Starting phenix.real_space_refine on Tue Sep 24 08:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/09_2024/6caa_7441.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5044 2.51 5 N 1158 2.21 5 O 1264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7508 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3754 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Restraints were copied for chains: B Time building chain proxies: 6.32, per 1000 atoms: 0.84 Number of scatterers: 7508 At special positions: 0 Unit cell: (131.92, 77.52, 93.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1264 8.00 N 1158 7.00 C 5044 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 67.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 402 through 410 removed outlier: 4.307A pdb=" N ARG A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.708A pdb=" N PHE A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.587A pdb=" N SER A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.712A pdb=" N ASP A 449 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.813A pdb=" N LEU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 499 removed outlier: 3.667A pdb=" N LEU A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 528 removed outlier: 3.707A pdb=" N TRP A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 516 " --> pdb=" O TRP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 541 through 567 removed outlier: 4.058A pdb=" N LEU A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 669 removed outlier: 3.790A pdb=" N ILE A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 676 through 684 removed outlier: 4.194A pdb=" N LEU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.616A pdb=" N PHE A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 740 Processing helix chain 'A' and resid 740 through 764 removed outlier: 3.542A pdb=" N ALA A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 756 " --> pdb=" O PHE A 752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 762 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 792 removed outlier: 3.635A pdb=" N ALA A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 811 removed outlier: 3.506A pdb=" N ASP A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.958A pdb=" N VAL A 839 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.067A pdb=" N PHE A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 removed outlier: 3.821A pdb=" N LEU A 861 " --> pdb=" O PRO A 857 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 873 " --> pdb=" O GLY A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 883 removed outlier: 4.041A pdb=" N ASP A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 926 removed outlier: 3.816A pdb=" N VAL A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 911 " --> pdb=" O HIS A 907 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 946 removed outlier: 3.540A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 939 " --> pdb=" O MET A 935 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 944 " --> pdb=" O VAL A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'B' and resid 402 through 410 removed outlier: 4.307A pdb=" N ARG B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 removed outlier: 3.707A pdb=" N PHE B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.587A pdb=" N SER B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.711A pdb=" N ASP B 449 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.813A pdb=" N LEU B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 499 removed outlier: 3.668A pdb=" N LEU B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 528 removed outlier: 3.708A pdb=" N TRP B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 516 " --> pdb=" O TRP B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 541 through 567 removed outlier: 4.059A pdb=" N LEU B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 669 removed outlier: 3.790A pdb=" N ILE B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 676 through 684 removed outlier: 4.194A pdb=" N LEU B 682 " --> pdb=" O THR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 702 removed outlier: 3.615A pdb=" N PHE B 695 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 740 Processing helix chain 'B' and resid 740 through 764 removed outlier: 3.542A pdb=" N ALA B 744 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 756 " --> pdb=" O PHE B 752 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 757 " --> pdb=" O MET B 753 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 761 " --> pdb=" O ILE B 757 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL B 762 " --> pdb=" O THR B 758 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 764 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 792 removed outlier: 3.635A pdb=" N ALA B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 811 removed outlier: 3.506A pdb=" N ASP B 809 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 811 " --> pdb=" O HIS B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.958A pdb=" N VAL B 839 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE B 840 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 4.066A pdb=" N PHE B 855 " --> pdb=" O PRO B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 873 removed outlier: 3.821A pdb=" N LEU B 861 " --> pdb=" O PRO B 857 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 863 " --> pdb=" O PRO B 859 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 883 removed outlier: 4.041A pdb=" N ASP B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 926 removed outlier: 3.816A pdb=" N VAL B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 911 " --> pdb=" O HIS B 907 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 919 " --> pdb=" O LEU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 946 removed outlier: 3.540A pdb=" N ALA B 938 " --> pdb=" O VAL B 934 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 939 " --> pdb=" O MET B 935 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 942 " --> pdb=" O ALA B 938 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 944 " --> pdb=" O VAL B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 949 No H-bonds generated for 'chain 'B' and resid 947 through 949' 342 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2090 1.34 - 1.45: 1412 1.45 - 1.57: 4120 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 7694 Sorted by residual: bond pdb=" CA ALA A 410 " pdb=" C ALA A 410 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.26e-02 6.30e+03 6.65e+00 bond pdb=" CA ALA B 410 " pdb=" C ALA B 410 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.26e-02 6.30e+03 6.51e+00 bond pdb=" CG1 ILE A 432 " pdb=" CD1 ILE A 432 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.07e+00 bond pdb=" CG1 ILE B 432 " pdb=" CD1 ILE B 432 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 5.03e+00 bond pdb=" CG MET B 560 " pdb=" SD MET B 560 " ideal model delta sigma weight residual 1.803 1.752 0.051 2.50e-02 1.60e+03 4.19e+00 ... (remaining 7689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 10215 3.85 - 7.70: 209 7.70 - 11.55: 26 11.55 - 15.40: 4 15.40 - 19.26: 2 Bond angle restraints: 10456 Sorted by residual: angle pdb=" CA LEU B 898 " pdb=" CB LEU B 898 " pdb=" CG LEU B 898 " ideal model delta sigma weight residual 116.30 135.56 -19.26 3.50e+00 8.16e-02 3.03e+01 angle pdb=" CA LEU A 898 " pdb=" CB LEU A 898 " pdb=" CG LEU A 898 " ideal model delta sigma weight residual 116.30 135.55 -19.25 3.50e+00 8.16e-02 3.02e+01 angle pdb=" C PRO A 646 " pdb=" N ASP A 647 " pdb=" CA ASP A 647 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C PRO B 646 " pdb=" N ASP B 647 " pdb=" CA ASP B 647 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" N TYR A 897 " pdb=" CA TYR A 897 " pdb=" CB TYR A 897 " ideal model delta sigma weight residual 114.17 108.91 5.26 1.14e+00 7.69e-01 2.13e+01 ... (remaining 10451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 4174 16.77 - 33.53: 256 33.53 - 50.30: 58 50.30 - 67.07: 2 67.07 - 83.83: 8 Dihedral angle restraints: 4498 sinusoidal: 1708 harmonic: 2790 Sorted by residual: dihedral pdb=" CA PRO B 888 " pdb=" C PRO B 888 " pdb=" N LEU B 889 " pdb=" CA LEU B 889 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA PRO A 888 " pdb=" C PRO A 888 " pdb=" N LEU A 889 " pdb=" CA LEU A 889 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA GLU B 541 " pdb=" C GLU B 541 " pdb=" N GLU B 542 " pdb=" CA GLU B 542 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 4495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1002 0.080 - 0.159: 220 0.159 - 0.238: 34 0.238 - 0.318: 2 0.318 - 0.397: 2 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB ILE A 710 " pdb=" CA ILE A 710 " pdb=" CG1 ILE A 710 " pdb=" CG2 ILE A 710 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE B 710 " pdb=" CA ILE B 710 " pdb=" CG1 ILE B 710 " pdb=" CG2 ILE B 710 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ASP A 647 " pdb=" N ASP A 647 " pdb=" C ASP A 647 " pdb=" CB ASP A 647 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1257 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 829 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C VAL A 829 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL A 829 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 830 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 829 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.15e+00 pdb=" C VAL B 829 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL B 829 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG B 830 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 850 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 851 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " -0.039 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 32 2.49 - 3.09: 5123 3.09 - 3.69: 11730 3.69 - 4.30: 15665 4.30 - 4.90: 24962 Nonbonded interactions: 57512 Sorted by model distance: nonbonded pdb=" O TYR B 674 " pdb=" CD1 PHE B 675 " model vdw 1.886 3.340 nonbonded pdb=" O TYR A 674 " pdb=" CD1 PHE A 675 " model vdw 1.886 3.340 nonbonded pdb=" O GLN A 424 " pdb=" OG SER A 427 " model vdw 2.279 3.040 nonbonded pdb=" O GLN B 424 " pdb=" OG SER B 427 " model vdw 2.280 3.040 nonbonded pdb=" O ILE A 922 " pdb=" OG SER A 925 " model vdw 2.311 3.040 ... (remaining 57507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.009 0.088 7694 Z= 0.539 Angle : 1.328 19.256 10456 Z= 0.670 Chirality : 0.068 0.397 1260 Planarity : 0.009 0.070 1260 Dihedral : 12.406 83.834 2686 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.23 (0.18), residues: 938 helix: -4.19 (0.11), residues: 546 sheet: None (None), residues: 0 loop : -3.91 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 512 HIS 0.017 0.004 HIS B 900 PHE 0.042 0.004 PHE A 855 TYR 0.017 0.003 TYR B 797 ARG 0.006 0.001 ARG A 830 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.883 Fit side-chains REVERT: A 430 LEU cc_start: 0.8199 (pp) cc_final: 0.7721 (tp) REVERT: A 454 MET cc_start: 0.4217 (mmm) cc_final: 0.2570 (tmm) REVERT: A 473 LEU cc_start: 0.7235 (mt) cc_final: 0.6835 (mt) REVERT: A 493 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7301 (mmp-170) REVERT: A 494 LEU cc_start: 0.8783 (tp) cc_final: 0.8487 (tp) REVERT: A 502 ASN cc_start: 0.8454 (t0) cc_final: 0.7791 (t0) REVERT: A 506 TYR cc_start: 0.7558 (t80) cc_final: 0.7358 (t80) REVERT: A 699 ASP cc_start: 0.8197 (t0) cc_final: 0.7865 (t0) REVERT: A 754 ASP cc_start: 0.8774 (t0) cc_final: 0.8253 (t0) REVERT: A 858 MET cc_start: 0.9184 (tpt) cc_final: 0.8545 (tpp) REVERT: A 887 MET cc_start: 0.7605 (ttt) cc_final: 0.7404 (tmm) REVERT: A 924 LYS cc_start: 0.8493 (tppp) cc_final: 0.8213 (tptt) REVERT: B 430 LEU cc_start: 0.8241 (pp) cc_final: 0.7772 (tp) REVERT: B 454 MET cc_start: 0.4111 (mmm) cc_final: 0.2414 (tmm) REVERT: B 473 LEU cc_start: 0.7246 (mt) cc_final: 0.6852 (mt) REVERT: B 493 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7349 (mmp-170) REVERT: B 494 LEU cc_start: 0.8779 (tp) cc_final: 0.8482 (tp) REVERT: B 502 ASN cc_start: 0.8373 (t0) cc_final: 0.7690 (t0) REVERT: B 506 TYR cc_start: 0.7494 (t80) cc_final: 0.7282 (t80) REVERT: B 699 ASP cc_start: 0.8233 (t0) cc_final: 0.7883 (t0) REVERT: B 754 ASP cc_start: 0.8775 (t0) cc_final: 0.8384 (t0) REVERT: B 854 LYS cc_start: 0.8779 (tmtm) cc_final: 0.8479 (tppt) REVERT: B 858 MET cc_start: 0.9170 (tpt) cc_final: 0.8535 (tpp) REVERT: B 887 MET cc_start: 0.7674 (ttt) cc_final: 0.7441 (tmm) REVERT: B 924 LYS cc_start: 0.8491 (tppp) cc_final: 0.8212 (tptt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2195 time to fit residues: 65.8779 Evaluate side-chains 131 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 763 ASN A 767 HIS B 572 ASN B 763 ASN B 767 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7694 Z= 0.211 Angle : 0.808 10.000 10456 Z= 0.407 Chirality : 0.046 0.189 1260 Planarity : 0.007 0.061 1260 Dihedral : 6.546 23.624 1002 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 3.82 % Allowed : 13.92 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.22), residues: 938 helix: -2.12 (0.17), residues: 586 sheet: None (None), residues: 0 loop : -3.82 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 512 HIS 0.003 0.001 HIS A 953 PHE 0.015 0.002 PHE B 531 TYR 0.035 0.002 TYR B 577 ARG 0.005 0.001 ARG B 830 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 0.872 Fit side-chains REVERT: A 413 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: A 430 LEU cc_start: 0.8860 (pp) cc_final: 0.8379 (tp) REVERT: A 454 MET cc_start: 0.4399 (mmm) cc_final: 0.3773 (tpt) REVERT: A 542 GLU cc_start: 0.7632 (mp0) cc_final: 0.6557 (mp0) REVERT: A 699 ASP cc_start: 0.8533 (t0) cc_final: 0.8225 (t0) REVERT: A 754 ASP cc_start: 0.8925 (t0) cc_final: 0.8703 (t0) REVERT: A 808 ILE cc_start: 0.9203 (pt) cc_final: 0.8975 (tp) REVERT: A 874 ASN cc_start: 0.8069 (t0) cc_final: 0.7844 (t0) REVERT: A 924 LYS cc_start: 0.8442 (tppp) cc_final: 0.8079 (tptt) REVERT: B 413 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 430 LEU cc_start: 0.8843 (pp) cc_final: 0.8388 (tp) REVERT: B 454 MET cc_start: 0.4339 (mmm) cc_final: 0.3722 (tpt) REVERT: B 542 GLU cc_start: 0.7635 (mp0) cc_final: 0.6449 (mp0) REVERT: B 699 ASP cc_start: 0.8526 (t0) cc_final: 0.8204 (t0) REVERT: B 754 ASP cc_start: 0.8964 (t0) cc_final: 0.8690 (t0) REVERT: B 808 ILE cc_start: 0.9190 (pt) cc_final: 0.8972 (tp) REVERT: B 874 ASN cc_start: 0.8062 (t0) cc_final: 0.7838 (t0) REVERT: B 924 LYS cc_start: 0.8502 (tppp) cc_final: 0.8055 (tptt) outliers start: 31 outliers final: 13 residues processed: 190 average time/residue: 0.1705 time to fit residues: 44.8346 Evaluate side-chains 152 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 68 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 572 ASN B 422 ASN B 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7694 Z= 0.181 Angle : 0.758 11.299 10456 Z= 0.372 Chirality : 0.044 0.173 1260 Planarity : 0.005 0.055 1260 Dihedral : 5.984 22.380 1002 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 4.56 % Allowed : 15.39 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.25), residues: 938 helix: -1.03 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -3.50 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 516 HIS 0.003 0.001 HIS A 953 PHE 0.037 0.002 PHE A 848 TYR 0.012 0.001 TYR B 867 ARG 0.002 0.000 ARG B 943 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: A 430 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 454 MET cc_start: 0.4518 (mmm) cc_final: 0.3869 (tpt) REVERT: A 754 ASP cc_start: 0.8973 (t0) cc_final: 0.8727 (t0) REVERT: A 764 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7844 (mmm-85) REVERT: B 413 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 430 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 454 MET cc_start: 0.4301 (mmm) cc_final: 0.3667 (tpt) REVERT: B 675 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: B 699 ASP cc_start: 0.8555 (t0) cc_final: 0.8163 (t0) REVERT: B 754 ASP cc_start: 0.8973 (t0) cc_final: 0.8656 (t0) REVERT: B 757 ILE cc_start: 0.8820 (pp) cc_final: 0.8466 (pp) REVERT: B 764 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7821 (mmm-85) outliers start: 37 outliers final: 12 residues processed: 187 average time/residue: 0.1617 time to fit residues: 42.4861 Evaluate side-chains 156 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 763 ASN Chi-restraints excluded: chain B residue 801 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 477 GLN B 572 ASN B 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7694 Z= 0.204 Angle : 0.797 12.920 10456 Z= 0.383 Chirality : 0.045 0.170 1260 Planarity : 0.005 0.057 1260 Dihedral : 5.725 22.859 1002 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 6.03 % Allowed : 17.24 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.27), residues: 938 helix: -0.60 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -3.37 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.004 0.001 HIS A 900 PHE 0.039 0.002 PHE A 848 TYR 0.023 0.002 TYR A 577 ARG 0.002 0.000 ARG A 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 152 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 430 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 454 MET cc_start: 0.4020 (mmm) cc_final: 0.3327 (tpt) REVERT: A 541 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: A 542 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: A 699 ASP cc_start: 0.8590 (t0) cc_final: 0.8270 (t0) REVERT: A 753 MET cc_start: 0.8311 (mtp) cc_final: 0.8070 (mtp) REVERT: A 754 ASP cc_start: 0.9045 (t0) cc_final: 0.8819 (t0) REVERT: A 756 GLN cc_start: 0.8391 (mp10) cc_final: 0.7622 (mp10) REVERT: A 764 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7695 (mmm-85) REVERT: B 413 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: B 430 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8271 (tp) REVERT: B 454 MET cc_start: 0.3991 (mmm) cc_final: 0.3279 (tpt) REVERT: B 542 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 699 ASP cc_start: 0.8488 (t0) cc_final: 0.8069 (t0) REVERT: B 753 MET cc_start: 0.8348 (mtp) cc_final: 0.8123 (mtp) REVERT: B 754 ASP cc_start: 0.9050 (t0) cc_final: 0.8682 (t0) REVERT: B 756 GLN cc_start: 0.8507 (mp10) cc_final: 0.7684 (mp10) REVERT: B 757 ILE cc_start: 0.8801 (pp) cc_final: 0.8343 (pp) REVERT: B 764 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7166 (mmm-85) REVERT: B 911 PHE cc_start: 0.8117 (t80) cc_final: 0.7536 (m-80) outliers start: 49 outliers final: 20 residues processed: 191 average time/residue: 0.1673 time to fit residues: 44.8443 Evaluate side-chains 157 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 763 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 908 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.0020 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN ** A 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN B 572 ASN B 763 ASN B 900 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7694 Z= 0.183 Angle : 0.774 10.668 10456 Z= 0.373 Chirality : 0.044 0.165 1260 Planarity : 0.005 0.053 1260 Dihedral : 5.480 22.907 1002 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 5.67 % Allowed : 17.49 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 938 helix: -0.34 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.31 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 516 HIS 0.003 0.001 HIS A 767 PHE 0.057 0.002 PHE A 848 TYR 0.013 0.001 TYR B 897 ARG 0.008 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 163 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 430 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8251 (tp) REVERT: A 454 MET cc_start: 0.4078 (mmm) cc_final: 0.3386 (tpt) REVERT: A 493 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7519 (mmp-170) REVERT: A 510 ARG cc_start: 0.8413 (mtp180) cc_final: 0.7937 (ttt-90) REVERT: A 531 PHE cc_start: 0.7814 (m-10) cc_final: 0.7521 (m-10) REVERT: A 542 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: A 749 ILE cc_start: 0.8791 (mt) cc_final: 0.8445 (tt) REVERT: A 753 MET cc_start: 0.8348 (mtp) cc_final: 0.8078 (mtp) REVERT: A 756 GLN cc_start: 0.8445 (mp10) cc_final: 0.7564 (mp10) REVERT: A 911 PHE cc_start: 0.8106 (t80) cc_final: 0.7542 (m-80) REVERT: A 957 PHE cc_start: 0.7315 (p90) cc_final: 0.6737 (p90) REVERT: B 413 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 430 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 454 MET cc_start: 0.4051 (mmm) cc_final: 0.3366 (tpt) REVERT: B 493 ARG cc_start: 0.7886 (mtt180) cc_final: 0.7533 (mmp-170) REVERT: B 510 ARG cc_start: 0.8403 (mtp180) cc_final: 0.7946 (ttt-90) REVERT: B 542 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: B 699 ASP cc_start: 0.8455 (t0) cc_final: 0.8063 (t0) REVERT: B 753 MET cc_start: 0.8439 (mtp) cc_final: 0.8167 (mtp) REVERT: B 754 ASP cc_start: 0.9052 (t0) cc_final: 0.8769 (t0) REVERT: B 756 GLN cc_start: 0.8408 (mp10) cc_final: 0.7422 (mp10) REVERT: B 757 ILE cc_start: 0.8818 (pp) cc_final: 0.8527 (pp) REVERT: B 874 ASN cc_start: 0.8063 (t0) cc_final: 0.7834 (t0) REVERT: B 911 PHE cc_start: 0.8116 (t80) cc_final: 0.7517 (m-80) outliers start: 46 outliers final: 19 residues processed: 193 average time/residue: 0.1827 time to fit residues: 47.4687 Evaluate side-chains 165 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN A 900 HIS B 477 GLN B 572 ASN B 763 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7694 Z= 0.200 Angle : 0.794 10.993 10456 Z= 0.379 Chirality : 0.045 0.203 1260 Planarity : 0.005 0.053 1260 Dihedral : 5.361 21.066 1002 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 5.54 % Allowed : 18.60 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 938 helix: -0.19 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -3.05 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.002 0.001 HIS B 807 PHE 0.029 0.002 PHE A 848 TYR 0.015 0.001 TYR A 897 ARG 0.006 0.001 ARG A 899 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: A 430 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 454 MET cc_start: 0.4229 (mmm) cc_final: 0.3461 (tpt) REVERT: A 510 ARG cc_start: 0.8446 (mtp180) cc_final: 0.8008 (ttt-90) REVERT: A 532 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7599 (pp) REVERT: A 542 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: A 699 ASP cc_start: 0.8571 (t0) cc_final: 0.8257 (t0) REVERT: A 749 ILE cc_start: 0.8801 (mt) cc_final: 0.8575 (tt) REVERT: A 753 MET cc_start: 0.8311 (mtp) cc_final: 0.7999 (mtp) REVERT: A 756 GLN cc_start: 0.8201 (mp10) cc_final: 0.7519 (mp10) REVERT: A 911 PHE cc_start: 0.8129 (t80) cc_final: 0.7516 (m-80) REVERT: B 413 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: B 430 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8164 (tp) REVERT: B 454 MET cc_start: 0.4199 (mmm) cc_final: 0.3448 (tpt) REVERT: B 510 ARG cc_start: 0.8436 (mtp180) cc_final: 0.8001 (ttt-90) REVERT: B 699 ASP cc_start: 0.8465 (t0) cc_final: 0.8060 (t0) REVERT: B 753 MET cc_start: 0.8488 (mtp) cc_final: 0.8130 (mtp) REVERT: B 754 ASP cc_start: 0.9078 (t0) cc_final: 0.8821 (t0) REVERT: B 756 GLN cc_start: 0.8525 (mp10) cc_final: 0.7649 (mp10) REVERT: B 757 ILE cc_start: 0.8853 (pp) cc_final: 0.8620 (pp) REVERT: B 911 PHE cc_start: 0.8108 (t80) cc_final: 0.7490 (m-80) REVERT: B 930 ILE cc_start: 0.8742 (pt) cc_final: 0.8450 (mp) outliers start: 45 outliers final: 24 residues processed: 181 average time/residue: 0.1596 time to fit residues: 40.7610 Evaluate side-chains 168 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 0.0470 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7694 Z= 0.187 Angle : 0.782 13.493 10456 Z= 0.371 Chirality : 0.045 0.176 1260 Planarity : 0.005 0.051 1260 Dihedral : 5.315 20.543 1002 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 5.17 % Allowed : 20.20 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.28), residues: 938 helix: -0.04 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -2.98 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 516 HIS 0.002 0.001 HIS A 807 PHE 0.028 0.002 PHE B 848 TYR 0.010 0.001 TYR A 867 ARG 0.004 0.000 ARG A 899 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 147 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: A 430 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8155 (tp) REVERT: A 454 MET cc_start: 0.4066 (mmm) cc_final: 0.3378 (tpt) REVERT: A 510 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8040 (ttt-90) REVERT: A 542 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: A 753 MET cc_start: 0.8340 (mtp) cc_final: 0.8052 (mtp) REVERT: A 911 PHE cc_start: 0.8188 (t80) cc_final: 0.7555 (m-80) REVERT: A 930 ILE cc_start: 0.8722 (pt) cc_final: 0.8444 (mp) REVERT: B 413 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 430 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 454 MET cc_start: 0.4062 (mmm) cc_final: 0.3369 (tpt) REVERT: B 493 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7581 (mmp-170) REVERT: B 510 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7979 (ttt-90) REVERT: B 699 ASP cc_start: 0.8461 (t0) cc_final: 0.8070 (t0) REVERT: B 753 MET cc_start: 0.8495 (mtp) cc_final: 0.8149 (mtp) REVERT: B 754 ASP cc_start: 0.9073 (t0) cc_final: 0.8870 (t0) REVERT: B 756 GLN cc_start: 0.8497 (mp10) cc_final: 0.7659 (mp10) REVERT: B 911 PHE cc_start: 0.8176 (t80) cc_final: 0.7541 (m-80) REVERT: B 930 ILE cc_start: 0.8755 (pt) cc_final: 0.8486 (mp) outliers start: 42 outliers final: 27 residues processed: 178 average time/residue: 0.1801 time to fit residues: 43.7247 Evaluate side-chains 168 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 572 ASN B 572 ASN B 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7694 Z= 0.205 Angle : 0.810 12.281 10456 Z= 0.383 Chirality : 0.045 0.177 1260 Planarity : 0.005 0.051 1260 Dihedral : 5.272 20.880 1002 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 5.05 % Allowed : 20.81 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.28), residues: 938 helix: 0.03 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -3.00 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 516 HIS 0.002 0.001 HIS A 807 PHE 0.030 0.002 PHE B 957 TYR 0.009 0.001 TYR A 867 ARG 0.021 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: A 430 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.7993 (tp) REVERT: A 454 MET cc_start: 0.4167 (mmm) cc_final: 0.3414 (tpt) REVERT: A 510 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8028 (ttt-90) REVERT: A 542 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: A 753 MET cc_start: 0.8315 (mtp) cc_final: 0.8112 (mtp) REVERT: A 911 PHE cc_start: 0.8215 (t80) cc_final: 0.7574 (m-80) REVERT: A 930 ILE cc_start: 0.8734 (pt) cc_final: 0.8493 (mp) REVERT: B 413 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: B 430 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 454 MET cc_start: 0.4168 (mmm) cc_final: 0.3400 (tpt) REVERT: B 510 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7994 (ttt-90) REVERT: B 699 ASP cc_start: 0.8461 (t0) cc_final: 0.8082 (t0) REVERT: B 753 MET cc_start: 0.8416 (mtp) cc_final: 0.8173 (mtp) REVERT: B 756 GLN cc_start: 0.8259 (mp10) cc_final: 0.7466 (mp10) REVERT: B 911 PHE cc_start: 0.8078 (t80) cc_final: 0.7450 (m-80) REVERT: B 930 ILE cc_start: 0.8755 (pt) cc_final: 0.8491 (mp) outliers start: 41 outliers final: 26 residues processed: 177 average time/residue: 0.1537 time to fit residues: 38.5946 Evaluate side-chains 166 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 958 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 25 optimal weight: 0.0270 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7694 Z= 0.186 Angle : 0.792 11.445 10456 Z= 0.376 Chirality : 0.044 0.158 1260 Planarity : 0.005 0.067 1260 Dihedral : 5.142 20.424 1002 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 4.19 % Allowed : 22.41 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.28), residues: 938 helix: 0.17 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.03 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 516 HIS 0.002 0.001 HIS A 807 PHE 0.024 0.002 PHE A 957 TYR 0.011 0.001 TYR A 867 ARG 0.014 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: A 430 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 454 MET cc_start: 0.4209 (mmm) cc_final: 0.3589 (tpt) REVERT: A 510 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8026 (ttt-90) REVERT: A 532 LEU cc_start: 0.7792 (pt) cc_final: 0.7525 (pp) REVERT: A 911 PHE cc_start: 0.8147 (t80) cc_final: 0.7497 (m-80) REVERT: A 930 ILE cc_start: 0.8711 (pt) cc_final: 0.8470 (mp) REVERT: B 413 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7436 (m-80) REVERT: B 430 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.7944 (tp) REVERT: B 454 MET cc_start: 0.4210 (mmm) cc_final: 0.3569 (tpt) REVERT: B 493 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7480 (mmp-170) REVERT: B 510 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7942 (ttt-90) REVERT: B 699 ASP cc_start: 0.8542 (t0) cc_final: 0.8203 (t0) REVERT: B 753 MET cc_start: 0.8466 (mtp) cc_final: 0.8203 (mtp) REVERT: B 756 GLN cc_start: 0.8274 (mp10) cc_final: 0.7490 (mp10) REVERT: B 911 PHE cc_start: 0.8052 (t80) cc_final: 0.7438 (m-80) outliers start: 34 outliers final: 23 residues processed: 173 average time/residue: 0.1584 time to fit residues: 38.3778 Evaluate side-chains 166 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 572 ASN A 763 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.235 7694 Z= 0.393 Angle : 1.106 59.173 10456 Z= 0.598 Chirality : 0.050 0.456 1260 Planarity : 0.006 0.082 1260 Dihedral : 5.194 20.413 1002 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 3.94 % Allowed : 23.15 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 938 helix: 0.18 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.01 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 516 HIS 0.002 0.001 HIS A 807 PHE 0.021 0.002 PHE B 848 TYR 0.018 0.001 TYR A 775 ARG 0.024 0.001 ARG A 899 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 430 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.7907 (tp) REVERT: A 454 MET cc_start: 0.4218 (mmm) cc_final: 0.3585 (tpt) REVERT: A 510 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8019 (ttt-90) REVERT: A 532 LEU cc_start: 0.7774 (pt) cc_final: 0.7528 (pp) REVERT: A 572 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.6505 (p0) REVERT: A 675 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: A 911 PHE cc_start: 0.8182 (t80) cc_final: 0.7542 (m-80) REVERT: A 930 ILE cc_start: 0.8735 (pt) cc_final: 0.8486 (mp) REVERT: B 413 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 430 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.7942 (tp) REVERT: B 454 MET cc_start: 0.4205 (mmm) cc_final: 0.3566 (tpt) REVERT: B 493 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7480 (mmp-170) REVERT: B 510 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7933 (ttt-90) REVERT: B 699 ASP cc_start: 0.8518 (t0) cc_final: 0.8204 (t0) REVERT: B 753 MET cc_start: 0.8474 (mtp) cc_final: 0.8161 (mtp) REVERT: B 756 GLN cc_start: 0.8372 (mp10) cc_final: 0.7616 (mp10) REVERT: B 911 PHE cc_start: 0.8055 (t80) cc_final: 0.7430 (m-80) outliers start: 32 outliers final: 24 residues processed: 162 average time/residue: 0.1630 time to fit residues: 37.1356 Evaluate side-chains 167 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 516 TRP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** 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 = 0.3688 r_free = 0.3688 target = 0.124545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099607 restraints weight = 14786.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101549 restraints weight = 10459.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102671 restraints weight = 8355.551| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.522 7694 Z= 0.730 Angle : 1.017 44.139 10456 Z= 0.633 Chirality : 0.050 0.455 1260 Planarity : 0.008 0.185 1260 Dihedral : 5.193 20.413 1002 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 3.69 % Allowed : 23.52 % Favored : 72.78 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 938 helix: 0.18 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -3.01 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 516 HIS 0.002 0.001 HIS A 807 PHE 0.021 0.002 PHE B 848 TYR 0.018 0.001 TYR A 775 ARG 0.024 0.001 ARG A 899 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.01 seconds wall clock time: 30 minutes 2.73 seconds (1802.73 seconds total)