Starting phenix.real_space_refine on Mon Mar 11 07:06:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/03_2024/6caa_7441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/03_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_7441/03_2024/6caa_7441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/03_2024/6caa_7441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/03_2024/6caa_7441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caa_7441/03_2024/6caa_7441.pdb" } 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 Residue "A ARG 493": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7508 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "B" 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 Time building chain proxies: 4.37, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 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: 0.81 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: 1.91 Time building geometry restraints manager: 2.93 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: 98.65 - 106.44: 218 106.44 - 114.23: 4446 114.23 - 122.01: 4530 122.01 - 129.80: 1202 129.80 - 137.59: 60 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 2.440 nonbonded pdb=" O GLN B 424 " pdb=" OG SER B 427 " model vdw 2.280 2.440 nonbonded pdb=" O ILE A 922 " pdb=" OG SER A 925 " model vdw 2.311 2.440 ... (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 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.010 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.390 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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 : 0.808 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: 0.2218 time to fit residues: 66.4303 Evaluate side-chains 131 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 763 ASN A 767 HIS B 572 ASN B 763 ASN B 767 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3148 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= 0.205 Angle : 0.791 9.428 10456 Z= 0.398 Chirality : 0.045 0.186 1260 Planarity : 0.006 0.061 1260 Dihedral : 6.528 22.695 1002 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 3.69 % Allowed : 14.53 % Favored : 81.77 % 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: -4.16 (0.23), residues: 938 helix: -2.07 (0.17), residues: 586 sheet: None (None), residues: 0 loop : -3.88 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 512 HIS 0.004 0.001 HIS A 900 PHE 0.015 0.002 PHE B 531 TYR 0.036 0.002 TYR B 577 ARG 0.003 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 192 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.849 Fit side-chains REVERT: A 413 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 430 LEU cc_start: 0.8840 (pp) cc_final: 0.8348 (tp) REVERT: A 454 MET cc_start: 0.4399 (mmm) cc_final: 0.3828 (tpt) REVERT: A 699 ASP cc_start: 0.8522 (t0) cc_final: 0.8205 (t0) REVERT: A 754 ASP cc_start: 0.8889 (t0) cc_final: 0.8657 (t0) REVERT: A 808 ILE cc_start: 0.9201 (pt) cc_final: 0.8961 (tp) REVERT: A 874 ASN cc_start: 0.8050 (t0) cc_final: 0.7821 (t0) REVERT: A 924 LYS cc_start: 0.8482 (tppp) cc_final: 0.8057 (tptt) REVERT: B 413 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: B 430 LEU cc_start: 0.8848 (pp) cc_final: 0.8393 (tp) REVERT: B 454 MET cc_start: 0.4534 (mmm) cc_final: 0.4020 (tpt) REVERT: B 699 ASP cc_start: 0.8513 (t0) cc_final: 0.8181 (t0) REVERT: B 754 ASP cc_start: 0.8924 (t0) cc_final: 0.8651 (t0) REVERT: B 808 ILE cc_start: 0.9187 (pt) cc_final: 0.8977 (tp) REVERT: B 924 LYS cc_start: 0.8529 (tppp) cc_final: 0.8078 (tptt) outliers start: 30 outliers final: 14 residues processed: 184 average time/residue: 0.1765 time to fit residues: 44.5421 Evaluate side-chains 155 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 742 ILE Chi-restraints excluded: chain A residue 763 ASN 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 763 ASN 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: 9.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.0070 chunk 92 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 B 422 ASN B 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7694 Z= 0.178 Angle : 0.753 11.737 10456 Z= 0.367 Chirality : 0.043 0.174 1260 Planarity : 0.005 0.056 1260 Dihedral : 5.966 20.390 1002 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 4.56 % Allowed : 14.90 % Favored : 80.54 % 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: -2.94 (0.25), residues: 938 helix: -0.98 (0.20), residues: 590 sheet: None (None), residues: 0 loop : -3.66 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 516 HIS 0.004 0.001 HIS A 900 PHE 0.039 0.002 PHE A 848 TYR 0.011 0.001 TYR B 867 ARG 0.002 0.000 ARG A 899 *********************** 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 194 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: A 430 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8357 (tp) REVERT: A 454 MET cc_start: 0.4433 (mmm) cc_final: 0.3965 (tpt) REVERT: B 413 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 430 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 454 MET cc_start: 0.4198 (mmm) cc_final: 0.3777 (tpt) REVERT: B 754 ASP cc_start: 0.8884 (t0) cc_final: 0.8510 (t0) REVERT: B 873 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.9003 (pp) outliers start: 37 outliers final: 13 residues processed: 187 average time/residue: 0.1506 time to fit residues: 40.1325 Evaluate side-chains 154 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 537 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7694 Z= 0.228 Angle : 0.784 13.382 10456 Z= 0.381 Chirality : 0.045 0.171 1260 Planarity : 0.005 0.057 1260 Dihedral : 5.814 22.181 1002 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.79 % Allowed : 17.36 % 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: -2.37 (0.26), residues: 938 helix: -0.50 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -3.51 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 516 HIS 0.009 0.001 HIS A 900 PHE 0.039 0.002 PHE A 848 TYR 0.021 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 197 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 150 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.7227 (mmtt) cc_final: 0.6938 (mmtm) REVERT: A 413 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: A 430 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 454 MET cc_start: 0.4306 (mmm) cc_final: 0.3579 (tpt) REVERT: A 699 ASP cc_start: 0.8605 (t0) cc_final: 0.8286 (t0) REVERT: A 738 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7527 (mm) REVERT: B 413 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 430 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8262 (tp) REVERT: B 454 MET cc_start: 0.4175 (mmm) cc_final: 0.3419 (tpt) REVERT: B 699 ASP cc_start: 0.8579 (t0) cc_final: 0.8256 (t0) REVERT: B 738 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7392 (mm) REVERT: B 754 ASP cc_start: 0.8953 (t0) cc_final: 0.8648 (t0) REVERT: B 899 ARG cc_start: 0.7262 (mtp85) cc_final: 0.6980 (mtp85) REVERT: B 911 PHE cc_start: 0.8158 (t80) cc_final: 0.7713 (m-80) outliers start: 47 outliers final: 20 residues processed: 187 average time/residue: 0.1521 time to fit residues: 40.4862 Evaluate side-chains 157 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 432 ILE Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 ILE 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 B residue 413 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 432 ILE 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 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE 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: 0.9980 chunk 1 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4560 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= 0.180 Angle : 0.747 10.298 10456 Z= 0.361 Chirality : 0.043 0.162 1260 Planarity : 0.005 0.052 1260 Dihedral : 5.479 20.677 1002 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 4.68 % Allowed : 18.97 % Favored : 76.35 % 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: -1.95 (0.27), residues: 938 helix: -0.14 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -3.37 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 516 HIS 0.004 0.001 HIS B 900 PHE 0.056 0.002 PHE A 848 TYR 0.016 0.001 TYR A 897 ARG 0.004 0.000 ARG A 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 195 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6695 (mmtm) REVERT: A 413 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: A 430 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8151 (tp) REVERT: A 454 MET cc_start: 0.3998 (mmm) cc_final: 0.3398 (tpt) REVERT: A 510 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8077 (ttt-90) REVERT: A 542 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 911 PHE cc_start: 0.8204 (t80) cc_final: 0.7609 (m-80) REVERT: B 413 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: B 430 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 454 MET cc_start: 0.3972 (mmm) cc_final: 0.3382 (tpt) REVERT: B 493 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7483 (mmp-170) REVERT: B 510 ARG cc_start: 0.8401 (mtp180) cc_final: 0.7986 (ttt-90) REVERT: B 699 ASP cc_start: 0.8560 (t0) cc_final: 0.8348 (t0) REVERT: B 830 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8138 (mmt180) REVERT: B 899 ARG cc_start: 0.7103 (mtp85) cc_final: 0.6697 (mtp85) REVERT: B 911 PHE cc_start: 0.8102 (t80) cc_final: 0.7507 (m-80) outliers start: 38 outliers final: 23 residues processed: 183 average time/residue: 0.1863 time to fit residues: 46.3332 Evaluate side-chains 159 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 804 SER 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 915 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 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 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 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: 4.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 0.0040 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7694 Z= 0.186 Angle : 0.766 10.370 10456 Z= 0.365 Chirality : 0.044 0.204 1260 Planarity : 0.005 0.051 1260 Dihedral : 5.364 20.947 1002 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 6.16 % Allowed : 20.07 % Favored : 73.77 % 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: -1.73 (0.27), residues: 938 helix: 0.03 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -3.29 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.003 0.001 HIS B 900 PHE 0.028 0.002 PHE A 848 TYR 0.013 0.001 TYR A 797 ARG 0.004 0.000 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 197 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6957 (mmtt) cc_final: 0.6646 (mmtm) REVERT: A 413 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: A 430 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8052 (tp) REVERT: A 454 MET cc_start: 0.4059 (mmm) cc_final: 0.3515 (tpt) REVERT: A 510 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7984 (ttt-90) REVERT: A 560 MET cc_start: 0.9090 (mtp) cc_final: 0.8819 (mtm) REVERT: A 764 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7999 (mmm-85) REVERT: A 911 PHE cc_start: 0.8167 (t80) cc_final: 0.7547 (m-80) REVERT: A 930 ILE cc_start: 0.8753 (pt) cc_final: 0.8538 (mp) REVERT: B 413 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: B 430 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8173 (tp) REVERT: B 454 MET cc_start: 0.3922 (mmm) cc_final: 0.3464 (tpt) REVERT: B 510 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8075 (ttt-90) REVERT: B 738 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 764 ARG cc_start: 0.8357 (mmt180) cc_final: 0.8060 (mmm-85) REVERT: B 899 ARG cc_start: 0.7047 (mtp85) cc_final: 0.6519 (mtp85) REVERT: B 911 PHE cc_start: 0.8128 (t80) cc_final: 0.7501 (m-80) outliers start: 50 outliers final: 28 residues processed: 182 average time/residue: 0.1629 time to fit residues: 41.6194 Evaluate side-chains 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 804 SER 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 894 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 915 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 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 894 ASP 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: 3.9990 chunk 51 optimal weight: 0.0010 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.0060 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5117 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= 0.172 Angle : 0.749 11.708 10456 Z= 0.357 Chirality : 0.043 0.158 1260 Planarity : 0.005 0.048 1260 Dihedral : 5.166 19.949 1002 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 5.79 % Allowed : 20.69 % Favored : 73.52 % 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: -1.39 (0.28), residues: 938 helix: 0.33 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -3.15 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.003 0.001 HIS B 900 PHE 0.028 0.002 PHE A 848 TYR 0.011 0.001 TYR A 867 ARG 0.001 0.000 ARG B 830 *********************** 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 203 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 156 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6587 (mmtm) REVERT: A 413 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 430 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8036 (tp) REVERT: A 454 MET cc_start: 0.3987 (mmm) cc_final: 0.3466 (tpt) REVERT: A 510 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8048 (ttt-90) REVERT: A 560 MET cc_start: 0.9071 (mtp) cc_final: 0.8859 (mtm) REVERT: A 858 MET cc_start: 0.8759 (mmm) cc_final: 0.8509 (mmt) REVERT: A 911 PHE cc_start: 0.8155 (t80) cc_final: 0.7550 (m-80) REVERT: A 930 ILE cc_start: 0.8789 (pt) cc_final: 0.8536 (mp) REVERT: B 413 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 430 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 454 MET cc_start: 0.3962 (mmm) cc_final: 0.3453 (tpt) REVERT: B 510 ARG cc_start: 0.8320 (mtp180) cc_final: 0.8048 (ttt-90) REVERT: B 540 THR cc_start: 0.7810 (m) cc_final: 0.7486 (p) REVERT: B 738 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7102 (mm) REVERT: B 764 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7893 (mmm-85) REVERT: B 858 MET cc_start: 0.8753 (mmm) cc_final: 0.8502 (mmt) REVERT: B 899 ARG cc_start: 0.6928 (mtp85) cc_final: 0.6412 (mtp85) REVERT: B 911 PHE cc_start: 0.8088 (t80) cc_final: 0.7493 (m-80) outliers start: 47 outliers final: 29 residues processed: 191 average time/residue: 0.1659 time to fit residues: 44.2906 Evaluate side-chains 167 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 649 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 915 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 572 ASN Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 894 ASP 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: 2.9990 chunk 57 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7694 Z= 0.185 Angle : 0.764 12.863 10456 Z= 0.362 Chirality : 0.044 0.215 1260 Planarity : 0.005 0.049 1260 Dihedral : 5.088 19.143 1002 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 5.42 % Allowed : 20.94 % Favored : 73.65 % 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: -1.27 (0.28), residues: 938 helix: 0.33 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 344 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 0.028 0.002 PHE A 498 TYR 0.010 0.001 TYR B 867 ARG 0.002 0.000 ARG B 538 *********************** 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 181 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6581 (mmtm) REVERT: A 413 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: A 430 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.7930 (tp) REVERT: A 454 MET cc_start: 0.3938 (mmm) cc_final: 0.3416 (tpt) REVERT: A 510 ARG cc_start: 0.8402 (mtp180) cc_final: 0.8000 (ttt-90) REVERT: A 858 MET cc_start: 0.8763 (mmm) cc_final: 0.8493 (mmt) REVERT: A 911 PHE cc_start: 0.8151 (t80) cc_final: 0.7539 (m-80) REVERT: B 413 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: B 430 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 454 MET cc_start: 0.3920 (mmm) cc_final: 0.3407 (tpt) REVERT: B 510 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8024 (ttt-90) REVERT: B 699 ASP cc_start: 0.8477 (t0) cc_final: 0.8152 (t0) REVERT: B 738 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7089 (mm) REVERT: B 764 ARG cc_start: 0.8198 (mmt180) cc_final: 0.7928 (mmm-85) REVERT: B 858 MET cc_start: 0.8779 (mmm) cc_final: 0.8487 (mmt) REVERT: B 899 ARG cc_start: 0.6649 (mtp85) cc_final: 0.6038 (mtp85) REVERT: B 911 PHE cc_start: 0.8111 (t80) cc_final: 0.7495 (m-80) outliers start: 44 outliers final: 33 residues processed: 172 average time/residue: 0.1651 time to fit residues: 39.7434 Evaluate side-chains 169 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 480 THR 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 804 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 915 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 480 THR 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 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 949 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 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 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7694 Z= 0.194 Angle : 0.776 12.532 10456 Z= 0.362 Chirality : 0.045 0.230 1260 Planarity : 0.004 0.047 1260 Dihedral : 5.030 19.094 1002 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 5.30 % Allowed : 21.55 % Favored : 73.15 % 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: -1.16 (0.28), residues: 938 helix: 0.40 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -2.95 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.004 0.001 HIS B 900 PHE 0.022 0.002 PHE A 848 TYR 0.009 0.001 TYR B 867 ARG 0.002 0.000 ARG B 899 *********************** 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 181 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6839 (mmtt) cc_final: 0.6553 (mmtm) REVERT: A 413 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: A 430 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.7905 (tp) REVERT: A 454 MET cc_start: 0.3893 (mmm) cc_final: 0.3410 (tpt) REVERT: A 510 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8088 (ttt-90) REVERT: A 699 ASP cc_start: 0.8483 (t0) cc_final: 0.8241 (t0) REVERT: A 858 MET cc_start: 0.8780 (mmm) cc_final: 0.8495 (mmt) REVERT: A 911 PHE cc_start: 0.8060 (t80) cc_final: 0.7425 (m-80) REVERT: B 413 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 430 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8102 (tp) REVERT: B 454 MET cc_start: 0.4133 (mmm) cc_final: 0.3567 (tpt) REVERT: B 510 ARG cc_start: 0.8349 (mtp180) cc_final: 0.8019 (ttt-90) REVERT: B 541 GLU cc_start: 0.8553 (pm20) cc_final: 0.8330 (pm20) REVERT: B 699 ASP cc_start: 0.8510 (t0) cc_final: 0.8183 (t0) REVERT: B 738 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7137 (mm) REVERT: B 764 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7967 (mmm-85) REVERT: B 858 MET cc_start: 0.8789 (mmm) cc_final: 0.8513 (mmt) REVERT: B 911 PHE cc_start: 0.8128 (t80) cc_final: 0.7501 (m-80) outliers start: 43 outliers final: 32 residues processed: 173 average time/residue: 0.1741 time to fit residues: 42.6624 Evaluate side-chains 170 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 480 THR 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 804 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 915 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 480 THR 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 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 894 ASP 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: 6.9990 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7694 Z= 0.201 Angle : 0.763 11.442 10456 Z= 0.363 Chirality : 0.045 0.240 1260 Planarity : 0.005 0.047 1260 Dihedral : 5.028 19.055 1002 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 4.68 % Allowed : 22.54 % Favored : 72.78 % 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: -1.13 (0.28), residues: 938 helix: 0.43 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.95 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.004 0.001 HIS B 900 PHE 0.023 0.002 PHE A 957 TYR 0.008 0.001 TYR B 867 ARG 0.002 0.000 ARG B 905 ********************** 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 175 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 LYS cc_start: 0.6869 (mmtt) cc_final: 0.6575 (mmtm) REVERT: A 413 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: A 430 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.7961 (tp) REVERT: A 454 MET cc_start: 0.4151 (mmm) cc_final: 0.3582 (tpt) REVERT: A 493 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7548 (mmp-170) REVERT: A 510 ARG cc_start: 0.8437 (mtp180) cc_final: 0.8105 (ttt-90) REVERT: A 699 ASP cc_start: 0.8419 (t0) cc_final: 0.8179 (t0) REVERT: A 858 MET cc_start: 0.8792 (mmm) cc_final: 0.8479 (mmt) REVERT: A 911 PHE cc_start: 0.8175 (t80) cc_final: 0.7553 (m-80) REVERT: B 413 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: B 430 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 454 MET cc_start: 0.4139 (mmm) cc_final: 0.3574 (tpt) REVERT: B 510 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8003 (ttt-90) REVERT: B 532 LEU cc_start: 0.7908 (pt) cc_final: 0.7675 (pp) REVERT: B 699 ASP cc_start: 0.8523 (t0) cc_final: 0.8190 (t0) REVERT: B 738 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 858 MET cc_start: 0.8794 (mmm) cc_final: 0.8505 (mmt) REVERT: B 911 PHE cc_start: 0.8135 (t80) cc_final: 0.7523 (m-80) outliers start: 38 outliers final: 31 residues processed: 167 average time/residue: 0.1639 time to fit residues: 38.3174 Evaluate side-chains 169 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 480 THR Chi-restraints excluded: chain A residue 516 TRP Chi-restraints excluded: chain A residue 537 THR 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 804 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 865 PHE Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 915 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 480 THR 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 738 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 801 THR Chi-restraints excluded: chain B residue 804 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 894 ASP 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: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.0000 chunk 65 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094066 restraints weight = 14990.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096083 restraints weight = 10216.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097479 restraints weight = 7983.336| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7694 Z= 0.243 Angle : 0.794 10.459 10456 Z= 0.382 Chirality : 0.046 0.221 1260 Planarity : 0.005 0.047 1260 Dihedral : 5.212 20.562 1002 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 5.05 % Allowed : 22.66 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.28), residues: 938 helix: 0.35 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.90 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 516 HIS 0.005 0.001 HIS B 900 PHE 0.019 0.002 PHE A 848 TYR 0.008 0.001 TYR A 567 ARG 0.002 0.001 ARG B 830 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.82 seconds wall clock time: 31 minutes 27.19 seconds (1887.19 seconds total)