Starting phenix.real_space_refine on Thu Feb 5 14:04:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8n_63715/02_2026/9m8n_63715.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.063 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 128 5.16 5 C 11568 2.51 5 N 2916 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17620 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4405 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 532} Chain breaks: 5 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 27 Restraints were copied for chains: B, C, D Time building chain proxies: 3.71, per 1000 atoms: 0.21 Number of scatterers: 17620 At special positions: 0 Unit cell: (111.28, 111.28, 138.32, 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 128 16.00 O 3008 8.00 N 2916 7.00 C 11568 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: 1.54 Conformation dependent library (CDL) restraints added in 758.0 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 77.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.803A pdb=" N TRP A 515 " --> pdb=" O HIS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.504A pdb=" N MET A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.594A pdb=" N MET A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.372A pdb=" N PHE A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.776A pdb=" N MET A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 714 through 740 removed outlier: 3.910A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 768 through 790 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 854 removed outlier: 4.080A pdb=" N GLU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 892 removed outlier: 3.976A pdb=" N GLU A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 865 " --> pdb=" O VAL A 861 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.621A pdb=" N PHE A 898 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 914 Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.788A pdb=" N SER A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.761A pdb=" N TYR A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 927 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 928' Processing helix chain 'A' and resid 933 through 946 Processing helix chain 'A' and resid 947 through 989 removed outlier: 3.970A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.304A pdb=" N LEU A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 3.667A pdb=" N LYS A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.803A pdb=" N TRP B 515 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.504A pdb=" N MET B 523 " --> pdb=" O HIS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.594A pdb=" N MET B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 590 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 604 through 612 removed outlier: 4.373A pdb=" N PHE B 612 " --> pdb=" O CYS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.776A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 Processing helix chain 'B' and resid 714 through 740 removed outlier: 3.910A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 768 through 790 Processing helix chain 'B' and resid 803 through 820 Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 854 removed outlier: 4.081A pdb=" N GLU B 854 " --> pdb=" O LEU B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 892 removed outlier: 3.976A pdb=" N GLU B 864 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 865 " --> pdb=" O VAL B 861 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.620A pdb=" N PHE B 898 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 914 Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.788A pdb=" N SER B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 928 removed outlier: 3.760A pdb=" N TYR B 926 " --> pdb=" O PHE B 922 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 928 " --> pdb=" O GLU B 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 922 through 928' Processing helix chain 'B' and resid 933 through 946 Processing helix chain 'B' and resid 947 through 989 removed outlier: 3.969A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 4.304A pdb=" N LEU B 995 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 3.668A pdb=" N LYS B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.802A pdb=" N TRP C 515 " --> pdb=" O HIS C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.504A pdb=" N MET C 523 " --> pdb=" O HIS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.595A pdb=" N MET C 530 " --> pdb=" O TYR C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 590 Processing helix chain 'C' and resid 593 through 602 Processing helix chain 'C' and resid 604 through 612 removed outlier: 4.373A pdb=" N PHE C 612 " --> pdb=" O CYS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.776A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 714 through 740 removed outlier: 3.910A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 768 through 790 Processing helix chain 'C' and resid 803 through 820 Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 854 removed outlier: 4.081A pdb=" N GLU C 854 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 892 removed outlier: 3.976A pdb=" N GLU C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL C 865 " --> pdb=" O VAL C 861 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.621A pdb=" N PHE C 898 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 914 Processing helix chain 'C' and resid 917 through 922 removed outlier: 3.787A pdb=" N SER C 921 " --> pdb=" O ASN C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 928 removed outlier: 3.761A pdb=" N TYR C 926 " --> pdb=" O PHE C 922 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 927 " --> pdb=" O LEU C 923 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 928 " --> pdb=" O GLU C 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 922 through 928' Processing helix chain 'C' and resid 933 through 946 Processing helix chain 'C' and resid 947 through 989 removed outlier: 3.969A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA C 977 " --> pdb=" O LEU C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 removed outlier: 4.304A pdb=" N LEU C 995 " --> pdb=" O PRO C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 3.668A pdb=" N LYS C1071 " --> pdb=" O LEU C1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.803A pdb=" N TRP D 515 " --> pdb=" O HIS D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.504A pdb=" N MET D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.594A pdb=" N MET D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 590 Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 604 through 612 removed outlier: 4.373A pdb=" N PHE D 612 " --> pdb=" O CYS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.776A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 691 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 Processing helix chain 'D' and resid 714 through 740 removed outlier: 3.910A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 768 through 790 Processing helix chain 'D' and resid 803 through 820 Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 854 removed outlier: 4.080A pdb=" N GLU D 854 " --> pdb=" O LEU D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 892 removed outlier: 3.975A pdb=" N GLU D 864 " --> pdb=" O ILE D 860 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL D 865 " --> pdb=" O VAL D 861 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 878 " --> pdb=" O THR D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.620A pdb=" N PHE D 898 " --> pdb=" O GLN D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 914 Processing helix chain 'D' and resid 917 through 922 removed outlier: 3.788A pdb=" N SER D 921 " --> pdb=" O ASN D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 928 removed outlier: 3.760A pdb=" N TYR D 926 " --> pdb=" O PHE D 922 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 927 " --> pdb=" O LEU D 923 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 928 " --> pdb=" O GLU D 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 922 through 928' Processing helix chain 'D' and resid 933 through 946 Processing helix chain 'D' and resid 947 through 989 removed outlier: 3.970A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALA D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 4.304A pdb=" N LEU D 995 " --> pdb=" O PRO D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 3.667A pdb=" N LYS D1071 " --> pdb=" O LEU D1067 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 643 removed outlier: 3.872A pdb=" N ILE A 656 " --> pdb=" O VAL A1005 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A1003 " --> pdb=" O TYR A 658 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 642 through 643 removed outlier: 3.872A pdb=" N ILE B 656 " --> pdb=" O VAL B1005 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B1003 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 642 through 643 removed outlier: 3.872A pdb=" N ILE C 656 " --> pdb=" O VAL C1005 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C1003 " --> pdb=" O TYR C 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 642 through 643 removed outlier: 3.872A pdb=" N ILE D 656 " --> pdb=" O VAL D1005 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D1003 " --> pdb=" O TYR D 658 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5452 1.34 - 1.46: 4054 1.46 - 1.58: 8294 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18008 Sorted by residual: bond pdb=" CG1 ILE A1069 " pdb=" CD1 ILE A1069 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.91e+00 bond pdb=" CG1 ILE B1069 " pdb=" CD1 ILE B1069 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.90e+00 bond pdb=" CG1 ILE D1069 " pdb=" CD1 ILE D1069 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.85e+00 bond pdb=" CG1 ILE C1069 " pdb=" CD1 ILE C1069 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.83e+00 bond pdb=" C LEU B 820 " pdb=" N PRO B 821 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.77e+00 ... (remaining 18003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 23981 2.65 - 5.29: 331 5.29 - 7.94: 48 7.94 - 10.58: 10 10.58 - 13.23: 10 Bond angle restraints: 24380 Sorted by residual: angle pdb=" CA MET C 978 " pdb=" CB MET C 978 " pdb=" CG MET C 978 " ideal model delta sigma weight residual 114.10 121.73 -7.63 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA MET A 978 " pdb=" CB MET A 978 " pdb=" CG MET A 978 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA MET B 978 " pdb=" CB MET B 978 " pdb=" CG MET B 978 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA MET D 978 " pdb=" CB MET D 978 " pdb=" CG MET D 978 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA LEU B 982 " pdb=" CB LEU B 982 " pdb=" CG LEU B 982 " ideal model delta sigma weight residual 116.30 129.53 -13.23 3.50e+00 8.16e-02 1.43e+01 ... (remaining 24375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8943 17.87 - 35.74: 1340 35.74 - 53.61: 401 53.61 - 71.48: 56 71.48 - 89.35: 24 Dihedral angle restraints: 10764 sinusoidal: 4272 harmonic: 6492 Sorted by residual: dihedral pdb=" CA ARG B 464 " pdb=" C ARG B 464 " pdb=" N LEU B 465 " pdb=" CA LEU B 465 " ideal model delta harmonic sigma weight residual 180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG C 464 " pdb=" C ARG C 464 " pdb=" N LEU C 465 " pdb=" CA LEU C 465 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG D 464 " pdb=" C ARG D 464 " pdb=" N LEU D 465 " pdb=" CA LEU D 465 " ideal model delta harmonic sigma weight residual 180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 10761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1974 0.040 - 0.080: 643 0.080 - 0.120: 180 0.120 - 0.161: 43 0.161 - 0.201: 20 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CB THR C 984 " pdb=" CA THR C 984 " pdb=" OG1 THR C 984 " pdb=" CG2 THR C 984 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR B 984 " pdb=" CA THR B 984 " pdb=" OG1 THR B 984 " pdb=" CG2 THR B 984 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB THR A 984 " pdb=" CA THR A 984 " pdb=" OG1 THR A 984 " pdb=" CG2 THR A 984 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 2857 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " -0.020 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP A 605 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 605 " -0.019 2.00e-02 2.50e+03 1.65e-02 6.77e+00 pdb=" CG TRP C 605 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 605 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 605 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 605 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 605 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 605 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 605 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 605 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 605 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 605 " 0.020 2.00e-02 2.50e+03 1.65e-02 6.77e+00 pdb=" CG TRP D 605 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 605 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 605 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 605 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 605 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 605 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 605 " -0.000 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 10607 3.01 - 3.48: 19896 3.48 - 3.96: 27393 3.96 - 4.43: 32369 4.43 - 4.90: 47990 Nonbonded interactions: 138255 Sorted by model distance: nonbonded pdb=" N ASP D 542 " pdb=" OD1 ASP D 542 " model vdw 2.542 3.120 nonbonded pdb=" N ASP C 542 " pdb=" OD1 ASP C 542 " model vdw 2.542 3.120 nonbonded pdb=" N ASP B 542 " pdb=" OD1 ASP B 542 " model vdw 2.542 3.120 nonbonded pdb=" N ASP A 542 " pdb=" OD1 ASP A 542 " model vdw 2.542 3.120 nonbonded pdb=" N ASP B 606 " pdb=" OD1 ASP B 606 " model vdw 2.567 3.120 ... (remaining 138250 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.090 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.004 0.077 18008 Z= 0.184 Angle : 0.808 13.229 24380 Z= 0.397 Chirality : 0.046 0.201 2860 Planarity : 0.005 0.043 2984 Dihedral : 18.598 89.352 6540 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.86 % Allowed : 34.99 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2160 helix: 0.61 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 928 TYR 0.012 0.002 TYR D 889 PHE 0.021 0.002 PHE D 944 TRP 0.044 0.003 TRP A 605 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00426 (18008) covalent geometry : angle 0.80814 (24380) hydrogen bonds : bond 0.12293 ( 1141) hydrogen bonds : angle 5.56126 ( 3399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 376 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 LYS cc_start: 0.8080 (pttm) cc_final: 0.7634 (pttm) REVERT: A 597 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7920 (tt) REVERT: A 610 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8289 (tptp) REVERT: A 842 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7585 (t80) REVERT: A 1072 MET cc_start: 0.4401 (tpp) cc_final: 0.3684 (tpp) REVERT: B 531 LYS cc_start: 0.8007 (pttm) cc_final: 0.7541 (pttm) REVERT: B 543 ARG cc_start: 0.7396 (ptt180) cc_final: 0.6950 (ptt180) REVERT: B 610 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8298 (tptp) REVERT: B 842 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 1072 MET cc_start: 0.4406 (tpp) cc_final: 0.3605 (tpp) REVERT: C 531 LYS cc_start: 0.8011 (pttm) cc_final: 0.7541 (pttm) REVERT: C 543 ARG cc_start: 0.7449 (ptt180) cc_final: 0.7001 (ptt180) REVERT: C 610 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8297 (tptp) REVERT: C 842 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 1072 MET cc_start: 0.4396 (tpp) cc_final: 0.3594 (tpp) REVERT: D 531 LYS cc_start: 0.8081 (pttm) cc_final: 0.7633 (pttm) REVERT: D 610 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8290 (tptp) REVERT: D 842 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7576 (t80) REVERT: D 1072 MET cc_start: 0.4410 (tpp) cc_final: 0.3693 (tpp) outliers start: 112 outliers final: 92 residues processed: 453 average time/residue: 0.1105 time to fit residues: 79.4245 Evaluate side-chains 465 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 364 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 970 HIS Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 970 HIS Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1068 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 610 LYS Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 970 HIS Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1068 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 727 CYS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 970 HIS Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1068 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.0970 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 GLN ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN ** C1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN ** D1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.162993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144259 restraints weight = 35710.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146791 restraints weight = 23263.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.148658 restraints weight = 17353.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.149876 restraints weight = 14071.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150619 restraints weight = 12124.077| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18008 Z= 0.169 Angle : 0.688 10.471 24380 Z= 0.338 Chirality : 0.042 0.165 2860 Planarity : 0.004 0.047 2984 Dihedral : 9.390 56.448 2522 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.32 % Allowed : 30.44 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2160 helix: 0.67 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 928 TYR 0.012 0.001 TYR B 658 PHE 0.021 0.002 PHE D 944 TRP 0.019 0.002 TRP A 605 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00393 (18008) covalent geometry : angle 0.68808 (24380) hydrogen bonds : bond 0.04614 ( 1141) hydrogen bonds : angle 4.56973 ( 3399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 416 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8400 (tptp) REVERT: A 720 MET cc_start: 0.8299 (tpp) cc_final: 0.7686 (mmm) REVERT: A 842 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7605 (t80) REVERT: B 597 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7934 (tt) REVERT: B 610 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8394 (tptp) REVERT: B 720 MET cc_start: 0.8284 (tpp) cc_final: 0.7675 (mmm) REVERT: B 842 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7635 (t80) REVERT: C 597 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7948 (tt) REVERT: C 610 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8406 (tptp) REVERT: C 720 MET cc_start: 0.8293 (tpp) cc_final: 0.7682 (mmm) REVERT: C 842 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7626 (t80) REVERT: D 597 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (tt) REVERT: D 610 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8395 (tptp) REVERT: D 720 MET cc_start: 0.8293 (tpp) cc_final: 0.7681 (mmm) REVERT: D 842 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7608 (t80) REVERT: D 907 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7691 (tm130) outliers start: 159 outliers final: 88 residues processed: 531 average time/residue: 0.1137 time to fit residues: 95.1248 Evaluate side-chains 486 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 386 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 610 LYS Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 727 CYS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1045 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 211 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 200 optimal weight: 8.9990 chunk 64 optimal weight: 0.0470 chunk 60 optimal weight: 0.0470 chunk 149 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN A 855 ASN A1047 GLN A1070 GLN B 571 ASN B1047 GLN ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN C 855 ASN C1047 GLN C1070 GLN D 571 ASN D1047 GLN D1070 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148235 restraints weight = 36572.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.150977 restraints weight = 23614.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.152735 restraints weight = 17255.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154163 restraints weight = 13929.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154968 restraints weight = 11823.457| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18008 Z= 0.129 Angle : 0.690 11.894 24380 Z= 0.327 Chirality : 0.042 0.219 2860 Planarity : 0.004 0.050 2984 Dihedral : 7.902 56.839 2440 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.01 % Allowed : 32.37 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2160 helix: 0.71 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 928 TYR 0.013 0.001 TYR A1049 PHE 0.015 0.001 PHE C 909 TRP 0.011 0.001 TRP C 809 HIS 0.002 0.001 HIS C 560 Details of bonding type rmsd covalent geometry : bond 0.00283 (18008) covalent geometry : angle 0.68970 (24380) hydrogen bonds : bond 0.04332 ( 1141) hydrogen bonds : angle 4.33588 ( 3399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 428 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8177 (tptp) REVERT: A 720 MET cc_start: 0.8215 (tpp) cc_final: 0.7664 (mmm) REVERT: A 842 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7344 (t80) REVERT: B 528 GLN cc_start: 0.6921 (mp10) cc_final: 0.6698 (mp10) REVERT: B 610 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8210 (tptp) REVERT: B 720 MET cc_start: 0.8219 (tpp) cc_final: 0.7625 (mmm) REVERT: B 842 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7411 (t80) REVERT: C 528 GLN cc_start: 0.6937 (mp10) cc_final: 0.6709 (mp10) REVERT: C 610 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8235 (tptp) REVERT: C 720 MET cc_start: 0.8225 (tpp) cc_final: 0.7633 (mmm) REVERT: C 842 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7418 (t80) REVERT: D 543 ARG cc_start: 0.7194 (ptt180) cc_final: 0.6637 (ptt180) REVERT: D 610 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8176 (tptp) REVERT: D 720 MET cc_start: 0.8209 (tpp) cc_final: 0.7653 (mmm) REVERT: D 842 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7338 (t80) outliers start: 134 outliers final: 105 residues processed: 515 average time/residue: 0.1085 time to fit residues: 88.7591 Evaluate side-chains 509 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 396 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1070 GLN Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 727 CYS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 610 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1070 GLN Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 727 CYS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 837 ILE Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1070 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 3 optimal weight: 0.0020 chunk 112 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 855 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.165810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.147630 restraints weight = 36734.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.150297 restraints weight = 23687.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.152181 restraints weight = 17390.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153516 restraints weight = 13970.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154372 restraints weight = 11908.350| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18008 Z= 0.129 Angle : 0.671 11.582 24380 Z= 0.322 Chirality : 0.041 0.184 2860 Planarity : 0.004 0.051 2984 Dihedral : 7.758 59.936 2436 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.00 % Allowed : 32.74 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2160 helix: 0.73 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 928 TYR 0.010 0.001 TYR A 785 PHE 0.018 0.001 PHE A 452 TRP 0.018 0.001 TRP C 809 HIS 0.003 0.000 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00292 (18008) covalent geometry : angle 0.67093 (24380) hydrogen bonds : bond 0.04165 ( 1141) hydrogen bonds : angle 4.17470 ( 3399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 420 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 LYS cc_start: 0.8113 (pttm) cc_final: 0.7891 (pttm) REVERT: A 542 ASP cc_start: 0.7382 (p0) cc_final: 0.6955 (p0) REVERT: A 543 ARG cc_start: 0.7155 (ptt180) cc_final: 0.6461 (ptt180) REVERT: A 610 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8094 (tptp) REVERT: A 720 MET cc_start: 0.8218 (tpp) cc_final: 0.7632 (mmm) REVERT: A 842 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 542 ASP cc_start: 0.7377 (p0) cc_final: 0.6935 (p0) REVERT: B 597 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7825 (tt) REVERT: B 610 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8087 (tptp) REVERT: B 720 MET cc_start: 0.8208 (tpp) cc_final: 0.7627 (mmm) REVERT: B 842 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 953 MET cc_start: 0.7941 (mmp) cc_final: 0.7407 (mmp) REVERT: B 1072 MET cc_start: 0.3878 (tpp) cc_final: 0.3633 (tpp) REVERT: C 542 ASP cc_start: 0.7377 (p0) cc_final: 0.6951 (p0) REVERT: C 597 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7829 (tt) REVERT: C 610 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: C 720 MET cc_start: 0.8212 (tpp) cc_final: 0.7642 (mmm) REVERT: C 842 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7308 (t80) REVERT: C 953 MET cc_start: 0.7944 (mmp) cc_final: 0.7406 (mmp) REVERT: C 1047 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: D 531 LYS cc_start: 0.8110 (pttm) cc_final: 0.7889 (pttm) REVERT: D 542 ASP cc_start: 0.7393 (p0) cc_final: 0.6957 (p0) REVERT: D 597 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7845 (tt) REVERT: D 610 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8094 (tptp) REVERT: D 720 MET cc_start: 0.8224 (tpp) cc_final: 0.7634 (mmm) REVERT: D 842 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7270 (t80) outliers start: 153 outliers final: 109 residues processed: 523 average time/residue: 0.1081 time to fit residues: 89.5771 Evaluate side-chains 513 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 392 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 610 LYS Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1047 GLN Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 907 GLN Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 130 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** D 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.159293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141490 restraints weight = 39801.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144336 restraints weight = 24417.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.146331 restraints weight = 17428.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.147679 restraints weight = 13813.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.148509 restraints weight = 11750.933| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 18008 Z= 0.252 Angle : 0.770 7.469 24380 Z= 0.382 Chirality : 0.046 0.200 2860 Planarity : 0.005 0.054 2984 Dihedral : 7.749 59.529 2424 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 10.25 % Allowed : 30.91 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2160 helix: 0.58 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 694 TYR 0.013 0.002 TYR C 658 PHE 0.025 0.002 PHE A 944 TRP 0.019 0.002 TRP A 809 HIS 0.006 0.001 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00587 (18008) covalent geometry : angle 0.76968 (24380) hydrogen bonds : bond 0.04767 ( 1141) hydrogen bonds : angle 4.60933 ( 3399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 401 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.7387 (mmm) cc_final: 0.7169 (mmm) REVERT: A 531 LYS cc_start: 0.8336 (pttm) cc_final: 0.7828 (pttm) REVERT: A 842 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 1072 MET cc_start: 0.3372 (OUTLIER) cc_final: 0.2705 (mpp) REVERT: B 531 LYS cc_start: 0.8337 (pttm) cc_final: 0.8044 (pttm) REVERT: B 543 ARG cc_start: 0.7194 (ptt180) cc_final: 0.6832 (ptt180) REVERT: B 597 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8111 (tt) REVERT: B 842 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7555 (t80) REVERT: C 531 LYS cc_start: 0.8346 (pttm) cc_final: 0.8054 (pttm) REVERT: C 543 ARG cc_start: 0.7194 (ptt180) cc_final: 0.6832 (ptt180) REVERT: C 597 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8115 (tt) REVERT: C 842 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 1072 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.2574 (mpp) REVERT: D 530 MET cc_start: 0.7371 (mmm) cc_final: 0.7146 (mmm) REVERT: D 531 LYS cc_start: 0.8335 (pttm) cc_final: 0.7824 (pttm) REVERT: D 543 ARG cc_start: 0.7165 (ptt180) cc_final: 0.6687 (ptt180) REVERT: D 597 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8120 (tt) REVERT: D 610 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (tmtt) REVERT: D 842 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7555 (t80) REVERT: D 1072 MET cc_start: 0.3333 (OUTLIER) cc_final: 0.2649 (mpp) outliers start: 196 outliers final: 133 residues processed: 528 average time/residue: 0.1030 time to fit residues: 87.0484 Evaluate side-chains 527 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 383 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 876 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1072 MET Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 876 VAL Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 905 ILE Chi-restraints excluded: chain D residue 913 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 945 THR Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1072 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 50 optimal weight: 20.0000 chunk 64 optimal weight: 0.0980 chunk 181 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 855 ASN ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.163623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.145402 restraints weight = 36473.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148064 restraints weight = 23449.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149799 restraints weight = 17261.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151302 restraints weight = 13993.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.152123 restraints weight = 11878.112| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18008 Z= 0.133 Angle : 0.710 13.422 24380 Z= 0.338 Chirality : 0.042 0.171 2860 Planarity : 0.004 0.056 2984 Dihedral : 7.388 59.586 2412 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 7.53 % Allowed : 33.84 % Favored : 58.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2160 helix: 0.81 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 928 TYR 0.008 0.001 TYR B 456 PHE 0.022 0.002 PHE C 452 TRP 0.013 0.001 TRP A 809 HIS 0.002 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00298 (18008) covalent geometry : angle 0.70989 (24380) hydrogen bonds : bond 0.04182 ( 1141) hydrogen bonds : angle 4.25002 ( 3399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 432 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 LYS cc_start: 0.8190 (pttm) cc_final: 0.7713 (pttm) REVERT: A 543 ARG cc_start: 0.7063 (ptt180) cc_final: 0.6832 (ptt180) REVERT: A 842 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 872 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7228 (mtt90) REVERT: B 528 GLN cc_start: 0.6980 (mp10) cc_final: 0.6492 (mp10) REVERT: B 531 LYS cc_start: 0.8149 (pttm) cc_final: 0.7688 (pttm) REVERT: B 543 ARG cc_start: 0.7133 (ptt180) cc_final: 0.6825 (ptt180) REVERT: B 721 MET cc_start: 0.8367 (tpp) cc_final: 0.8156 (tpp) REVERT: B 842 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7400 (t80) REVERT: B 872 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7244 (mtt90) REVERT: B 937 SER cc_start: 0.9070 (m) cc_final: 0.8722 (p) REVERT: B 1072 MET cc_start: 0.3621 (tpp) cc_final: 0.2868 (mpp) REVERT: C 528 GLN cc_start: 0.7010 (mp10) cc_final: 0.6515 (mp10) REVERT: C 531 LYS cc_start: 0.8163 (pttm) cc_final: 0.7696 (pttm) REVERT: C 543 ARG cc_start: 0.7133 (ptt180) cc_final: 0.6831 (ptt180) REVERT: C 721 MET cc_start: 0.8372 (tpp) cc_final: 0.8161 (tpp) REVERT: C 842 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 872 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7289 (mtt90) REVERT: C 937 SER cc_start: 0.9066 (m) cc_final: 0.8716 (p) REVERT: D 531 LYS cc_start: 0.8179 (pttm) cc_final: 0.7702 (pttm) REVERT: D 610 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8151 (tptp) REVERT: D 842 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7418 (t80) REVERT: D 872 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7227 (mtt90) outliers start: 144 outliers final: 110 residues processed: 528 average time/residue: 0.1048 time to fit residues: 87.1516 Evaluate side-chains 510 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 391 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 837 ILE Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 610 LYS Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 144 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 158 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.164656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.146033 restraints weight = 36037.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.148573 restraints weight = 23144.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150605 restraints weight = 17173.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.151685 restraints weight = 13774.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152689 restraints weight = 11960.869| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18008 Z= 0.151 Angle : 0.749 13.502 24380 Z= 0.356 Chirality : 0.044 0.198 2860 Planarity : 0.004 0.056 2984 Dihedral : 7.432 57.642 2412 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 8.53 % Allowed : 33.68 % Favored : 57.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2160 helix: 0.78 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 543 TYR 0.012 0.001 TYR A 785 PHE 0.017 0.002 PHE C 922 TRP 0.041 0.003 TRP A 605 HIS 0.003 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00353 (18008) covalent geometry : angle 0.74875 (24380) hydrogen bonds : bond 0.04196 ( 1141) hydrogen bonds : angle 4.25196 ( 3399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 404 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.7083 (ptt180) cc_final: 0.6862 (ptt180) REVERT: A 842 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7360 (t80) REVERT: A 872 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7235 (mtt90) REVERT: B 531 LYS cc_start: 0.8174 (pttm) cc_final: 0.7734 (pttm) REVERT: B 543 ARG cc_start: 0.7144 (ptt180) cc_final: 0.6846 (ptt180) REVERT: B 597 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7862 (tt) REVERT: B 842 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 872 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7238 (mtt90) REVERT: C 531 LYS cc_start: 0.8174 (pttm) cc_final: 0.7734 (pttm) REVERT: C 543 ARG cc_start: 0.7146 (ptt180) cc_final: 0.6849 (ptt180) REVERT: C 597 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7856 (tt) REVERT: C 842 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7403 (t80) REVERT: C 872 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7300 (mtt90) REVERT: C 882 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5734 (tt) REVERT: D 597 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7846 (tt) REVERT: D 842 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7383 (t80) REVERT: D 872 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7236 (mtt90) outliers start: 163 outliers final: 137 residues processed: 506 average time/residue: 0.1105 time to fit residues: 88.4155 Evaluate side-chains 539 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 390 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 976 ILE Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 600 ILE Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 913 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 21 optimal weight: 9.9990 chunk 110 optimal weight: 0.0060 chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.166425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.147952 restraints weight = 35817.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150607 restraints weight = 22976.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.152534 restraints weight = 16927.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153700 restraints weight = 13624.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154693 restraints weight = 11725.463| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18008 Z= 0.135 Angle : 0.749 11.971 24380 Z= 0.355 Chirality : 0.042 0.232 2860 Planarity : 0.004 0.056 2984 Dihedral : 7.309 56.153 2408 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 7.53 % Allowed : 34.62 % Favored : 57.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2160 helix: 0.83 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -2.00 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 543 TYR 0.009 0.001 TYR B 456 PHE 0.018 0.002 PHE D 452 TRP 0.031 0.002 TRP D 605 HIS 0.002 0.000 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00309 (18008) covalent geometry : angle 0.74911 (24380) hydrogen bonds : bond 0.04010 ( 1141) hydrogen bonds : angle 4.17739 ( 3399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 400 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.6991 (ptt180) cc_final: 0.6767 (ptt180) REVERT: A 720 MET cc_start: 0.8292 (tpp) cc_final: 0.7515 (mmm) REVERT: A 842 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7231 (t80) REVERT: A 872 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7221 (mtt90) REVERT: A 937 SER cc_start: 0.9159 (m) cc_final: 0.8764 (p) REVERT: B 528 GLN cc_start: 0.7267 (mp10) cc_final: 0.6910 (mp10) REVERT: B 531 LYS cc_start: 0.8298 (pttm) cc_final: 0.7819 (pttm) REVERT: B 543 ARG cc_start: 0.7144 (ptt180) cc_final: 0.6805 (ptt180) REVERT: B 720 MET cc_start: 0.8286 (tpp) cc_final: 0.7520 (mmm) REVERT: B 842 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7228 (t80) REVERT: B 872 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7214 (mtt90) REVERT: C 528 GLN cc_start: 0.7262 (mp10) cc_final: 0.6894 (mp10) REVERT: C 531 LYS cc_start: 0.8287 (pttm) cc_final: 0.7803 (pttm) REVERT: C 543 ARG cc_start: 0.7127 (ptt180) cc_final: 0.6779 (ptt180) REVERT: C 720 MET cc_start: 0.8313 (tpp) cc_final: 0.7528 (mmm) REVERT: C 842 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7234 (t80) REVERT: C 872 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7218 (mtt90) REVERT: D 543 ARG cc_start: 0.7040 (ptt180) cc_final: 0.6781 (ptt180) REVERT: D 720 MET cc_start: 0.8288 (tpp) cc_final: 0.7516 (mmm) REVERT: D 842 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7229 (t80) REVERT: D 872 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7219 (mtt90) REVERT: D 937 SER cc_start: 0.9158 (m) cc_final: 0.8766 (p) outliers start: 144 outliers final: 118 residues processed: 492 average time/residue: 0.1139 time to fit residues: 88.1997 Evaluate side-chains 512 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 386 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 976 ILE Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139114 restraints weight = 36307.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141704 restraints weight = 23668.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143615 restraints weight = 17485.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144957 restraints weight = 14042.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145813 restraints weight = 11982.847| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18008 Z= 0.136 Angle : 0.752 11.277 24380 Z= 0.356 Chirality : 0.042 0.211 2860 Planarity : 0.004 0.057 2984 Dihedral : 7.292 55.881 2408 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 7.95 % Allowed : 34.10 % Favored : 57.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2160 helix: 0.84 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -2.00 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 543 TYR 0.015 0.001 TYR C 785 PHE 0.018 0.002 PHE B 944 TRP 0.025 0.002 TRP D 605 HIS 0.003 0.000 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00316 (18008) covalent geometry : angle 0.75205 (24380) hydrogen bonds : bond 0.04007 ( 1141) hydrogen bonds : angle 4.17325 ( 3399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 389 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7870 (pttm) REVERT: A 543 ARG cc_start: 0.7004 (ptt180) cc_final: 0.6801 (ptt180) REVERT: A 720 MET cc_start: 0.8247 (tpp) cc_final: 0.7472 (mmm) REVERT: A 842 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 872 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7211 (mtt90) REVERT: A 937 SER cc_start: 0.9087 (m) cc_final: 0.8725 (p) REVERT: B 531 LYS cc_start: 0.8148 (pttm) cc_final: 0.7706 (pttm) REVERT: B 543 ARG cc_start: 0.7160 (ptt180) cc_final: 0.6839 (ptt180) REVERT: B 597 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 720 MET cc_start: 0.8233 (tpp) cc_final: 0.7462 (mmm) REVERT: B 842 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 872 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7222 (mtt90) REVERT: C 531 LYS cc_start: 0.8118 (pttm) cc_final: 0.7677 (pttm) REVERT: C 543 ARG cc_start: 0.7154 (ptt180) cc_final: 0.6831 (ptt180) REVERT: C 720 MET cc_start: 0.8234 (tpp) cc_final: 0.7466 (mmm) REVERT: C 842 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7231 (t80) REVERT: C 872 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7198 (mtt90) REVERT: D 531 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7875 (pttm) REVERT: D 543 ARG cc_start: 0.7059 (ptt180) cc_final: 0.6836 (ptt180) REVERT: D 720 MET cc_start: 0.8245 (tpp) cc_final: 0.7471 (mmm) REVERT: D 842 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7332 (t80) REVERT: D 872 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7224 (mtt90) REVERT: D 937 SER cc_start: 0.9091 (m) cc_final: 0.8733 (p) outliers start: 152 outliers final: 117 residues processed: 491 average time/residue: 0.1289 time to fit residues: 99.1143 Evaluate side-chains 511 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 383 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 808 GLU Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 593 LYS Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.164199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145324 restraints weight = 35695.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.148009 restraints weight = 23176.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.149916 restraints weight = 17167.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150954 restraints weight = 13898.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.152049 restraints weight = 12136.378| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18008 Z= 0.169 Angle : 0.789 11.218 24380 Z= 0.377 Chirality : 0.045 0.245 2860 Planarity : 0.004 0.057 2984 Dihedral : 7.317 56.938 2400 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 7.64 % Allowed : 34.47 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2160 helix: 0.81 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -2.06 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 996 TYR 0.011 0.001 TYR B 456 PHE 0.021 0.002 PHE B 944 TRP 0.028 0.002 TRP D 605 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00400 (18008) covalent geometry : angle 0.78851 (24380) hydrogen bonds : bond 0.04222 ( 1141) hydrogen bonds : angle 4.33292 ( 3399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 396 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ARG cc_start: 0.7014 (ptt180) cc_final: 0.6776 (ptt180) REVERT: A 720 MET cc_start: 0.8331 (tpp) cc_final: 0.8051 (mmm) REVERT: A 842 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 872 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7303 (mtt90) REVERT: A 937 SER cc_start: 0.9183 (m) cc_final: 0.8799 (p) REVERT: B 543 ARG cc_start: 0.7170 (ptt180) cc_final: 0.6840 (ptt180) REVERT: B 597 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 720 MET cc_start: 0.8320 (tpp) cc_final: 0.8042 (mmm) REVERT: B 842 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 872 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7322 (mtt90) REVERT: C 543 ARG cc_start: 0.7195 (ptt180) cc_final: 0.6861 (ptt180) REVERT: C 597 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7911 (tt) REVERT: C 720 MET cc_start: 0.8332 (tpp) cc_final: 0.8048 (mmm) REVERT: C 842 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7403 (t80) REVERT: C 872 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7316 (mtt90) REVERT: D 543 ARG cc_start: 0.7094 (ptt180) cc_final: 0.6494 (ptt180) REVERT: D 597 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7907 (tt) REVERT: D 720 MET cc_start: 0.8320 (tpp) cc_final: 0.8045 (mmm) REVERT: D 842 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 872 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7332 (mtt90) REVERT: D 937 SER cc_start: 0.9177 (m) cc_final: 0.8787 (p) outliers start: 146 outliers final: 119 residues processed: 490 average time/residue: 0.1271 time to fit residues: 98.0224 Evaluate side-chains 518 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 388 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 644 HIS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 834 CYS Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 872 ARG Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 621 CYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 644 HIS Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 808 GLU Chi-restraints excluded: chain B residue 834 CYS Chi-restraints excluded: chain B residue 842 TYR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 903 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1003 THR Chi-restraints excluded: chain C residue 463 GLN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 621 CYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 644 HIS Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 834 CYS Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 LEU Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 973 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 574 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 621 CYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 644 HIS Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain D residue 834 CYS Chi-restraints excluded: chain D residue 842 TYR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 THR Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 915 ASP Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 946 ILE Chi-restraints excluded: chain D residue 948 VAL Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 1003 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 147 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS B 614 HIS ** B1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS D 614 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.160054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141990 restraints weight = 39759.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144923 restraints weight = 24207.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.146929 restraints weight = 17281.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148147 restraints weight = 13727.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.149161 restraints weight = 11784.263| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18008 Z= 0.208 Angle : 0.834 11.223 24380 Z= 0.404 Chirality : 0.046 0.250 2860 Planarity : 0.004 0.056 2984 Dihedral : 6.957 57.899 2388 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.53 % Allowed : 34.94 % Favored : 57.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2160 helix: 0.64 (0.13), residues: 1604 sheet: None (None), residues: 0 loop : -2.13 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 996 TYR 0.014 0.002 TYR A 785 PHE 0.027 0.002 PHE D 944 TRP 0.030 0.003 TRP A 605 HIS 0.005 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00488 (18008) covalent geometry : angle 0.83431 (24380) hydrogen bonds : bond 0.04511 ( 1141) hydrogen bonds : angle 4.51620 ( 3399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.36 seconds wall clock time: 48 minutes 23.94 seconds (2903.94 seconds total)