (tpp80) REVERT: A 117 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 62 MET cc_start: 0.8476 (mtp) cc_final: 0.8204 (mtm) REVERT: B 105 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9115 (tm) outliers start: 20 outliers final: 10 residues processed: 117 average time/residue: 1.4695 time to fit residues: 185.8262 Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 857 HIS B 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.093084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077535 restraints weight = 84275.640| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.41 r_work: 0.3323 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11934 Z= 0.199 Angle : 0.549 5.548 16154 Z= 0.295 Chirality : 0.045 0.179 1710 Planarity : 0.004 0.045 2084 Dihedral : 5.159 24.040 1594 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.75 % Allowed : 12.98 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.22), residues: 1432 helix: 0.06 (0.32), residues: 266 sheet: -0.62 (0.25), residues: 404 loop : -0.08 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.012 0.002 TYR A 910 PHE 0.016 0.002 PHE A 116 TRP 0.011 0.002 TRP B 55 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00449 (11934) covalent geometry : angle 0.54922 (16154) hydrogen bonds : bond 0.04093 ( 430) hydrogen bonds : angle 4.68535 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 382 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 857 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8230 (t70) REVERT: B 62 MET cc_start: 0.8499 (mtp) cc_final: 0.8247 (mtm) REVERT: B 105 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9136 (tm) outliers start: 22 outliers final: 10 residues processed: 118 average time/residue: 1.4390 time to fit residues: 183.0564 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 857 HIS Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 ASN ** 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 = 0.3729 r_free = 0.3729 target = 0.093956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.078387 restraints weight = 84349.956| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.42 r_work: 0.3321 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11934 Z= 0.140 Angle : 0.528 6.057 16154 Z= 0.282 Chirality : 0.044 0.177 1710 Planarity : 0.004 0.046 2084 Dihedral : 5.080 23.875 1594 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.35 % Allowed : 13.61 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1432 helix: 0.36 (0.33), residues: 256 sheet: -0.68 (0.24), residues: 410 loop : -0.06 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 114 TYR 0.010 0.001 TYR A 580 PHE 0.016 0.001 PHE A 888 TRP 0.011 0.001 TRP B 55 HIS 0.003 0.001 HIS A 857 Details of bonding type rmsd covalent geometry : bond 0.00318 (11934) covalent geometry : angle 0.52781 (16154) hydrogen bonds : bond 0.03809 ( 430) hydrogen bonds : angle 4.54782 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.7314 (t0) cc_final: 0.7019 (m-40) REVERT: A 117 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 382 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 62 MET cc_start: 0.8492 (mtp) cc_final: 0.8244 (mtm) REVERT: B 105 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9153 (tm) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 1.3868 time to fit residues: 171.4460 Evaluate side-chains 113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS B 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.096840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.080991 restraints weight = 83411.874| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.51 r_work: 0.3334 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11934 Z= 0.145 Angle : 0.535 6.262 16154 Z= 0.284 Chirality : 0.044 0.174 1710 Planarity : 0.004 0.047 2084 Dihedral : 4.999 23.461 1594 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 1.35 % Allowed : 14.09 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1432 helix: 0.43 (0.33), residues: 256 sheet: -0.63 (0.25), residues: 400 loop : -0.15 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 114 TYR 0.010 0.001 TYR A 580 PHE 0.017 0.001 PHE B 506 TRP 0.011 0.001 TRP B 55 HIS 0.003 0.001 HIS B 893 Details of bonding type rmsd covalent geometry : bond 0.00330 (11934) covalent geometry : angle 0.53503 (16154) hydrogen bonds : bond 0.03746 ( 430) hydrogen bonds : angle 4.52823 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.7294 (t0) cc_final: 0.6980 (m-40) REVERT: A 382 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 62 MET cc_start: 0.8485 (mtp) cc_final: 0.8231 (mtm) REVERT: B 105 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9165 (tm) outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 1.4747 time to fit residues: 181.3313 Evaluate side-chains 112 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS B 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080056 restraints weight = 83816.788| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.44 r_work: 0.3318 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11934 Z= 0.201 Angle : 0.558 5.959 16154 Z= 0.298 Chirality : 0.044 0.176 1710 Planarity : 0.004 0.051 2084 Dihedral : 5.107 23.330 1594 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.07 % Favored : 96.86 % Rotamer: Outliers : 1.19 % Allowed : 14.49 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.22), residues: 1432 helix: 0.26 (0.33), residues: 254 sheet: -0.64 (0.25), residues: 408 loop : -0.26 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 310 TYR 0.011 0.002 TYR A 483 PHE 0.023 0.002 PHE B 506 TRP 0.011 0.002 TRP B 55 HIS 0.003 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00452 (11934) covalent geometry : angle 0.55779 (16154) hydrogen bonds : bond 0.04028 ( 430) hydrogen bonds : angle 4.66639 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8427.33 seconds wall clock time: 143 minutes 12.64 seconds (8592.64 seconds total)