Starting phenix.real_space_refine on Thu Feb 5 16:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.map" model { file = "/net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mpo_48497/02_2026/9mpo_48497.cif" } resolution = 3.62 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= 0.017 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 Zn 12 6.06 5 S 172 5.16 5 C 11628 2.51 5 N 3254 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18326 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3412 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2255 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 167 SG CYS A 494 76.253 66.144 86.873 1.00300.00 S ATOM 187 SG CYS A 497 77.980 70.024 85.469 1.00300.00 S ATOM 309 SG CYS A 514 76.841 66.985 83.201 1.00300.00 S ATOM 332 SG CYS A 517 79.858 66.933 85.070 1.00300.00 S ATOM 500 SG CYS A 537 86.444 66.141 94.444 1.00300.00 S ATOM 521 SG CYS A 540 85.008 68.543 91.026 1.00300.00 S ATOM 658 SG CYS A 559 86.532 69.966 94.654 1.00300.00 S ATOM 680 SG CYS A 562 83.342 68.300 94.575 1.00300.00 S ATOM 584 SG CYS A 549 91.842 58.707 102.927 1.00300.00 S ATOM 618 SG CYS A 554 91.407 56.392 99.790 1.00300.00 S ATOM 831 SG CYS A 583 88.696 58.355 101.166 1.00300.00 S ATOM 857 SG CYS A 586 89.269 54.727 102.133 1.00300.00 S Restraints were copied for chains: D, E, F, C Time building chain proxies: 3.59, per 1000 atoms: 0.20 Number of scatterers: 18326 At special positions: 0 Unit cell: (169.74, 207.828, 136.62, 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) Zn 12 29.99 S 172 16.00 O 3260 8.00 N 3254 7.00 C 11628 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: 1.34 Conformation dependent library (CDL) restraints added in 728.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 494 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 497 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 517 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 514 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 559 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 537 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 540 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 562 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 549 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 586 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 583 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 494 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 497 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 517 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 514 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 537 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 559 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 540 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 562 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 549 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 554 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 586 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 583 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 494 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 497 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 517 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 514 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 559 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 537 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 540 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 562 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 549 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 554 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 586 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 583 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 494 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 497 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 517 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 514 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 537 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 559 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 540 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 562 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 549 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 554 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 586 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 583 " Number of angles added : 72 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 26 sheets defined 39.9% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.784A pdb=" N LEU A 565 " --> pdb=" O GLU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.881A pdb=" N LYS A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.977A pdb=" N PHE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.517A pdb=" N PHE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 860 through 869 Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 894 through 903 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 686 through 690 Processing helix chain 'B' and resid 691 through 698 Processing helix chain 'B' and resid 726 through 742 removed outlier: 3.518A pdb=" N PHE B 732 " --> pdb=" O GLY B 728 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 774 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 860 through 869 Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 894 through 903 Processing helix chain 'B' and resid 904 through 908 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 666 through 677 Processing helix chain 'C' and resid 686 through 690 Processing helix chain 'C' and resid 691 through 698 Processing helix chain 'C' and resid 726 through 742 removed outlier: 3.518A pdb=" N PHE C 732 " --> pdb=" O GLY C 728 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 733 " --> pdb=" O ARG C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 774 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 860 through 869 Processing helix chain 'C' and resid 881 through 891 Processing helix chain 'C' and resid 894 through 903 Processing helix chain 'C' and resid 904 through 908 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 514 through 525 Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.783A pdb=" N LEU D 565 " --> pdb=" O GLU D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 577 removed outlier: 3.881A pdb=" N LYS D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 removed outlier: 3.978A pdb=" N PHE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 610 " --> pdb=" O GLN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 631 Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 666 through 677 Processing helix chain 'D' and resid 686 through 690 Processing helix chain 'D' and resid 691 through 698 Processing helix chain 'D' and resid 726 through 742 removed outlier: 3.517A pdb=" N PHE D 732 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 733 " --> pdb=" O ARG D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 774 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 860 through 869 Processing helix chain 'D' and resid 881 through 891 Processing helix chain 'D' and resid 894 through 903 Processing helix chain 'D' and resid 904 through 908 Processing helix chain 'E' and resid 477 through 485 Processing helix chain 'E' and resid 489 through 493 Processing helix chain 'E' and resid 514 through 525 Processing helix chain 'E' and resid 560 through 567 removed outlier: 3.783A pdb=" N LEU E 565 " --> pdb=" O GLU E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.881A pdb=" N LYS E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 611 removed outlier: 3.977A pdb=" N PHE E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA E 610 " --> pdb=" O GLN E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 631 Processing helix chain 'E' and resid 644 through 653 Processing helix chain 'E' and resid 666 through 677 Processing helix chain 'E' and resid 686 through 690 Processing helix chain 'E' and resid 691 through 698 Processing helix chain 'E' and resid 726 through 742 removed outlier: 3.518A pdb=" N PHE E 732 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 733 " --> pdb=" O ARG E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 774 Processing helix chain 'E' and resid 783 through 785 No H-bonds generated for 'chain 'E' and resid 783 through 785' Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 860 through 869 Processing helix chain 'E' and resid 881 through 891 Processing helix chain 'E' and resid 894 through 903 Processing helix chain 'E' and resid 904 through 908 Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'F' and resid 489 through 493 Processing helix chain 'F' and resid 514 through 525 Processing helix chain 'F' and resid 560 through 567 removed outlier: 3.783A pdb=" N LEU F 565 " --> pdb=" O GLU F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.881A pdb=" N LYS F 577 " --> pdb=" O GLN F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 611 removed outlier: 3.977A pdb=" N PHE F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 610 " --> pdb=" O GLN F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 Processing helix chain 'F' and resid 644 through 653 Processing helix chain 'F' and resid 666 through 677 Processing helix chain 'F' and resid 686 through 690 Processing helix chain 'F' and resid 691 through 698 Processing helix chain 'F' and resid 726 through 742 removed outlier: 3.517A pdb=" N PHE F 732 " --> pdb=" O GLY F 728 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 774 Processing helix chain 'F' and resid 783 through 785 No H-bonds generated for 'chain 'F' and resid 783 through 785' Processing helix chain 'F' and resid 815 through 819 Processing helix chain 'F' and resid 860 through 869 Processing helix chain 'F' and resid 881 through 891 Processing helix chain 'F' and resid 894 through 903 Processing helix chain 'F' and resid 904 through 908 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA2, first strand: chain 'A' and resid 546 through 548 Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 684 removed outlier: 8.753A pdb=" N MET A 682 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR A 660 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 684 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 662 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE A 634 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 659 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 707 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 788 through 789 Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 852 Processing sheet with id=AA6, first strand: chain 'B' and resid 682 through 684 removed outlier: 8.753A pdb=" N MET B 682 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR B 660 " --> pdb=" O MET B 682 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL B 684 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 662 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE B 634 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 659 " --> pdb=" O ILE B 634 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 707 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 788 through 789 Processing sheet with id=AA8, first strand: chain 'B' and resid 850 through 852 Processing sheet with id=AA9, first strand: chain 'C' and resid 682 through 684 removed outlier: 8.752A pdb=" N MET C 682 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR C 660 " --> pdb=" O MET C 682 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 684 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 662 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE C 634 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 659 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY C 707 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 788 through 789 Processing sheet with id=AB2, first strand: chain 'C' and resid 850 through 852 Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 505 Processing sheet with id=AB4, first strand: chain 'D' and resid 546 through 548 Processing sheet with id=AB5, first strand: chain 'D' and resid 682 through 684 removed outlier: 8.753A pdb=" N MET D 682 " --> pdb=" O ASP D 658 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR D 660 " --> pdb=" O MET D 682 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL D 684 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA D 662 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE D 634 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG D 659 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 707 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 788 through 789 Processing sheet with id=AB7, first strand: chain 'D' and resid 850 through 852 Processing sheet with id=AB8, first strand: chain 'E' and resid 504 through 505 Processing sheet with id=AB9, first strand: chain 'E' and resid 546 through 548 Processing sheet with id=AC1, first strand: chain 'E' and resid 682 through 684 removed outlier: 8.752A pdb=" N MET E 682 " --> pdb=" O ASP E 658 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR E 660 " --> pdb=" O MET E 682 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL E 684 " --> pdb=" O TYR E 660 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA E 662 " --> pdb=" O VAL E 684 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE E 634 " --> pdb=" O VAL E 657 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG E 659 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY E 707 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 788 through 789 Processing sheet with id=AC3, first strand: chain 'E' and resid 850 through 852 Processing sheet with id=AC4, first strand: chain 'F' and resid 504 through 505 Processing sheet with id=AC5, first strand: chain 'F' and resid 546 through 548 Processing sheet with id=AC6, first strand: chain 'F' and resid 682 through 684 removed outlier: 8.753A pdb=" N MET F 682 " --> pdb=" O ASP F 658 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR F 660 " --> pdb=" O MET F 682 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL F 684 " --> pdb=" O TYR F 660 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA F 662 " --> pdb=" O VAL F 684 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE F 634 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG F 659 " --> pdb=" O ILE F 634 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY F 707 " --> pdb=" O LEU F 639 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 788 through 789 Processing sheet with id=AC8, first strand: chain 'F' and resid 850 through 852 665 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 1.81 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: 5940 1.34 - 1.47: 4442 1.47 - 1.59: 8148 1.59 - 1.71: 0 1.71 - 1.83: 242 Bond restraints: 18772 Sorted by residual: bond pdb=" C8 SAH F1004 " pdb=" N7 SAH F1004 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C8 SAH C1001 " pdb=" N7 SAH C1001 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.48e+00 bond pdb=" C8 SAH D1004 " pdb=" N7 SAH D1004 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C8 SAH A1004 " pdb=" N7 SAH A1004 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C8 SAH B1001 " pdb=" N7 SAH B1001 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 18767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 23395 2.07 - 4.15: 1631 4.15 - 6.22: 238 6.22 - 8.30: 92 8.30 - 10.37: 28 Bond angle restraints: 25384 Sorted by residual: angle pdb=" N VAL D 684 " pdb=" CA VAL D 684 " pdb=" CB VAL D 684 " ideal model delta sigma weight residual 112.07 107.41 4.66 1.14e+00 7.69e-01 1.67e+01 angle pdb=" N VAL B 684 " pdb=" CA VAL B 684 " pdb=" CB VAL B 684 " ideal model delta sigma weight residual 112.07 107.44 4.63 1.14e+00 7.69e-01 1.65e+01 angle pdb=" N VAL F 684 " pdb=" CA VAL F 684 " pdb=" CB VAL F 684 " ideal model delta sigma weight residual 112.07 107.44 4.63 1.14e+00 7.69e-01 1.65e+01 angle pdb=" CA ARG E 790 " pdb=" CB ARG E 790 " pdb=" CG ARG E 790 " ideal model delta sigma weight residual 114.10 122.21 -8.11 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CA ARG A 790 " pdb=" CB ARG A 790 " pdb=" CG ARG A 790 " ideal model delta sigma weight residual 114.10 122.21 -8.11 2.00e+00 2.50e-01 1.64e+01 ... (remaining 25379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.14: 9811 9.14 - 18.27: 1096 18.27 - 27.41: 165 27.41 - 36.55: 82 36.55 - 45.68: 24 Dihedral angle restraints: 11178 sinusoidal: 4652 harmonic: 6526 Sorted by residual: dihedral pdb=" CA HIS E 677 " pdb=" C HIS E 677 " pdb=" N GLN E 678 " pdb=" CA GLN E 678 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA HIS D 677 " pdb=" C HIS D 677 " pdb=" N GLN D 678 " pdb=" CA GLN D 678 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA HIS A 677 " pdb=" C HIS A 677 " pdb=" N GLN A 678 " pdb=" CA GLN A 678 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 11175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1792 0.050 - 0.100: 666 0.100 - 0.150: 183 0.150 - 0.200: 28 0.200 - 0.250: 15 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA ILE F 858 " pdb=" N ILE F 858 " pdb=" C ILE F 858 " pdb=" CB ILE F 858 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE E 858 " pdb=" N ILE E 858 " pdb=" C ILE E 858 " pdb=" CB ILE E 858 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 858 " pdb=" N ILE A 858 " pdb=" C ILE A 858 " pdb=" CB ILE A 858 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2681 not shown) Planarity restraints: 3300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 735 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C TYR A 735 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR A 735 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 736 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 735 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR D 735 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR D 735 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG D 736 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 735 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR E 735 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR E 735 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG E 736 " -0.021 2.00e-02 2.50e+03 ... (remaining 3297 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5724 2.85 - 3.36: 16993 3.36 - 3.87: 30237 3.87 - 4.39: 35393 4.39 - 4.90: 59084 Nonbonded interactions: 147431 Sorted by model distance: nonbonded pdb=" OG SER B 663 " pdb=" O GLY B 685 " model vdw 2.335 3.040 nonbonded pdb=" OG SER D 663 " pdb=" O GLY D 685 " model vdw 2.335 3.040 nonbonded pdb=" OG SER F 663 " pdb=" O GLY F 685 " model vdw 2.336 3.040 nonbonded pdb=" OG SER C 663 " pdb=" O GLY C 685 " model vdw 2.336 3.040 nonbonded pdb=" OG SER E 663 " pdb=" O GLY E 685 " model vdw 2.336 3.040 ... (remaining 147426 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.71 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: 5.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.010 0.170 18820 Z= 0.407 Angle : 1.515 45.989 25456 Z= 0.707 Chirality : 0.058 0.250 2684 Planarity : 0.008 0.047 3300 Dihedral : 8.275 45.684 6974 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.30 % Allowed : 0.20 % Favored : 99.50 % 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: -1.32 (0.16), residues: 2234 helix: -1.26 (0.17), residues: 734 sheet: -0.83 (0.35), residues: 204 loop : -0.55 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG F 659 TYR 0.026 0.003 TYR A 683 PHE 0.042 0.005 PHE F 755 TRP 0.018 0.003 TRP D 860 HIS 0.018 0.004 HIS E 789 Details of bonding type rmsd covalent geometry : bond 0.00709 (18772) covalent geometry : angle 1.23626 (25384) hydrogen bonds : bond 0.16379 ( 665) hydrogen bonds : angle 7.00636 ( 1743) metal coordination : bond 0.12595 ( 48) metal coordination : angle 16.51813 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 519 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.6569 (ttt) cc_final: 0.6317 (ttt) REVERT: A 732 PHE cc_start: 0.9092 (m-80) cc_final: 0.8863 (m-80) REVERT: A 758 VAL cc_start: 0.6967 (m) cc_final: 0.6480 (t) REVERT: A 759 VAL cc_start: 0.7452 (t) cc_final: 0.7212 (m) REVERT: A 794 PHE cc_start: 0.7629 (m-80) cc_final: 0.7323 (m-80) REVERT: A 812 LYS cc_start: 0.7673 (mttp) cc_final: 0.7446 (mmmm) REVERT: A 829 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7940 (mmmt) REVERT: A 885 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7999 (ttt-90) REVERT: A 898 ILE cc_start: 0.8989 (mm) cc_final: 0.8680 (tp) REVERT: B 641 ASP cc_start: 0.3192 (t0) cc_final: 0.2863 (t0) REVERT: B 647 LEU cc_start: 0.8452 (tp) cc_final: 0.8210 (tp) REVERT: B 694 HIS cc_start: 0.7996 (m170) cc_final: 0.7191 (m-70) REVERT: B 696 GLN cc_start: 0.8710 (mt0) cc_final: 0.8480 (pt0) REVERT: B 753 TRP cc_start: 0.7326 (p-90) cc_final: 0.6249 (p-90) REVERT: B 780 ILE cc_start: 0.8729 (mt) cc_final: 0.8499 (tp) REVERT: B 781 ASP cc_start: 0.8358 (t0) cc_final: 0.6746 (t0) REVERT: C 647 LEU cc_start: 0.8739 (tp) cc_final: 0.8527 (tp) REVERT: C 753 TRP cc_start: 0.7360 (p-90) cc_final: 0.6200 (p-90) REVERT: C 780 ILE cc_start: 0.8716 (mt) cc_final: 0.8367 (tp) REVERT: C 781 ASP cc_start: 0.8494 (t0) cc_final: 0.7153 (t0) REVERT: C 860 TRP cc_start: 0.4866 (m-10) cc_final: 0.4386 (m-10) REVERT: D 513 MET cc_start: 0.7394 (ttt) cc_final: 0.7154 (ttt) REVERT: D 616 GLU cc_start: 0.8521 (tt0) cc_final: 0.8149 (tm-30) REVERT: D 643 ILE cc_start: 0.6356 (pt) cc_final: 0.6125 (pt) REVERT: D 674 MET cc_start: 0.8188 (mtp) cc_final: 0.7818 (mmm) REVERT: D 678 GLN cc_start: 0.8821 (mp10) cc_final: 0.8319 (pp30) REVERT: D 765 ASP cc_start: 0.8320 (t0) cc_final: 0.8011 (t0) REVERT: D 774 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8242 (tm-30) REVERT: D 868 PHE cc_start: 0.8089 (m-10) cc_final: 0.7859 (m-10) REVERT: D 870 PHE cc_start: 0.8698 (m-80) cc_final: 0.8296 (m-80) REVERT: D 878 SER cc_start: 0.7707 (p) cc_final: 0.7451 (p) REVERT: E 481 TYR cc_start: 0.8513 (t80) cc_final: 0.8290 (t80) REVERT: E 513 MET cc_start: 0.8535 (ttt) cc_final: 0.7670 (ppp) REVERT: E 548 MET cc_start: 0.3757 (mtm) cc_final: 0.3505 (mtm) REVERT: E 607 MET cc_start: 0.5131 (mtp) cc_final: 0.4492 (mtp) REVERT: E 621 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8719 (tptp) REVERT: E 623 TYR cc_start: 0.8733 (m-80) cc_final: 0.8462 (m-80) REVERT: E 638 SER cc_start: 0.8773 (t) cc_final: 0.8342 (p) REVERT: E 666 CYS cc_start: 0.7555 (t) cc_final: 0.7159 (t) REVERT: E 733 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 736 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8584 (tmm-80) REVERT: E 737 LEU cc_start: 0.8981 (mt) cc_final: 0.8754 (mt) REVERT: E 784 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8445 (tt0) REVERT: E 792 ARG cc_start: 0.7233 (mmt-90) cc_final: 0.7025 (mmt-90) REVERT: E 802 ASN cc_start: 0.8325 (t0) cc_final: 0.7960 (p0) REVERT: E 812 LYS cc_start: 0.8172 (mttp) cc_final: 0.7971 (mtpp) REVERT: E 823 ARG cc_start: 0.6805 (mtp180) cc_final: 0.6307 (mtt180) REVERT: E 852 MET cc_start: 0.8873 (ttt) cc_final: 0.8268 (ttt) REVERT: E 853 ASN cc_start: 0.8432 (m-40) cc_final: 0.7727 (p0) REVERT: E 865 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7446 (pt0) REVERT: E 899 ARG cc_start: 0.8446 (ttt90) cc_final: 0.8220 (ttp-110) REVERT: E 906 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8340 (mtpp) REVERT: F 481 TYR cc_start: 0.8815 (t80) cc_final: 0.8610 (t80) REVERT: F 515 GLN cc_start: 0.9175 (mt0) cc_final: 0.8929 (mp10) REVERT: F 548 MET cc_start: 0.3559 (mtm) cc_final: 0.3175 (mtm) REVERT: F 607 MET cc_start: 0.5708 (mtp) cc_final: 0.5032 (mtp) REVERT: F 617 PHE cc_start: 0.8663 (m-80) cc_final: 0.8427 (m-10) REVERT: F 621 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8604 (ttmt) REVERT: F 623 TYR cc_start: 0.8815 (m-80) cc_final: 0.8504 (m-80) REVERT: F 638 SER cc_start: 0.8522 (t) cc_final: 0.8061 (p) REVERT: F 658 ASP cc_start: 0.8516 (t0) cc_final: 0.8210 (t0) REVERT: F 659 ARG cc_start: 0.8921 (ptp90) cc_final: 0.8711 (ttp-110) REVERT: F 729 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7500 (mmt180) REVERT: F 735 TYR cc_start: 0.8164 (t80) cc_final: 0.7769 (t80) REVERT: F 736 ARG cc_start: 0.8998 (ttp-170) cc_final: 0.8554 (ttp80) REVERT: F 737 LEU cc_start: 0.8919 (mt) cc_final: 0.8617 (mt) REVERT: F 784 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8518 (tt0) REVERT: F 812 LYS cc_start: 0.8403 (mttp) cc_final: 0.8022 (mtpp) REVERT: F 817 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8574 (mt-10) REVERT: F 853 ASN cc_start: 0.8749 (m-40) cc_final: 0.8314 (p0) REVERT: F 855 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8503 (ttmm) REVERT: F 863 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7407 (tt0) REVERT: F 872 VAL cc_start: 0.8324 (t) cc_final: 0.8035 (m) REVERT: F 899 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8208 (ttp-110) outliers start: 6 outliers final: 0 residues processed: 521 average time/residue: 0.1641 time to fit residues: 121.8689 Evaluate side-chains 453 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 40.0000 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.0980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 873 HIS B 853 ASN B 873 HIS B 900 HIS C 873 HIS C 900 HIS D 516 ASN ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 810 ASN ** E 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.247191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.196684 restraints weight = 32143.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.206979 restraints weight = 17594.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.208447 restraints weight = 10338.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.210178 restraints weight = 8458.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.210599 restraints weight = 7942.120| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4578 r_free = 0.4578 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4577 r_free = 0.4577 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18820 Z= 0.176 Angle : 0.699 9.311 25456 Z= 0.347 Chirality : 0.043 0.200 2684 Planarity : 0.005 0.087 3300 Dihedral : 5.458 57.985 2512 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.21 % Allowed : 6.71 % Favored : 92.08 % 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: 0.13 (0.17), residues: 2234 helix: 0.34 (0.19), residues: 738 sheet: -0.17 (0.36), residues: 206 loop : 0.11 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 891 TYR 0.023 0.002 TYR B 683 PHE 0.019 0.002 PHE D 909 TRP 0.026 0.002 TRP B 698 HIS 0.007 0.001 HIS E 677 Details of bonding type rmsd covalent geometry : bond 0.00368 (18772) covalent geometry : angle 0.66104 (25384) hydrogen bonds : bond 0.04524 ( 665) hydrogen bonds : angle 5.59987 ( 1743) metal coordination : bond 0.00904 ( 48) metal coordination : angle 4.34364 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 460 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ILE cc_start: 0.7369 (mt) cc_final: 0.7135 (mt) REVERT: A 705 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8147 (pt) REVERT: A 732 PHE cc_start: 0.7683 (m-80) cc_final: 0.7382 (m-80) REVERT: A 758 VAL cc_start: 0.6385 (m) cc_final: 0.5956 (t) REVERT: A 771 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7313 (mtm-85) REVERT: A 801 MET cc_start: 0.6279 (mtp) cc_final: 0.5955 (mtp) REVERT: A 812 LYS cc_start: 0.7802 (mttp) cc_final: 0.7546 (mmmm) REVERT: A 885 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7872 (ttt-90) REVERT: A 887 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: A 898 ILE cc_start: 0.8008 (mm) cc_final: 0.7772 (mm) REVERT: A 899 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6716 (mtt180) REVERT: B 647 LEU cc_start: 0.8325 (tp) cc_final: 0.7979 (tp) REVERT: B 694 HIS cc_start: 0.7094 (m170) cc_final: 0.5927 (m-70) REVERT: B 736 ARG cc_start: 0.4033 (OUTLIER) cc_final: 0.3730 (ptp-170) REVERT: B 753 TRP cc_start: 0.6202 (p-90) cc_final: 0.5726 (p-90) REVERT: B 781 ASP cc_start: 0.8042 (t0) cc_final: 0.7629 (t0) REVERT: B 831 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8207 (ttp80) REVERT: B 848 PHE cc_start: 0.7221 (m-10) cc_final: 0.6648 (m-10) REVERT: C 647 LEU cc_start: 0.8499 (tp) cc_final: 0.8226 (tp) REVERT: C 652 ASP cc_start: 0.7527 (t0) cc_final: 0.7303 (t0) REVERT: C 674 MET cc_start: 0.7255 (mtt) cc_final: 0.7046 (mtm) REVERT: C 753 TRP cc_start: 0.6143 (p-90) cc_final: 0.5750 (p-90) REVERT: C 781 ASP cc_start: 0.8035 (t0) cc_final: 0.7536 (t0) REVERT: C 798 LEU cc_start: 0.7330 (mp) cc_final: 0.7101 (mp) REVERT: D 513 MET cc_start: 0.7354 (ttt) cc_final: 0.7139 (ttt) REVERT: D 732 PHE cc_start: 0.7814 (m-80) cc_final: 0.7356 (m-80) REVERT: D 765 ASP cc_start: 0.7680 (t0) cc_final: 0.7139 (t0) REVERT: D 769 ILE cc_start: 0.8670 (mt) cc_final: 0.8431 (mt) REVERT: D 812 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8496 (mmmm) REVERT: D 864 MET cc_start: 0.8835 (mmt) cc_final: 0.8571 (mmm) REVERT: E 481 TYR cc_start: 0.8077 (t80) cc_final: 0.7823 (t80) REVERT: E 521 PHE cc_start: 0.8184 (t80) cc_final: 0.7884 (t80) REVERT: E 607 MET cc_start: 0.5228 (mtp) cc_final: 0.4680 (mtp) REVERT: E 621 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8529 (ptmm) REVERT: E 623 TYR cc_start: 0.7256 (m-80) cc_final: 0.6115 (m-80) REVERT: E 638 SER cc_start: 0.8644 (t) cc_final: 0.7866 (p) REVERT: E 666 CYS cc_start: 0.6809 (t) cc_final: 0.6418 (t) REVERT: E 686 ASP cc_start: 0.7343 (t0) cc_final: 0.7117 (t70) REVERT: E 693 LYS cc_start: 0.8662 (tttt) cc_final: 0.8303 (mttt) REVERT: E 733 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7376 (mm-30) REVERT: E 735 TYR cc_start: 0.7698 (t80) cc_final: 0.7253 (t80) REVERT: E 737 LEU cc_start: 0.8449 (mt) cc_final: 0.7973 (mt) REVERT: E 740 ASP cc_start: 0.7293 (m-30) cc_final: 0.7073 (m-30) REVERT: E 765 ASP cc_start: 0.7698 (t0) cc_final: 0.7474 (t0) REVERT: E 768 ASP cc_start: 0.6947 (m-30) cc_final: 0.6496 (m-30) REVERT: E 772 PHE cc_start: 0.7590 (m-80) cc_final: 0.7371 (m-80) REVERT: E 774 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7111 (mt-10) REVERT: E 812 LYS cc_start: 0.7958 (mttp) cc_final: 0.7666 (mtpp) REVERT: E 818 CYS cc_start: 0.8514 (m) cc_final: 0.8168 (m) REVERT: E 820 GLU cc_start: 0.7775 (tp30) cc_final: 0.7557 (tp30) REVERT: E 853 ASN cc_start: 0.7917 (m-40) cc_final: 0.7412 (p0) REVERT: E 865 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7078 (pt0) REVERT: F 481 TYR cc_start: 0.8322 (t80) cc_final: 0.8061 (t80) REVERT: F 515 GLN cc_start: 0.8759 (mt0) cc_final: 0.8432 (mm-40) REVERT: F 521 PHE cc_start: 0.8317 (t80) cc_final: 0.8045 (t80) REVERT: F 548 MET cc_start: 0.3459 (mtm) cc_final: 0.3238 (mtm) REVERT: F 607 MET cc_start: 0.5564 (mtp) cc_final: 0.5045 (mtp) REVERT: F 617 PHE cc_start: 0.8050 (m-80) cc_final: 0.7690 (m-10) REVERT: F 621 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8399 (ttmt) REVERT: F 623 TYR cc_start: 0.7348 (m-80) cc_final: 0.6577 (m-80) REVERT: F 643 ILE cc_start: 0.7422 (pt) cc_final: 0.7009 (tt) REVERT: F 729 ARG cc_start: 0.7543 (mmt180) cc_final: 0.6751 (mmt180) REVERT: F 733 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7396 (mm-30) REVERT: F 736 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8179 (ttp80) REVERT: F 737 LEU cc_start: 0.8534 (mt) cc_final: 0.8220 (mt) REVERT: F 742 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7416 (mmm-85) REVERT: F 765 ASP cc_start: 0.7920 (t0) cc_final: 0.7679 (t0) REVERT: F 812 LYS cc_start: 0.7952 (mttp) cc_final: 0.7282 (mtpp) REVERT: F 817 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7556 (mt-10) REVERT: F 853 ASN cc_start: 0.8542 (m-40) cc_final: 0.8098 (p0) REVERT: F 855 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8283 (ttmm) REVERT: F 865 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7081 (pt0) REVERT: F 887 ARG cc_start: 0.7688 (tmm-80) cc_final: 0.7336 (tmm-80) outliers start: 24 outliers final: 13 residues processed: 466 average time/residue: 0.1745 time to fit residues: 115.4520 Evaluate side-chains 454 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 439 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 736 ARG Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 779 MET Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 814 GLU Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 878 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 174 optimal weight: 0.6980 chunk 220 optimal weight: 0.3980 chunk 206 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 218 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 28 optimal weight: 0.0970 chunk 202 optimal weight: 0.1980 chunk 196 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 677 HIS ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 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 = 0.5065 r_free = 0.5065 target = 0.248138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.198224 restraints weight = 32649.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.205196 restraints weight = 15551.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.210323 restraints weight = 9710.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.211269 restraints weight = 7186.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.212077 restraints weight = 6642.374| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18820 Z= 0.111 Angle : 0.633 12.735 25456 Z= 0.305 Chirality : 0.041 0.154 2684 Planarity : 0.005 0.081 3300 Dihedral : 5.094 59.078 2512 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.66 % Allowed : 8.83 % Favored : 89.51 % 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: 0.58 (0.18), residues: 2234 helix: 0.86 (0.19), residues: 738 sheet: 0.01 (0.35), residues: 206 loop : 0.29 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 891 TYR 0.015 0.001 TYR B 683 PHE 0.034 0.002 PHE E 731 TRP 0.042 0.002 TRP B 698 HIS 0.011 0.001 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00240 (18772) covalent geometry : angle 0.58257 (25384) hydrogen bonds : bond 0.03718 ( 665) hydrogen bonds : angle 5.17007 ( 1743) metal coordination : bond 0.00578 ( 48) metal coordination : angle 4.67724 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 447 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ILE cc_start: 0.7260 (mt) cc_final: 0.7038 (mt) REVERT: A 678 GLN cc_start: 0.7791 (mp-120) cc_final: 0.7056 (pp30) REVERT: A 732 PHE cc_start: 0.7607 (m-80) cc_final: 0.7272 (m-80) REVERT: A 758 VAL cc_start: 0.6419 (m) cc_final: 0.6057 (t) REVERT: A 812 LYS cc_start: 0.7809 (mttp) cc_final: 0.7568 (mmmm) REVERT: A 875 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7156 (m) REVERT: A 885 ARG cc_start: 0.8419 (ttt180) cc_final: 0.7814 (ttt-90) REVERT: A 887 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: A 898 ILE cc_start: 0.7947 (mm) cc_final: 0.7727 (mm) REVERT: B 647 LEU cc_start: 0.8234 (tp) cc_final: 0.7894 (tp) REVERT: B 753 TRP cc_start: 0.5904 (p-90) cc_final: 0.5572 (p-90) REVERT: B 780 ILE cc_start: 0.8146 (mt) cc_final: 0.7933 (tp) REVERT: B 781 ASP cc_start: 0.7891 (t0) cc_final: 0.7410 (t0) REVERT: B 860 TRP cc_start: 0.3714 (m-10) cc_final: 0.3273 (m-10) REVERT: C 652 ASP cc_start: 0.7352 (t0) cc_final: 0.7131 (t0) REVERT: C 781 ASP cc_start: 0.7828 (t0) cc_final: 0.7527 (t0) REVERT: D 617 PHE cc_start: 0.6915 (m-80) cc_final: 0.6652 (m-80) REVERT: D 639 LEU cc_start: 0.7968 (mp) cc_final: 0.7267 (mp) REVERT: D 732 PHE cc_start: 0.7804 (m-80) cc_final: 0.7284 (m-80) REVERT: D 742 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6882 (ttm110) REVERT: D 812 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8402 (mmmm) REVERT: D 864 MET cc_start: 0.8755 (mmt) cc_final: 0.8510 (mmm) REVERT: D 870 PHE cc_start: 0.7235 (m-80) cc_final: 0.6889 (m-80) REVERT: E 521 PHE cc_start: 0.8153 (t80) cc_final: 0.7791 (t80) REVERT: E 607 MET cc_start: 0.5253 (mtp) cc_final: 0.4710 (mtp) REVERT: E 623 TYR cc_start: 0.7320 (m-80) cc_final: 0.7118 (m-80) REVERT: E 638 SER cc_start: 0.8566 (t) cc_final: 0.7798 (p) REVERT: E 693 LYS cc_start: 0.8651 (tttt) cc_final: 0.8266 (mttt) REVERT: E 733 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7224 (mm-30) REVERT: E 735 TYR cc_start: 0.7642 (t80) cc_final: 0.7044 (t80) REVERT: E 737 LEU cc_start: 0.8284 (mt) cc_final: 0.7867 (mt) REVERT: E 765 ASP cc_start: 0.7624 (t0) cc_final: 0.7154 (t0) REVERT: E 768 ASP cc_start: 0.6989 (m-30) cc_final: 0.6519 (m-30) REVERT: E 769 ILE cc_start: 0.8748 (mt) cc_final: 0.8526 (mt) REVERT: E 772 PHE cc_start: 0.7559 (m-80) cc_final: 0.7359 (m-80) REVERT: E 784 GLU cc_start: 0.7770 (tt0) cc_final: 0.7570 (tt0) REVERT: E 812 LYS cc_start: 0.8032 (mttp) cc_final: 0.7676 (mtpp) REVERT: E 818 CYS cc_start: 0.8494 (m) cc_final: 0.8186 (m) REVERT: E 819 LEU cc_start: 0.8006 (mm) cc_final: 0.7700 (mt) REVERT: E 824 ILE cc_start: 0.8691 (tt) cc_final: 0.8452 (tt) REVERT: E 853 ASN cc_start: 0.7644 (m-40) cc_final: 0.7344 (p0) REVERT: E 865 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7224 (pt0) REVERT: F 481 TYR cc_start: 0.8254 (t80) cc_final: 0.8035 (t80) REVERT: F 515 GLN cc_start: 0.8721 (mt0) cc_final: 0.8470 (mm-40) REVERT: F 521 PHE cc_start: 0.8251 (t80) cc_final: 0.7965 (t80) REVERT: F 607 MET cc_start: 0.5532 (mtp) cc_final: 0.4983 (mtp) REVERT: F 617 PHE cc_start: 0.7995 (m-80) cc_final: 0.7679 (m-10) REVERT: F 621 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8446 (ttmt) REVERT: F 623 TYR cc_start: 0.7360 (m-80) cc_final: 0.6588 (m-80) REVERT: F 669 SER cc_start: 0.8535 (m) cc_final: 0.8001 (p) REVERT: F 729 ARG cc_start: 0.7375 (mmt180) cc_final: 0.6485 (mmt180) REVERT: F 733 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7239 (mm-30) REVERT: F 737 LEU cc_start: 0.8443 (mt) cc_final: 0.8144 (mp) REVERT: F 742 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7334 (mmm-85) REVERT: F 765 ASP cc_start: 0.7780 (t0) cc_final: 0.7436 (t0) REVERT: F 768 ASP cc_start: 0.7203 (m-30) cc_final: 0.6790 (m-30) REVERT: F 812 LYS cc_start: 0.7990 (mttp) cc_final: 0.7277 (mtpp) REVERT: F 817 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 826 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7698 (ptpp) REVERT: F 851 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: F 853 ASN cc_start: 0.8355 (m-40) cc_final: 0.8047 (p0) REVERT: F 855 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8126 (ttmm) REVERT: F 866 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8013 (ttm110) REVERT: F 885 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7368 (ttt180) outliers start: 33 outliers final: 19 residues processed: 463 average time/residue: 0.1723 time to fit residues: 113.5731 Evaluate side-chains 449 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 428 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 693 LYS Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 814 GLU Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 851 PHE Chi-restraints excluded: chain F residue 878 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 14 optimal weight: 40.0000 chunk 178 optimal weight: 0.6980 chunk 109 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 chunk 117 optimal weight: 0.0040 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 678 GLN ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.248804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.196654 restraints weight = 32453.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.203556 restraints weight = 15831.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.208748 restraints weight = 10141.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.210532 restraints weight = 7651.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.212266 restraints weight = 6626.882| |-----------------------------------------------------------------------------| r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18820 Z= 0.132 Angle : 0.622 10.938 25456 Z= 0.304 Chirality : 0.041 0.163 2684 Planarity : 0.005 0.073 3300 Dihedral : 4.989 57.694 2512 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 9.84 % Favored : 88.14 % 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: 0.69 (0.18), residues: 2234 helix: 1.05 (0.19), residues: 738 sheet: -0.03 (0.35), residues: 208 loop : 0.32 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 891 TYR 0.015 0.001 TYR C 683 PHE 0.039 0.002 PHE E 731 TRP 0.053 0.002 TRP B 698 HIS 0.016 0.001 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00282 (18772) covalent geometry : angle 0.58314 (25384) hydrogen bonds : bond 0.03467 ( 665) hydrogen bonds : angle 5.07396 ( 1743) metal coordination : bond 0.00534 ( 48) metal coordination : angle 4.12791 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 438 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: -0.2591 (mmm) cc_final: -0.3668 (mmm) REVERT: A 661 ILE cc_start: 0.7339 (mt) cc_final: 0.7133 (mt) REVERT: A 687 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 705 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7952 (pt) REVERT: A 732 PHE cc_start: 0.7670 (m-80) cc_final: 0.7315 (m-80) REVERT: A 765 ASP cc_start: 0.6876 (t0) cc_final: 0.6610 (t0) REVERT: A 771 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7654 (mtm110) REVERT: A 885 ARG cc_start: 0.8478 (ttt180) cc_final: 0.7818 (ttt-90) REVERT: A 887 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7989 (mtm-85) REVERT: B 647 LEU cc_start: 0.8232 (tp) cc_final: 0.7876 (tp) REVERT: B 753 TRP cc_start: 0.5914 (p-90) cc_final: 0.5663 (p-90) REVERT: B 781 ASP cc_start: 0.7982 (t0) cc_final: 0.7511 (t0) REVERT: B 848 PHE cc_start: 0.7065 (m-10) cc_final: 0.6784 (m-10) REVERT: B 860 TRP cc_start: 0.3898 (m-10) cc_final: 0.3692 (m-90) REVERT: C 652 ASP cc_start: 0.7393 (t0) cc_final: 0.7169 (t0) REVERT: C 753 TRP cc_start: 0.5930 (p-90) cc_final: 0.5493 (p-90) REVERT: C 829 LYS cc_start: 0.5466 (tppt) cc_final: 0.4778 (tppt) REVERT: D 639 LEU cc_start: 0.7970 (mp) cc_final: 0.7442 (mp) REVERT: D 678 GLN cc_start: 0.7983 (mp10) cc_final: 0.7615 (pp30) REVERT: D 731 PHE cc_start: 0.8682 (t80) cc_final: 0.8411 (t80) REVERT: D 732 PHE cc_start: 0.7846 (m-80) cc_final: 0.7305 (m-80) REVERT: D 742 ARG cc_start: 0.7252 (ttm110) cc_final: 0.7024 (ttm110) REVERT: D 758 VAL cc_start: 0.6068 (m) cc_final: 0.5489 (t) REVERT: D 765 ASP cc_start: 0.7609 (t0) cc_final: 0.7197 (t0) REVERT: D 812 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8373 (mmmm) REVERT: D 864 MET cc_start: 0.8861 (mmt) cc_final: 0.8592 (mmm) REVERT: D 870 PHE cc_start: 0.7311 (m-80) cc_final: 0.6962 (m-80) REVERT: E 521 PHE cc_start: 0.8170 (t80) cc_final: 0.7763 (t80) REVERT: E 607 MET cc_start: 0.5289 (mtp) cc_final: 0.4746 (mtp) REVERT: E 638 SER cc_start: 0.8585 (t) cc_final: 0.7770 (p) REVERT: E 693 LYS cc_start: 0.8576 (tttt) cc_final: 0.8274 (mttt) REVERT: E 705 ILE cc_start: 0.8350 (pt) cc_final: 0.8035 (mm) REVERT: E 733 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7178 (mm-30) REVERT: E 735 TYR cc_start: 0.7656 (t80) cc_final: 0.7179 (t80) REVERT: E 737 LEU cc_start: 0.8307 (mt) cc_final: 0.7925 (mt) REVERT: E 765 ASP cc_start: 0.7687 (t0) cc_final: 0.7332 (t0) REVERT: E 768 ASP cc_start: 0.7046 (m-30) cc_final: 0.6580 (m-30) REVERT: E 812 LYS cc_start: 0.8086 (mttp) cc_final: 0.7672 (mtpp) REVERT: E 818 CYS cc_start: 0.8420 (m) cc_final: 0.8137 (m) REVERT: E 823 ARG cc_start: 0.6540 (ttm110) cc_final: 0.6228 (ttm-80) REVERT: E 853 ASN cc_start: 0.7608 (m-40) cc_final: 0.7353 (p0) REVERT: E 863 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7725 (mt-10) REVERT: E 865 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7220 (pt0) REVERT: E 885 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7709 (mmm-85) REVERT: F 481 TYR cc_start: 0.8305 (t80) cc_final: 0.8077 (t80) REVERT: F 515 GLN cc_start: 0.8752 (mt0) cc_final: 0.8487 (mm-40) REVERT: F 521 PHE cc_start: 0.8304 (t80) cc_final: 0.7976 (t80) REVERT: F 607 MET cc_start: 0.5562 (mtp) cc_final: 0.5013 (mtp) REVERT: F 617 PHE cc_start: 0.7986 (m-80) cc_final: 0.7678 (m-10) REVERT: F 621 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8503 (ttmt) REVERT: F 623 TYR cc_start: 0.7342 (m-80) cc_final: 0.6565 (m-80) REVERT: F 669 SER cc_start: 0.8591 (m) cc_final: 0.8021 (p) REVERT: F 729 ARG cc_start: 0.7376 (mmt180) cc_final: 0.6507 (mmt180) REVERT: F 733 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7464 (mm-30) REVERT: F 737 LEU cc_start: 0.8467 (mt) cc_final: 0.8132 (mt) REVERT: F 742 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7359 (mmm-85) REVERT: F 765 ASP cc_start: 0.7806 (t0) cc_final: 0.7548 (t0) REVERT: F 784 GLU cc_start: 0.7638 (tt0) cc_final: 0.6988 (tm-30) REVERT: F 812 LYS cc_start: 0.8098 (mttp) cc_final: 0.7768 (mtpp) REVERT: F 826 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7841 (ptpp) REVERT: F 853 ASN cc_start: 0.8346 (m-40) cc_final: 0.8031 (p0) REVERT: F 855 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8119 (ttmm) REVERT: F 866 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7898 (ttm110) REVERT: F 885 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7786 (mtp180) REVERT: F 900 HIS cc_start: 0.7480 (t70) cc_final: 0.6846 (t-170) outliers start: 40 outliers final: 27 residues processed: 458 average time/residue: 0.1813 time to fit residues: 118.1461 Evaluate side-chains 453 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 424 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 771 ARG Chi-restraints excluded: chain D residue 878 SER Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain D residue 880 MET Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 814 GLU Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 905 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 55 optimal weight: 8.9990 chunk 191 optimal weight: 0.0670 chunk 164 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 ASN ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 739 HIS ** F 789 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 = 0.5033 r_free = 0.5033 target = 0.246942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.193678 restraints weight = 32476.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.200937 restraints weight = 15550.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.205645 restraints weight = 9850.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.207621 restraints weight = 7352.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.210209 restraints weight = 6338.516| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18820 Z= 0.184 Angle : 0.638 10.586 25456 Z= 0.318 Chirality : 0.042 0.177 2684 Planarity : 0.005 0.074 3300 Dihedral : 4.960 56.716 2512 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.12 % Allowed : 11.40 % Favored : 86.48 % 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: 0.61 (0.18), residues: 2234 helix: 0.97 (0.20), residues: 740 sheet: -0.01 (0.35), residues: 208 loop : 0.26 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 771 TYR 0.012 0.001 TYR C 683 PHE 0.048 0.002 PHE E 731 TRP 0.050 0.002 TRP B 698 HIS 0.017 0.001 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00378 (18772) covalent geometry : angle 0.60687 (25384) hydrogen bonds : bond 0.03585 ( 665) hydrogen bonds : angle 5.20999 ( 1743) metal coordination : bond 0.00584 ( 48) metal coordination : angle 3.74610 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ILE cc_start: 0.7315 (mt) cc_final: 0.7098 (mt) REVERT: A 705 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 732 PHE cc_start: 0.7708 (m-80) cc_final: 0.7323 (m-80) REVERT: A 864 MET cc_start: 0.8350 (mmm) cc_final: 0.7838 (mmm) REVERT: A 875 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7383 (m) REVERT: A 885 ARG cc_start: 0.8517 (ttt180) cc_final: 0.7821 (ttt-90) REVERT: A 887 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: B 753 TRP cc_start: 0.6035 (p-90) cc_final: 0.5764 (p-90) REVERT: B 781 ASP cc_start: 0.8085 (t0) cc_final: 0.7627 (t0) REVERT: B 860 TRP cc_start: 0.4329 (m-10) cc_final: 0.4122 (m-90) REVERT: C 652 ASP cc_start: 0.7459 (t0) cc_final: 0.7240 (t0) REVERT: C 753 TRP cc_start: 0.6068 (p-90) cc_final: 0.5567 (p-90) REVERT: D 678 GLN cc_start: 0.8026 (mp10) cc_final: 0.7618 (pp30) REVERT: D 732 PHE cc_start: 0.7932 (m-80) cc_final: 0.7458 (m-80) REVERT: D 742 ARG cc_start: 0.7453 (ttm110) cc_final: 0.7133 (ttm110) REVERT: D 756 GLU cc_start: 0.6694 (tm-30) cc_final: 0.6095 (tm-30) REVERT: D 758 VAL cc_start: 0.6197 (m) cc_final: 0.5880 (t) REVERT: D 759 VAL cc_start: 0.6758 (t) cc_final: 0.6357 (m) REVERT: D 812 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8434 (mmmm) REVERT: D 852 MET cc_start: 0.5680 (mmm) cc_final: 0.5420 (mmm) REVERT: E 607 MET cc_start: 0.5323 (mtp) cc_final: 0.4772 (mtp) REVERT: E 621 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8582 (tmtt) REVERT: E 638 SER cc_start: 0.8549 (t) cc_final: 0.7774 (p) REVERT: E 639 LEU cc_start: 0.8357 (mt) cc_final: 0.8042 (mp) REVERT: E 653 LEU cc_start: 0.8425 (mt) cc_final: 0.8100 (mt) REVERT: E 669 SER cc_start: 0.8406 (m) cc_final: 0.7572 (t) REVERT: E 693 LYS cc_start: 0.8526 (tttt) cc_final: 0.8192 (mttt) REVERT: E 705 ILE cc_start: 0.8382 (pt) cc_final: 0.8167 (mm) REVERT: E 737 LEU cc_start: 0.8399 (mt) cc_final: 0.8000 (mt) REVERT: E 740 ASP cc_start: 0.7396 (m-30) cc_final: 0.7161 (m-30) REVERT: E 765 ASP cc_start: 0.7743 (t0) cc_final: 0.7510 (t0) REVERT: E 768 ASP cc_start: 0.6928 (m-30) cc_final: 0.6540 (m-30) REVERT: E 784 GLU cc_start: 0.7826 (tt0) cc_final: 0.7333 (tm-30) REVERT: E 812 LYS cc_start: 0.8163 (mttp) cc_final: 0.7660 (mtpp) REVERT: E 819 LEU cc_start: 0.8023 (mm) cc_final: 0.7534 (mm) REVERT: E 853 ASN cc_start: 0.7936 (m-40) cc_final: 0.7620 (p0) REVERT: E 863 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 865 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7278 (mt-10) REVERT: E 866 ARG cc_start: 0.8389 (mtp85) cc_final: 0.7866 (ttm110) REVERT: E 899 ARG cc_start: 0.7611 (ptp-110) cc_final: 0.7206 (ttp-110) REVERT: F 481 TYR cc_start: 0.8300 (t80) cc_final: 0.8090 (t80) REVERT: F 515 GLN cc_start: 0.8752 (mt0) cc_final: 0.8506 (mm-40) REVERT: F 521 PHE cc_start: 0.8341 (t80) cc_final: 0.7962 (t80) REVERT: F 607 MET cc_start: 0.5632 (mtp) cc_final: 0.5065 (mtp) REVERT: F 617 PHE cc_start: 0.8076 (m-80) cc_final: 0.7707 (m-10) REVERT: F 638 SER cc_start: 0.8632 (t) cc_final: 0.7910 (p) REVERT: F 663 SER cc_start: 0.8035 (t) cc_final: 0.7832 (t) REVERT: F 684 VAL cc_start: 0.5745 (OUTLIER) cc_final: 0.5354 (p) REVERT: F 729 ARG cc_start: 0.7411 (mmt180) cc_final: 0.6612 (mmt180) REVERT: F 733 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7599 (mm-30) REVERT: F 737 LEU cc_start: 0.8530 (mt) cc_final: 0.8246 (mt) REVERT: F 742 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: F 765 ASP cc_start: 0.7931 (t0) cc_final: 0.7700 (t0) REVERT: F 784 GLU cc_start: 0.7697 (tt0) cc_final: 0.7260 (tm-30) REVERT: F 812 LYS cc_start: 0.8191 (mttp) cc_final: 0.7871 (mtpp) REVERT: F 853 ASN cc_start: 0.8301 (m-40) cc_final: 0.8072 (p0) REVERT: F 855 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8135 (ttmm) REVERT: F 866 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8080 (ttm110) outliers start: 42 outliers final: 26 residues processed: 469 average time/residue: 0.1792 time to fit residues: 119.6273 Evaluate side-chains 455 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 426 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 696 GLN Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain E residue 872 VAL Chi-restraints excluded: chain E residue 907 GLU Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 814 GLU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 875 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 211 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 HIS ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN ** E 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 739 HIS ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 789 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.244766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.192690 restraints weight = 32411.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.199542 restraints weight = 16154.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.204034 restraints weight = 10408.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.206390 restraints weight = 7868.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.207463 restraints weight = 6648.259| |-----------------------------------------------------------------------------| r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18820 Z= 0.183 Angle : 0.643 10.683 25456 Z= 0.320 Chirality : 0.042 0.174 2684 Planarity : 0.005 0.068 3300 Dihedral : 4.916 58.105 2512 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.52 % Allowed : 12.56 % Favored : 84.91 % 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: 0.56 (0.18), residues: 2234 helix: 0.93 (0.19), residues: 740 sheet: -0.12 (0.34), residues: 208 loop : 0.25 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 803 TYR 0.036 0.001 TYR E 735 PHE 0.044 0.002 PHE E 731 TRP 0.045 0.002 TRP B 698 HIS 0.017 0.001 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00384 (18772) covalent geometry : angle 0.61192 (25384) hydrogen bonds : bond 0.03529 ( 665) hydrogen bonds : angle 5.16887 ( 1743) metal coordination : bond 0.00621 ( 48) metal coordination : angle 3.76212 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 443 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: -0.2986 (mmm) cc_final: -0.4005 (mmm) REVERT: A 661 ILE cc_start: 0.7281 (mt) cc_final: 0.7057 (mt) REVERT: A 705 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7985 (pt) REVERT: A 732 PHE cc_start: 0.7678 (m-80) cc_final: 0.7285 (m-80) REVERT: A 756 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6552 (tm-30) REVERT: A 864 MET cc_start: 0.8199 (mmm) cc_final: 0.7932 (mmm) REVERT: A 875 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7397 (m) REVERT: A 885 ARG cc_start: 0.8472 (ttt180) cc_final: 0.7560 (ttt-90) REVERT: A 887 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8100 (mtm-85) REVERT: A 899 ARG cc_start: 0.7309 (mtt-85) cc_final: 0.7095 (mtt-85) REVERT: B 656 GLN cc_start: 0.7238 (mm110) cc_final: 0.6513 (mp10) REVERT: B 753 TRP cc_start: 0.6021 (p-90) cc_final: 0.5730 (p-90) REVERT: B 781 ASP cc_start: 0.8042 (t0) cc_final: 0.7564 (t0) REVERT: C 652 ASP cc_start: 0.7565 (t0) cc_final: 0.7347 (t0) REVERT: C 753 TRP cc_start: 0.6108 (p-90) cc_final: 0.5565 (p-90) REVERT: C 761 MET cc_start: 0.5025 (mmm) cc_final: 0.4770 (mmm) REVERT: D 678 GLN cc_start: 0.8046 (mp10) cc_final: 0.7628 (pp30) REVERT: D 732 PHE cc_start: 0.7852 (m-80) cc_final: 0.7343 (m-80) REVERT: D 742 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7268 (ttm110) REVERT: D 756 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6114 (tm-30) REVERT: D 761 MET cc_start: 0.5404 (ptp) cc_final: 0.5020 (ptp) REVERT: D 765 ASP cc_start: 0.7682 (t0) cc_final: 0.7248 (t0) REVERT: D 812 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8511 (mmmm) REVERT: D 852 MET cc_start: 0.5652 (mmm) cc_final: 0.5361 (mmm) REVERT: D 902 PHE cc_start: 0.6902 (m-80) cc_final: 0.6659 (m-80) REVERT: E 607 MET cc_start: 0.5304 (mtp) cc_final: 0.4752 (mtp) REVERT: E 621 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8526 (tmtt) REVERT: E 638 SER cc_start: 0.8475 (t) cc_final: 0.7667 (p) REVERT: E 639 LEU cc_start: 0.8377 (mt) cc_final: 0.8065 (mp) REVERT: E 653 LEU cc_start: 0.8532 (mt) cc_final: 0.8119 (mt) REVERT: E 669 SER cc_start: 0.8447 (m) cc_final: 0.7592 (t) REVERT: E 693 LYS cc_start: 0.8560 (tttt) cc_final: 0.8230 (mttt) REVERT: E 731 PHE cc_start: 0.8001 (t80) cc_final: 0.7782 (t80) REVERT: E 737 LEU cc_start: 0.8434 (mt) cc_final: 0.7992 (mt) REVERT: E 740 ASP cc_start: 0.7399 (m-30) cc_final: 0.7108 (m-30) REVERT: E 768 ASP cc_start: 0.6855 (m-30) cc_final: 0.6504 (m-30) REVERT: E 784 GLU cc_start: 0.7858 (tt0) cc_final: 0.7631 (tt0) REVERT: E 812 LYS cc_start: 0.8233 (mttp) cc_final: 0.7741 (mtpp) REVERT: E 853 ASN cc_start: 0.7950 (m-40) cc_final: 0.7655 (p0) REVERT: E 863 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7502 (tt0) REVERT: E 865 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7328 (mt-10) REVERT: E 866 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7895 (ttm110) REVERT: E 899 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.7110 (ttp-110) REVERT: F 515 GLN cc_start: 0.8716 (mt0) cc_final: 0.8486 (mm-40) REVERT: F 521 PHE cc_start: 0.8352 (t80) cc_final: 0.7937 (t80) REVERT: F 607 MET cc_start: 0.5797 (mtp) cc_final: 0.5181 (mtp) REVERT: F 617 PHE cc_start: 0.8056 (m-80) cc_final: 0.7734 (m-10) REVERT: F 640 PHE cc_start: 0.8134 (m-80) cc_final: 0.7787 (m-80) REVERT: F 669 SER cc_start: 0.8543 (m) cc_final: 0.8069 (t) REVERT: F 684 VAL cc_start: 0.5873 (OUTLIER) cc_final: 0.5426 (p) REVERT: F 729 ARG cc_start: 0.7417 (mmt180) cc_final: 0.7002 (mmt180) REVERT: F 731 PHE cc_start: 0.8029 (t80) cc_final: 0.7801 (t80) REVERT: F 737 LEU cc_start: 0.8539 (mt) cc_final: 0.8264 (mt) REVERT: F 765 ASP cc_start: 0.7914 (t0) cc_final: 0.7656 (t0) REVERT: F 768 ASP cc_start: 0.6964 (m-30) cc_final: 0.6657 (m-30) REVERT: F 774 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7341 (mt-10) REVERT: F 784 GLU cc_start: 0.7702 (tt0) cc_final: 0.7287 (tm-30) REVERT: F 789 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7555 (m-70) REVERT: F 812 LYS cc_start: 0.8239 (mttp) cc_final: 0.7859 (mtpp) REVERT: F 853 ASN cc_start: 0.8334 (m-40) cc_final: 0.8112 (p0) REVERT: F 855 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8176 (ttmm) outliers start: 50 outliers final: 36 residues processed: 473 average time/residue: 0.1745 time to fit residues: 118.1742 Evaluate side-chains 468 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 696 GLN Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain E residue 872 VAL Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 789 HIS Chi-restraints excluded: chain F residue 814 GLU Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 862 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 HIS E 789 HIS ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 789 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.242113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.184748 restraints weight = 34332.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.193123 restraints weight = 17042.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196667 restraints weight = 10987.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.199037 restraints weight = 8006.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.199915 restraints weight = 6894.314| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 18820 Z= 0.469 Angle : 0.865 12.987 25456 Z= 0.456 Chirality : 0.050 0.213 2684 Planarity : 0.007 0.063 3300 Dihedral : 5.591 56.327 2512 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.88 % Allowed : 12.82 % Favored : 84.31 % 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: -0.39 (0.17), residues: 2234 helix: 0.01 (0.19), residues: 740 sheet: -0.62 (0.34), residues: 214 loop : -0.25 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 831 TYR 0.049 0.003 TYR E 735 PHE 0.071 0.003 PHE E 731 TRP 0.037 0.003 TRP E 795 HIS 0.021 0.002 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00954 (18772) covalent geometry : angle 0.83583 (25384) hydrogen bonds : bond 0.05460 ( 665) hydrogen bonds : angle 6.23586 ( 1743) metal coordination : bond 0.01079 ( 48) metal coordination : angle 4.27875 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 426 time to evaluate : 0.531 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: A 661 ILE cc_start: 0.7589 (mt) cc_final: 0.7347 (mt) REVERT: A 677 HIS cc_start: 0.7862 (m-70) cc_final: 0.7398 (m-70) REVERT: A 692 GLN cc_start: 0.7190 (mp10) cc_final: 0.6662 (mm110) REVERT: A 732 PHE cc_start: 0.7921 (m-80) cc_final: 0.7447 (m-80) REVERT: A 733 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 736 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.7430 (ttp-110) REVERT: A 756 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6501 (tm-30) REVERT: A 761 MET cc_start: 0.6859 (ppp) cc_final: 0.5818 (ptt) REVERT: A 875 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7502 (m) REVERT: A 885 ARG cc_start: 0.8426 (ttt180) cc_final: 0.8096 (ttt180) REVERT: A 899 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7090 (mtt-85) REVERT: B 753 TRP cc_start: 0.6868 (p-90) cc_final: 0.6245 (p-90) REVERT: B 781 ASP cc_start: 0.8338 (t0) cc_final: 0.8024 (t0) REVERT: C 652 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: C 753 TRP cc_start: 0.6782 (p-90) cc_final: 0.6177 (p-90) REVERT: C 781 ASP cc_start: 0.8066 (t0) cc_final: 0.7770 (t0) REVERT: C 872 VAL cc_start: 0.7856 (t) cc_final: 0.7548 (t) REVERT: D 631 ARG cc_start: 0.6437 (ttm110) cc_final: 0.6056 (mtm-85) REVERT: D 674 MET cc_start: 0.7035 (mmm) cc_final: 0.6803 (mmm) REVERT: D 692 GLN cc_start: 0.7223 (mp10) cc_final: 0.6867 (mp10) REVERT: D 732 PHE cc_start: 0.8076 (m-80) cc_final: 0.7549 (m-80) REVERT: D 756 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6566 (tm-30) REVERT: D 759 VAL cc_start: 0.7100 (t) cc_final: 0.6766 (p) REVERT: D 761 MET cc_start: 0.5918 (ptp) cc_final: 0.5256 (ptm) REVERT: D 769 ILE cc_start: 0.8801 (mt) cc_final: 0.8591 (pt) REVERT: D 812 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8531 (mmmm) REVERT: D 852 MET cc_start: 0.5756 (mmm) cc_final: 0.5496 (mmm) REVERT: D 902 PHE cc_start: 0.7168 (m-80) cc_final: 0.6915 (m-80) REVERT: E 521 PHE cc_start: 0.8248 (t80) cc_final: 0.7719 (t80) REVERT: E 607 MET cc_start: 0.5356 (mtp) cc_final: 0.4786 (mtp) REVERT: E 621 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8558 (tmtt) REVERT: E 638 SER cc_start: 0.8609 (t) cc_final: 0.7914 (p) REVERT: E 639 LEU cc_start: 0.8485 (mt) cc_final: 0.8186 (mp) REVERT: E 669 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.7764 (t) REVERT: E 693 LYS cc_start: 0.8602 (tttt) cc_final: 0.8307 (mttt) REVERT: E 737 LEU cc_start: 0.8618 (mt) cc_final: 0.8275 (mt) REVERT: E 740 ASP cc_start: 0.7355 (m-30) cc_final: 0.7151 (m-30) REVERT: E 768 ASP cc_start: 0.7024 (m-30) cc_final: 0.6685 (m-30) REVERT: E 812 LYS cc_start: 0.8339 (mttp) cc_final: 0.7855 (mtpp) REVERT: E 817 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: E 863 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7212 (tt0) REVERT: E 865 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7479 (mt-10) REVERT: E 899 ARG cc_start: 0.7746 (ptp-110) cc_final: 0.7190 (ttp-110) REVERT: F 521 PHE cc_start: 0.8325 (t80) cc_final: 0.7900 (t80) REVERT: F 607 MET cc_start: 0.5806 (mtp) cc_final: 0.5201 (mtp) REVERT: F 621 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8383 (tmtt) REVERT: F 623 TYR cc_start: 0.7475 (m-10) cc_final: 0.7111 (m-10) REVERT: F 669 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8043 (t) REVERT: F 684 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.5972 (p) REVERT: F 705 ILE cc_start: 0.8439 (pt) cc_final: 0.8200 (pt) REVERT: F 730 LEU cc_start: 0.8294 (mt) cc_final: 0.7946 (mt) REVERT: F 733 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7588 (mm-30) REVERT: F 737 LEU cc_start: 0.8625 (mt) cc_final: 0.8392 (mt) REVERT: F 768 ASP cc_start: 0.7082 (m-30) cc_final: 0.6866 (m-30) REVERT: F 803 ARG cc_start: 0.7329 (ptt-90) cc_final: 0.7036 (ptt-90) REVERT: F 812 LYS cc_start: 0.8275 (mttp) cc_final: 0.7740 (mtpp) REVERT: F 826 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (ptpp) REVERT: F 831 ARG cc_start: 0.6388 (mpt180) cc_final: 0.5955 (mpt180) REVERT: F 855 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8189 (ttmm) REVERT: F 863 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7375 (tt0) outliers start: 57 outliers final: 42 residues processed: 458 average time/residue: 0.1787 time to fit residues: 116.8394 Evaluate side-chains 461 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 413 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 661 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 774 GLU Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain E residue 641 ASP Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 669 SER Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 696 GLN Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 826 LYS Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain E residue 872 VAL Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 641 ASP Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 669 SER Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 710 CYS Chi-restraints excluded: chain F residue 758 VAL Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 817 GLU Chi-restraints excluded: chain F residue 826 LYS Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 875 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 153 optimal weight: 0.0570 chunk 184 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 75 optimal weight: 0.0040 chunk 143 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 ASN B 879 ASN ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 739 HIS ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.244878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.193049 restraints weight = 32486.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.199842 restraints weight = 16150.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.204442 restraints weight = 10471.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.206379 restraints weight = 7915.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.208421 restraints weight = 6807.238| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18820 Z= 0.133 Angle : 0.678 12.684 25456 Z= 0.340 Chirality : 0.043 0.171 2684 Planarity : 0.005 0.053 3300 Dihedral : 5.013 59.674 2512 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.02 % Allowed : 15.29 % Favored : 82.69 % 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: 0.24 (0.18), residues: 2234 helix: 0.62 (0.19), residues: 742 sheet: -0.21 (0.35), residues: 206 loop : 0.07 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 742 TYR 0.032 0.002 TYR E 735 PHE 0.051 0.002 PHE E 731 TRP 0.045 0.002 TRP B 698 HIS 0.017 0.002 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00294 (18772) covalent geometry : angle 0.65285 (25384) hydrogen bonds : bond 0.03469 ( 665) hydrogen bonds : angle 5.24639 ( 1743) metal coordination : bond 0.00466 ( 48) metal coordination : angle 3.52565 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 0.699 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: A 585 MET cc_start: -0.2982 (mmm) cc_final: -0.4027 (mmm) REVERT: A 661 ILE cc_start: 0.7174 (mt) cc_final: 0.6960 (mt) REVERT: A 732 PHE cc_start: 0.7583 (m-80) cc_final: 0.7237 (m-80) REVERT: A 733 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 736 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8210 (ttm170) REVERT: A 756 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6403 (tm-30) REVERT: A 864 MET cc_start: 0.8342 (mmm) cc_final: 0.8016 (mmm) REVERT: A 875 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7282 (m) REVERT: A 885 ARG cc_start: 0.8466 (ttt180) cc_final: 0.8173 (ttt180) REVERT: A 899 ARG cc_start: 0.7281 (mtt-85) cc_final: 0.6976 (mtt-85) REVERT: B 738 LEU cc_start: 0.6549 (tp) cc_final: 0.6189 (pp) REVERT: B 753 TRP cc_start: 0.5996 (p-90) cc_final: 0.5549 (p-90) REVERT: B 781 ASP cc_start: 0.7991 (t0) cc_final: 0.7557 (t0) REVERT: C 652 ASP cc_start: 0.7591 (t0) cc_final: 0.7360 (t0) REVERT: C 753 TRP cc_start: 0.6216 (p-90) cc_final: 0.5632 (p-90) REVERT: C 780 ILE cc_start: 0.7530 (mp) cc_final: 0.7228 (tp) REVERT: C 801 MET cc_start: 0.6043 (mpp) cc_final: 0.5669 (mpp) REVERT: C 864 MET cc_start: 0.5289 (ppp) cc_final: 0.5035 (ppp) REVERT: D 567 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (m) REVERT: D 674 MET cc_start: 0.7135 (mmm) cc_final: 0.6809 (mmm) REVERT: D 732 PHE cc_start: 0.7685 (m-80) cc_final: 0.7193 (m-80) REVERT: D 751 PHE cc_start: 0.8300 (t80) cc_final: 0.8075 (t80) REVERT: D 756 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6085 (tm-30) REVERT: D 759 VAL cc_start: 0.6581 (t) cc_final: 0.6168 (m) REVERT: D 761 MET cc_start: 0.5548 (ptp) cc_final: 0.4858 (ptm) REVERT: D 769 ILE cc_start: 0.8710 (mt) cc_final: 0.8448 (pt) REVERT: D 812 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8497 (mmmm) REVERT: D 902 PHE cc_start: 0.6807 (m-80) cc_final: 0.6506 (m-80) REVERT: E 482 GLU cc_start: 0.8217 (mp0) cc_final: 0.7985 (pm20) REVERT: E 521 PHE cc_start: 0.8238 (t80) cc_final: 0.7768 (t80) REVERT: E 607 MET cc_start: 0.5329 (mtp) cc_final: 0.4755 (mtp) REVERT: E 621 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8752 (tmtt) REVERT: E 638 SER cc_start: 0.8323 (t) cc_final: 0.8031 (t) REVERT: E 639 LEU cc_start: 0.8403 (mt) cc_final: 0.8133 (mp) REVERT: E 669 SER cc_start: 0.8428 (m) cc_final: 0.7456 (t) REVERT: E 693 LYS cc_start: 0.8550 (tttt) cc_final: 0.8281 (mttt) REVERT: E 737 LEU cc_start: 0.8472 (mt) cc_final: 0.7989 (mt) REVERT: E 740 ASP cc_start: 0.7453 (m-30) cc_final: 0.7130 (m-30) REVERT: E 768 ASP cc_start: 0.6717 (m-30) cc_final: 0.6369 (m-30) REVERT: E 784 GLU cc_start: 0.7748 (tt0) cc_final: 0.7320 (tm-30) REVERT: E 812 LYS cc_start: 0.8330 (mttp) cc_final: 0.7482 (mtpp) REVERT: E 865 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7376 (mt-10) REVERT: E 899 ARG cc_start: 0.7617 (ptp-110) cc_final: 0.7142 (ttp-110) REVERT: F 513 MET cc_start: 0.6992 (ttt) cc_final: 0.6327 (ttt) REVERT: F 521 PHE cc_start: 0.8328 (t80) cc_final: 0.7983 (t80) REVERT: F 584 TYR cc_start: 0.6840 (m-80) cc_final: 0.6592 (m-10) REVERT: F 607 MET cc_start: 0.5786 (mtp) cc_final: 0.5181 (mtp) REVERT: F 669 SER cc_start: 0.8625 (m) cc_final: 0.7929 (t) REVERT: F 684 VAL cc_start: 0.6074 (OUTLIER) cc_final: 0.5651 (p) REVERT: F 737 LEU cc_start: 0.8522 (mt) cc_final: 0.8249 (mt) REVERT: F 742 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7198 (mmm-85) REVERT: F 768 ASP cc_start: 0.7054 (m-30) cc_final: 0.6698 (m-30) REVERT: F 771 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7191 (ttp80) REVERT: F 784 GLU cc_start: 0.7533 (tt0) cc_final: 0.7074 (tm-30) REVERT: F 812 LYS cc_start: 0.8300 (mttp) cc_final: 0.7599 (mtpp) REVERT: F 855 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8174 (ttmm) REVERT: F 907 GLU cc_start: 0.7541 (tt0) cc_final: 0.7283 (tt0) outliers start: 40 outliers final: 32 residues processed: 454 average time/residue: 0.1635 time to fit residues: 105.7990 Evaluate side-chains 455 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 419 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain F residue 665 VAL Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 771 ARG Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 824 ILE Chi-restraints excluded: chain F residue 826 LYS Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 875 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 202 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.244233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192494 restraints weight = 32235.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.199061 restraints weight = 15996.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203790 restraints weight = 10299.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.205723 restraints weight = 7731.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.208049 restraints weight = 6644.757| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18820 Z= 0.187 Angle : 0.704 21.496 25456 Z= 0.354 Chirality : 0.044 0.222 2684 Planarity : 0.006 0.086 3300 Dihedral : 5.085 59.338 2512 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.02 % Allowed : 15.79 % Favored : 82.19 % 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: 0.21 (0.18), residues: 2234 helix: 0.59 (0.19), residues: 742 sheet: -0.21 (0.35), residues: 206 loop : 0.04 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 631 TYR 0.025 0.002 TYR F 735 PHE 0.048 0.002 PHE E 731 TRP 0.050 0.002 TRP B 698 HIS 0.015 0.001 HIS F 739 Details of bonding type rmsd covalent geometry : bond 0.00399 (18772) covalent geometry : angle 0.68040 (25384) hydrogen bonds : bond 0.03684 ( 665) hydrogen bonds : angle 5.33144 ( 1743) metal coordination : bond 0.00543 ( 48) metal coordination : angle 3.43581 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 0.579 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: A 661 ILE cc_start: 0.7296 (mt) cc_final: 0.7035 (mt) REVERT: A 705 ILE cc_start: 0.8063 (pt) cc_final: 0.7858 (mm) REVERT: A 732 PHE cc_start: 0.7635 (m-80) cc_final: 0.7258 (m-80) REVERT: A 733 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 736 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8258 (ttm170) REVERT: A 756 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6506 (tm-30) REVERT: A 812 LYS cc_start: 0.8206 (mttp) cc_final: 0.7864 (mttp) REVERT: A 864 MET cc_start: 0.8353 (mmm) cc_final: 0.8092 (mmp) REVERT: A 875 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7561 (m) REVERT: A 885 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8178 (ttt180) REVERT: A 899 ARG cc_start: 0.7370 (mtt-85) cc_final: 0.7092 (mtt-85) REVERT: B 738 LEU cc_start: 0.6655 (tp) cc_final: 0.6325 (pp) REVERT: B 753 TRP cc_start: 0.6065 (p-90) cc_final: 0.5601 (p-90) REVERT: B 781 ASP cc_start: 0.8070 (t0) cc_final: 0.7635 (t0) REVERT: C 652 ASP cc_start: 0.7632 (t0) cc_final: 0.7406 (t0) REVERT: C 753 TRP cc_start: 0.6229 (p-90) cc_final: 0.5646 (p-90) REVERT: C 780 ILE cc_start: 0.7554 (mp) cc_final: 0.7241 (tp) REVERT: C 781 ASP cc_start: 0.7817 (t0) cc_final: 0.7542 (t0) REVERT: C 864 MET cc_start: 0.5173 (ppp) cc_final: 0.4863 (ppp) REVERT: D 567 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7495 (m) REVERT: D 674 MET cc_start: 0.7139 (mmm) cc_final: 0.6833 (mmm) REVERT: D 732 PHE cc_start: 0.7727 (m-80) cc_final: 0.7284 (m-80) REVERT: D 751 PHE cc_start: 0.8442 (t80) cc_final: 0.8213 (t80) REVERT: D 756 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6357 (tm-30) REVERT: D 759 VAL cc_start: 0.6706 (t) cc_final: 0.6305 (m) REVERT: D 761 MET cc_start: 0.5578 (ptp) cc_final: 0.4796 (ptm) REVERT: D 769 ILE cc_start: 0.8744 (mt) cc_final: 0.8501 (pt) REVERT: D 812 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8453 (mmmm) REVERT: D 902 PHE cc_start: 0.6885 (m-80) cc_final: 0.6586 (m-80) REVERT: E 482 GLU cc_start: 0.8228 (mp0) cc_final: 0.8017 (pm20) REVERT: E 521 PHE cc_start: 0.8212 (t80) cc_final: 0.7757 (t80) REVERT: E 607 MET cc_start: 0.5335 (mtp) cc_final: 0.4769 (mtp) REVERT: E 617 PHE cc_start: 0.8159 (m-80) cc_final: 0.7949 (m-10) REVERT: E 621 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8711 (tmtt) REVERT: E 638 SER cc_start: 0.8368 (t) cc_final: 0.7562 (p) REVERT: E 653 LEU cc_start: 0.8490 (mt) cc_final: 0.8051 (mt) REVERT: E 664 GLU cc_start: 0.6271 (tp30) cc_final: 0.6036 (tp30) REVERT: E 669 SER cc_start: 0.8491 (m) cc_final: 0.7624 (t) REVERT: E 737 LEU cc_start: 0.8527 (mt) cc_final: 0.8204 (mp) REVERT: E 740 ASP cc_start: 0.7460 (m-30) cc_final: 0.7199 (m-30) REVERT: E 768 ASP cc_start: 0.6736 (m-30) cc_final: 0.6432 (m-30) REVERT: E 812 LYS cc_start: 0.8359 (mttp) cc_final: 0.7559 (mtpp) REVERT: E 863 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 865 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 899 ARG cc_start: 0.7650 (ptp-110) cc_final: 0.7162 (ttp-110) REVERT: E 901 LEU cc_start: 0.8702 (mt) cc_final: 0.8480 (mp) REVERT: F 521 PHE cc_start: 0.8321 (t80) cc_final: 0.7909 (t80) REVERT: F 584 TYR cc_start: 0.6858 (m-80) cc_final: 0.6583 (m-10) REVERT: F 607 MET cc_start: 0.5855 (mtp) cc_final: 0.5226 (mtp) REVERT: F 617 PHE cc_start: 0.7704 (m-80) cc_final: 0.7471 (m-10) REVERT: F 669 SER cc_start: 0.8649 (m) cc_final: 0.7883 (t) REVERT: F 694 HIS cc_start: 0.8187 (m170) cc_final: 0.7948 (m170) REVERT: F 731 PHE cc_start: 0.7974 (t80) cc_final: 0.7491 (t80) REVERT: F 737 LEU cc_start: 0.8549 (mt) cc_final: 0.8293 (mt) REVERT: F 742 ARG cc_start: 0.7678 (mmm-85) cc_final: 0.7168 (mmm-85) REVERT: F 768 ASP cc_start: 0.7139 (m-30) cc_final: 0.6774 (m-30) REVERT: F 771 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7334 (ttp80) REVERT: F 784 GLU cc_start: 0.7549 (tt0) cc_final: 0.7122 (tm-30) REVERT: F 812 LYS cc_start: 0.8328 (mttp) cc_final: 0.7631 (mtpp) REVERT: F 831 ARG cc_start: 0.6353 (mpt180) cc_final: 0.5912 (mpt180) REVERT: F 855 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8143 (ttmm) REVERT: F 866 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7976 (ttm110) REVERT: F 891 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7109 (mtm110) REVERT: F 907 GLU cc_start: 0.7576 (tt0) cc_final: 0.7341 (tt0) outliers start: 40 outliers final: 33 residues processed: 452 average time/residue: 0.1664 time to fit residues: 108.0083 Evaluate side-chains 458 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 422 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain E residue 851 PHE Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 771 ARG Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 817 GLU Chi-restraints excluded: chain F residue 826 LYS Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 875 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 114 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 168 optimal weight: 0.0040 chunk 83 optimal weight: 8.9990 chunk 202 optimal weight: 0.6980 chunk 157 optimal weight: 0.0470 overall best weight: 0.5092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.245280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.193797 restraints weight = 32681.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200359 restraints weight = 16165.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.205116 restraints weight = 10414.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.205967 restraints weight = 7805.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.207042 restraints weight = 7215.830| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18820 Z= 0.130 Angle : 0.681 16.456 25456 Z= 0.339 Chirality : 0.043 0.204 2684 Planarity : 0.005 0.074 3300 Dihedral : 4.888 58.929 2512 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.97 % Allowed : 15.99 % Favored : 82.04 % 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: 0.37 (0.18), residues: 2234 helix: 0.71 (0.20), residues: 746 sheet: -0.13 (0.35), residues: 208 loop : 0.16 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 631 TYR 0.023 0.001 TYR F 735 PHE 0.043 0.002 PHE E 731 TRP 0.052 0.002 TRP B 698 HIS 0.010 0.001 HIS E 900 Details of bonding type rmsd covalent geometry : bond 0.00290 (18772) covalent geometry : angle 0.65894 (25384) hydrogen bonds : bond 0.03326 ( 665) hydrogen bonds : angle 5.14054 ( 1743) metal coordination : bond 0.00438 ( 48) metal coordination : angle 3.31095 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4468 Ramachandran restraints generated. 2234 Oldfield, 0 Emsley, 2234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 424 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: -0.3123 (mmm) cc_final: -0.4140 (mmm) REVERT: A 661 ILE cc_start: 0.7207 (mt) cc_final: 0.6946 (mt) REVERT: A 705 ILE cc_start: 0.8068 (pt) cc_final: 0.7865 (mm) REVERT: A 732 PHE cc_start: 0.7483 (m-80) cc_final: 0.7238 (m-80) REVERT: A 756 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6508 (tm-30) REVERT: A 817 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 875 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7313 (m) REVERT: A 885 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8152 (ttt180) REVERT: A 899 ARG cc_start: 0.7361 (mtt-85) cc_final: 0.7083 (mtt-85) REVERT: B 738 LEU cc_start: 0.6675 (tp) cc_final: 0.6341 (pp) REVERT: B 753 TRP cc_start: 0.5905 (p-90) cc_final: 0.5490 (p-90) REVERT: B 781 ASP cc_start: 0.7961 (t0) cc_final: 0.7552 (t0) REVERT: C 647 LEU cc_start: 0.8317 (tp) cc_final: 0.8075 (tp) REVERT: C 753 TRP cc_start: 0.6143 (p-90) cc_final: 0.5564 (p-90) REVERT: C 780 ILE cc_start: 0.7516 (mp) cc_final: 0.7229 (tp) REVERT: C 864 MET cc_start: 0.5168 (ppp) cc_final: 0.4931 (ppp) REVERT: D 567 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7485 (m) REVERT: D 674 MET cc_start: 0.7084 (mmm) cc_final: 0.6723 (mmm) REVERT: D 732 PHE cc_start: 0.7737 (m-80) cc_final: 0.7312 (m-80) REVERT: D 751 PHE cc_start: 0.8223 (t80) cc_final: 0.7935 (t80) REVERT: D 756 GLU cc_start: 0.6642 (tm-30) cc_final: 0.6098 (tm-30) REVERT: D 759 VAL cc_start: 0.6390 (t) cc_final: 0.6014 (m) REVERT: D 761 MET cc_start: 0.5461 (ptp) cc_final: 0.4667 (ptm) REVERT: D 769 ILE cc_start: 0.8714 (mt) cc_final: 0.8469 (pt) REVERT: D 812 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8429 (mmmm) REVERT: D 902 PHE cc_start: 0.6707 (m-80) cc_final: 0.6409 (m-80) REVERT: E 521 PHE cc_start: 0.8242 (t80) cc_final: 0.7775 (t80) REVERT: E 607 MET cc_start: 0.5337 (mtp) cc_final: 0.4764 (mtp) REVERT: E 621 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8639 (tmtt) REVERT: E 638 SER cc_start: 0.8382 (t) cc_final: 0.7537 (p) REVERT: E 651 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7882 (mtpt) REVERT: E 664 GLU cc_start: 0.6200 (tp30) cc_final: 0.5926 (tp30) REVERT: E 669 SER cc_start: 0.8491 (m) cc_final: 0.7487 (t) REVERT: E 737 LEU cc_start: 0.8453 (mt) cc_final: 0.8098 (mt) REVERT: E 740 ASP cc_start: 0.7548 (m-30) cc_final: 0.7271 (m-30) REVERT: E 768 ASP cc_start: 0.6675 (m-30) cc_final: 0.6352 (m-30) REVERT: E 784 GLU cc_start: 0.7593 (tt0) cc_final: 0.7083 (tm-30) REVERT: E 812 LYS cc_start: 0.8325 (mttp) cc_final: 0.7484 (mtpp) REVERT: E 863 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7244 (tt0) REVERT: E 865 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7284 (mt-10) REVERT: E 899 ARG cc_start: 0.7644 (ptp-110) cc_final: 0.7066 (ttp-110) REVERT: F 513 MET cc_start: 0.7011 (ttt) cc_final: 0.6315 (ttt) REVERT: F 521 PHE cc_start: 0.8339 (t80) cc_final: 0.8000 (t80) REVERT: F 584 TYR cc_start: 0.6931 (m-80) cc_final: 0.6631 (m-10) REVERT: F 607 MET cc_start: 0.5793 (mtp) cc_final: 0.5201 (mtp) REVERT: F 617 PHE cc_start: 0.7793 (m-80) cc_final: 0.7518 (m-10) REVERT: F 737 LEU cc_start: 0.8522 (mt) cc_final: 0.8228 (mt) REVERT: F 742 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7133 (mmm-85) REVERT: F 768 ASP cc_start: 0.7132 (m-30) cc_final: 0.6791 (m-30) REVERT: F 784 GLU cc_start: 0.7424 (tt0) cc_final: 0.6985 (tm-30) REVERT: F 812 LYS cc_start: 0.8302 (mttp) cc_final: 0.7608 (mtpp) REVERT: F 823 ARG cc_start: 0.7265 (mtp85) cc_final: 0.5682 (mtm180) REVERT: F 831 ARG cc_start: 0.6383 (mpt180) cc_final: 0.5958 (mpt180) REVERT: F 855 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7972 (ttmm) REVERT: F 865 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7406 (mt-10) REVERT: F 907 GLU cc_start: 0.7501 (tt0) cc_final: 0.7274 (tt0) outliers start: 39 outliers final: 36 residues processed: 451 average time/residue: 0.1800 time to fit residues: 115.8776 Evaluate side-chains 457 residues out of total 1982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 419 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 803 ARG Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 481 TYR Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 817 GLU Chi-restraints excluded: chain D residue 879 ASN Chi-restraints excluded: chain E residue 567 VAL Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain E residue 657 VAL Chi-restraints excluded: chain E residue 666 CYS Chi-restraints excluded: chain E residue 684 VAL Chi-restraints excluded: chain E residue 739 HIS Chi-restraints excluded: chain E residue 775 SER Chi-restraints excluded: chain E residue 851 PHE Chi-restraints excluded: chain E residue 862 THR Chi-restraints excluded: chain E residue 892 SER Chi-restraints excluded: chain F residue 567 VAL Chi-restraints excluded: chain F residue 643 ILE Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 684 VAL Chi-restraints excluded: chain F residue 692 GLN Chi-restraints excluded: chain F residue 771 ARG Chi-restraints excluded: chain F residue 786 SER Chi-restraints excluded: chain F residue 826 LYS Chi-restraints excluded: chain F residue 830 VAL Chi-restraints excluded: chain F residue 875 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 188 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 209 optimal weight: 0.0970 chunk 78 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 678 GLN ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.242420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.185617 restraints weight = 33910.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.194230 restraints weight = 16860.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.197878 restraints weight = 10089.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.199863 restraints weight = 7518.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.200237 restraints weight = 6861.378| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.121 18820 Z= 0.488 Angle : 0.900 20.312 25456 Z= 0.477 Chirality : 0.051 0.219 2684 Planarity : 0.007 0.084 3300 Dihedral : 5.670 57.237 2512 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.42 % Allowed : 16.04 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2234 helix: -0.11 (0.19), residues: 740 sheet: -0.88 (0.34), residues: 224 loop : -0.27 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG F 899 TYR 0.060 0.003 TYR F 735 PHE 0.063 0.003 PHE E 731 TRP 0.045 0.003 TRP B 698 HIS 0.017 0.002 HIS F 900 Details of bonding type rmsd covalent geometry : bond 0.00997 (18772) covalent geometry : angle 0.87610 (25384) hydrogen bonds : bond 0.05506 ( 665) hydrogen bonds : angle 6.29393 ( 1743) metal coordination : bond 0.01079 ( 48) metal coordination : angle 3.93890 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5920.66 seconds wall clock time: 101 minutes 50.97 seconds (6110.97 seconds total)