Starting phenix.real_space_refine on Thu Mar 5 04:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.map" model { file = "/net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yeh_33773/03_2026/7yeh_33773.cif" } resolution = 3.92 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= 0.005 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 113 5.16 5 C 12137 2.51 5 N 3318 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19122 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8032 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 967} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 8032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 8032 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 967} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2773 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 245 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.26 Number of scatterers: 19122 At special positions: 0 Unit cell: (114.929, 162.747, 175.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 2 15.00 O 3552 8.00 N 3318 7.00 C 12137 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: 1.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 9 sheets defined 62.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 37 through 49 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 88 through 102 removed outlier: 4.053A pdb=" N TYR B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 123 through 137 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.731A pdb=" N ALA B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 172 through 187 Processing helix chain 'B' and resid 191 through 205 Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.534A pdb=" N TYR B 228 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.879A pdb=" N HIS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.599A pdb=" N TYR B 296 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 342 through 357 Processing helix chain 'B' and resid 360 through 374 removed outlier: 3.600A pdb=" N HIS B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 428 through 443 removed outlier: 3.858A pdb=" N HIS B 432 " --> pdb=" O PHE B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 462 through 476 Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 506 through 511 removed outlier: 4.028A pdb=" N MET B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 536 Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 707 through 712 removed outlier: 4.066A pdb=" N MET B 711 " --> pdb=" O ASP B 707 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 712 " --> pdb=" O HIS B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 712' Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.850A pdb=" N LYS B 717 " --> pdb=" O HIS B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 removed outlier: 4.280A pdb=" N LYS B 742 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 748 removed outlier: 4.324A pdb=" N SER B 747 " --> pdb=" O ALA B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 780 through 793 Processing helix chain 'B' and resid 808 through 813 removed outlier: 5.528A pdb=" N THR B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 833 through 836 Processing helix chain 'B' and resid 854 through 868 Processing helix chain 'B' and resid 881 through 893 removed outlier: 4.217A pdb=" N ASN B 885 " --> pdb=" O VAL B 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 889 " --> pdb=" O ASN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 918 removed outlier: 4.406A pdb=" N GLY B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN B 916 " --> pdb=" O VAL B 912 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 917 " --> pdb=" O ARG B 913 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 918 " --> pdb=" O ARG B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 940 removed outlier: 3.768A pdb=" N MET B 934 " --> pdb=" O HIS B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 964 removed outlier: 3.993A pdb=" N ALA B 956 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 958 " --> pdb=" O ARG B 954 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 969 removed outlier: 3.761A pdb=" N LEU B 968 " --> pdb=" O CYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 987 removed outlier: 4.068A pdb=" N LEU B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1004 removed outlier: 4.728A pdb=" N ILE B1002 " --> pdb=" O TRP B 998 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1028 removed outlier: 4.229A pdb=" N TYR B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 88 through 102 removed outlier: 4.052A pdb=" N TYR A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.731A pdb=" N ALA A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 172 through 187 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.534A pdb=" N TYR A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 Processing helix chain 'A' and resid 258 through 273 removed outlier: 3.879A pdb=" N HIS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.599A pdb=" N TYR A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.600A pdb=" N HIS A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 428 through 443 removed outlier: 3.858A pdb=" N HIS A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 506 through 511 removed outlier: 4.028A pdb=" N MET A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 536 Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 648 through 654 Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 707 through 712 removed outlier: 4.066A pdb=" N MET A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 707 through 712' Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.850A pdb=" N LYS A 717 " --> pdb=" O HIS A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.280A pdb=" N LYS A 742 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 748 removed outlier: 4.324A pdb=" N SER A 747 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 771 No H-bonds generated for 'chain 'A' and resid 769 through 771' Processing helix chain 'A' and resid 780 through 793 Processing helix chain 'A' and resid 808 through 813 removed outlier: 5.528A pdb=" N THR A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 833 through 836 Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 881 through 893 removed outlier: 4.216A pdb=" N ASN A 885 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 889 " --> pdb=" O ASN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 918 removed outlier: 4.405A pdb=" N GLY A 915 " --> pdb=" O HIS A 911 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 916 " --> pdb=" O VAL A 912 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 918 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 940 removed outlier: 3.769A pdb=" N MET A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 964 removed outlier: 3.993A pdb=" N ALA A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 969 removed outlier: 3.760A pdb=" N LEU A 968 " --> pdb=" O CYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 removed outlier: 4.068A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1004 removed outlier: 4.729A pdb=" N ILE A1002 " --> pdb=" O TRP A 998 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1028 removed outlier: 4.229A pdb=" N TYR A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.566A pdb=" N ARG C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 190 through 206 removed outlier: 3.512A pdb=" N ALA C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.500A pdb=" N ILE C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 4.157A pdb=" N ARG C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 333 Processing helix chain 'C' and resid 376 through 391 Processing helix chain 'C' and resid 394 through 398 Processing sheet with id=AA1, first strand: chain 'B' and resid 611 through 612 removed outlier: 6.344A pdb=" N ARG B 557 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL B 637 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 559 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 720 through 721 Processing sheet with id=AA3, first strand: chain 'B' and resid 734 through 737 removed outlier: 6.028A pdb=" N SER B 803 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 829 " --> pdb=" O SER B 803 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER B 805 " --> pdb=" O VAL B 829 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR B 831 " --> pdb=" O SER B 805 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 900 through 903 removed outlier: 7.523A pdb=" N ILE B 901 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 873 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 903 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 875 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 842 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TRP B 874 " --> pdb=" O ILE B 842 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR B 844 " --> pdb=" O TRP B 874 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU B 876 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 843 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 922 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N CYS B 845 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N CYS B 921 " --> pdb=" O VAL B 944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 611 through 612 removed outlier: 6.344A pdb=" N ARG A 557 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 637 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY A 559 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 721 Processing sheet with id=AA7, first strand: chain 'A' and resid 734 through 737 removed outlier: 6.027A pdb=" N SER A 803 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 829 " --> pdb=" O SER A 803 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 805 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR A 831 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 900 through 903 removed outlier: 7.523A pdb=" N ILE A 901 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU A 873 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER A 903 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 875 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 842 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TRP A 874 " --> pdb=" O ILE A 842 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR A 844 " --> pdb=" O TRP A 874 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU A 876 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 843 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A 922 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N CYS A 845 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS A 921 " --> pdb=" O VAL A 944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.685A pdb=" N TYR C 93 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA C 136 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR C 95 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N ALA C 170 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR C 135 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 172 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 137 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE C 169 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS C 215 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU C 171 " --> pdb=" O CYS C 215 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE C 214 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP C 278 " --> pdb=" O TRP C 249 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 61 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N THR C 312 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 63 " --> pdb=" O THR C 312 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 3009 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: 3.83 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6350 1.34 - 1.46: 4374 1.46 - 1.59: 8671 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 19570 Sorted by residual: bond pdb=" O1A UDP A1101 " pdb=" PA UDP A1101 " ideal model delta sigma weight residual 1.482 1.525 -0.043 1.00e-02 1.00e+04 1.84e+01 bond pdb=" O1B UDP A1101 " pdb=" PB UDP A1101 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.00e-02 1.00e+04 1.64e+01 bond pdb=" CB ASN A 500 " pdb=" CG ASN A 500 " ideal model delta sigma weight residual 1.516 1.585 -0.069 2.50e-02 1.60e+03 7.71e+00 bond pdb=" CB ASN B 500 " pdb=" CG ASN B 500 " ideal model delta sigma weight residual 1.516 1.585 -0.069 2.50e-02 1.60e+03 7.64e+00 bond pdb=" CA ILE B 577 " pdb=" CB ILE B 577 " ideal model delta sigma weight residual 1.537 1.550 -0.014 5.00e-03 4.00e+04 7.44e+00 ... (remaining 19565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 26204 3.38 - 6.76: 311 6.76 - 10.14: 42 10.14 - 13.52: 10 13.52 - 16.90: 12 Bond angle restraints: 26579 Sorted by residual: angle pdb=" O1B UDP A1101 " pdb=" PB UDP A1101 " pdb=" O3A UDP A1101 " ideal model delta sigma weight residual 102.95 112.03 -9.08 1.00e+00 1.00e+00 8.25e+01 angle pdb=" O3A UDP A1101 " pdb=" PB UDP A1101 " pdb=" O3B UDP A1101 " ideal model delta sigma weight residual 112.01 102.99 9.02 1.00e+00 1.00e+00 8.13e+01 angle pdb=" CA LYS A 83 " pdb=" CB LYS A 83 " pdb=" CG LYS A 83 " ideal model delta sigma weight residual 114.10 131.00 -16.90 2.00e+00 2.50e-01 7.14e+01 angle pdb=" CA LYS B 83 " pdb=" CB LYS B 83 " pdb=" CG LYS B 83 " ideal model delta sigma weight residual 114.10 130.98 -16.88 2.00e+00 2.50e-01 7.13e+01 angle pdb=" CB ARG B 113 " pdb=" CG ARG B 113 " pdb=" CD ARG B 113 " ideal model delta sigma weight residual 111.30 127.73 -16.43 2.30e+00 1.89e-01 5.11e+01 ... (remaining 26574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10475 17.80 - 35.61: 956 35.61 - 53.41: 255 53.41 - 71.21: 139 71.21 - 89.01: 18 Dihedral angle restraints: 11843 sinusoidal: 4750 harmonic: 7093 Sorted by residual: dihedral pdb=" CA GLN A 630 " pdb=" C GLN A 630 " pdb=" N ASP A 631 " pdb=" CA ASP A 631 " ideal model delta harmonic sigma weight residual 180.00 137.19 42.81 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA GLN B 630 " pdb=" C GLN B 630 " pdb=" N ASP B 631 " pdb=" CA ASP B 631 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ARG A 501 " pdb=" C ARG A 501 " pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta harmonic sigma weight residual -180.00 -137.67 -42.33 0 5.00e+00 4.00e-02 7.17e+01 ... (remaining 11840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2355 0.060 - 0.119: 516 0.119 - 0.179: 49 0.179 - 0.239: 1 0.239 - 0.298: 6 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CA ARG A 501 " pdb=" N ARG A 501 " pdb=" C ARG A 501 " pdb=" CB ARG A 501 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ARG B 501 " pdb=" N ARG B 501 " pdb=" C ARG B 501 " pdb=" CB ARG B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN B 500 " pdb=" N ASN B 500 " pdb=" C ASN B 500 " pdb=" CB ASN B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2924 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1102 " -0.091 2.00e-02 2.50e+03 7.44e-02 6.93e+01 pdb=" C7 NAG A1102 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG A1102 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG A1102 " 0.117 2.00e-02 2.50e+03 pdb=" O7 NAG A1102 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 861 " 0.024 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP B 861 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B 861 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 861 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 861 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 861 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 861 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 861 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 861 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 861 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 861 " -0.024 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP A 861 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 861 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 861 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 861 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 861 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 861 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 861 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 861 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 861 " 0.001 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 416 2.59 - 3.17: 19117 3.17 - 3.74: 33445 3.74 - 4.32: 44723 4.32 - 4.90: 67151 Nonbonded interactions: 164852 Sorted by model distance: nonbonded pdb=" N GLU B 344 " pdb=" OE1 GLU B 344 " model vdw 2.011 3.120 nonbonded pdb=" N GLU A 344 " pdb=" OE1 GLU A 344 " model vdw 2.012 3.120 nonbonded pdb=" OE1 GLU C 66 " pdb=" OH TYR C 93 " model vdw 2.074 3.040 nonbonded pdb=" N GLN A 630 " pdb=" OE1 GLN A 630 " model vdw 2.077 3.120 nonbonded pdb=" N GLN B 630 " pdb=" OE1 GLN B 630 " model vdw 2.078 3.120 ... (remaining 164847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 1039) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.006 0.069 19570 Z= 0.283 Angle : 1.004 16.897 26579 Z= 0.554 Chirality : 0.049 0.298 2927 Planarity : 0.006 0.074 3469 Dihedral : 16.733 89.013 7267 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 28.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.09 % Allowed : 1.42 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2409 helix: 0.06 (0.14), residues: 1299 sheet: -1.21 (0.43), residues: 165 loop : -1.79 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 877 TYR 0.021 0.002 TYR B 398 PHE 0.015 0.002 PHE C 133 TRP 0.071 0.005 TRP A 861 HIS 0.008 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00583 (19570) covalent geometry : angle 1.00425 (26579) hydrogen bonds : bond 0.14433 ( 1030) hydrogen bonds : angle 7.06962 ( 3009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 160 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7787 (mmm) REVERT: B 46 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7180 (pt0) REVERT: B 237 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: B 320 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8333 (pp) REVERT: B 401 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8670 (ppp) REVERT: B 466 TYR cc_start: 0.8453 (t80) cc_final: 0.7831 (t80) REVERT: B 606 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.5208 (tpp) REVERT: B 877 ARG cc_start: 0.4429 (OUTLIER) cc_final: 0.3309 (ptm-80) REVERT: B 893 MET cc_start: 0.3023 (ppp) cc_final: 0.2813 (ppp) REVERT: B 934 MET cc_start: 0.5467 (ttt) cc_final: 0.5220 (ptt) REVERT: B 1036 MET cc_start: -0.0531 (OUTLIER) cc_final: -0.2766 (ttp) REVERT: B 1038 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6682 (mmtt) REVERT: A 45 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7645 (mmm) REVERT: A 756 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8048 (mmm) REVERT: A 850 LEU cc_start: 0.9156 (mt) cc_final: 0.8952 (mt) REVERT: A 861 TRP cc_start: 0.8022 (m-90) cc_final: 0.7479 (m-90) REVERT: C 75 MET cc_start: 0.8907 (tpt) cc_final: 0.8639 (tpp) outliers start: 104 outliers final: 10 residues processed: 208 average time/residue: 0.1863 time to fit residues: 55.6967 Evaluate side-chains 124 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 792 ARG Chi-restraints excluded: chain B residue 877 ARG Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 1038 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN B 708 HIS ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 885 ASN ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 200 ASN C 404 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051903 restraints weight = 128862.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051367 restraints weight = 90004.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051745 restraints weight = 60566.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051871 restraints weight = 54025.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051914 restraints weight = 46864.517| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19570 Z= 0.201 Angle : 0.752 14.389 26579 Z= 0.394 Chirality : 0.047 0.205 2927 Planarity : 0.006 0.061 3469 Dihedral : 8.899 118.379 2743 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.76 % Allowed : 10.77 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.75 (0.17), residues: 2409 helix: 0.38 (0.14), residues: 1363 sheet: -1.32 (0.39), residues: 190 loop : -1.66 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.026 0.002 TYR B 851 PHE 0.030 0.002 PHE B 673 TRP 0.033 0.003 TRP A 874 HIS 0.005 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00433 (19570) covalent geometry : angle 0.75236 (26579) hydrogen bonds : bond 0.04546 ( 1030) hydrogen bonds : angle 5.55447 ( 3009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 466 TYR cc_start: 0.8555 (t80) cc_final: 0.7882 (t80) REVERT: B 774 MET cc_start: 0.4570 (mmt) cc_final: 0.4298 (mmp) REVERT: B 851 TYR cc_start: 0.6860 (p90) cc_final: 0.6371 (p90) REVERT: B 877 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3451 (ptm160) REVERT: B 893 MET cc_start: 0.3278 (ppp) cc_final: 0.2919 (ppp) REVERT: B 1023 MET cc_start: 0.7053 (mpp) cc_final: 0.6677 (mtt) REVERT: A 408 MET cc_start: 0.9092 (pmm) cc_final: 0.8664 (pmm) REVERT: A 606 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8630 (mmm) REVERT: A 736 LEU cc_start: 0.9310 (tp) cc_final: 0.9088 (tp) REVERT: A 792 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: A 850 LEU cc_start: 0.9318 (mt) cc_final: 0.9002 (mt) REVERT: A 861 TRP cc_start: 0.8383 (m-90) cc_final: 0.7679 (m-90) REVERT: C 75 MET cc_start: 0.8975 (tpt) cc_final: 0.8769 (tpp) REVERT: C 120 MET cc_start: 0.9134 (mmp) cc_final: 0.8833 (mmp) outliers start: 36 outliers final: 9 residues processed: 148 average time/residue: 0.1545 time to fit residues: 35.0270 Evaluate side-chains 114 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 877 ARG Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 792 ARG Chi-restraints excluded: chain A residue 877 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 239 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN B 264 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 897 GLN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.072543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.051550 restraints weight = 129444.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051836 restraints weight = 80572.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.052002 restraints weight = 52101.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.052105 restraints weight = 49816.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052158 restraints weight = 43326.406| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19570 Z= 0.166 Angle : 0.675 12.450 26579 Z= 0.352 Chirality : 0.044 0.185 2927 Planarity : 0.005 0.060 3469 Dihedral : 7.065 82.616 2699 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.86 % Allowed : 14.59 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.44 (0.18), residues: 2409 helix: 0.60 (0.14), residues: 1361 sheet: -1.25 (0.41), residues: 184 loop : -1.43 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.021 0.002 TYR C 286 PHE 0.023 0.002 PHE B 673 TRP 0.024 0.002 TRP A 874 HIS 0.006 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00360 (19570) covalent geometry : angle 0.67543 (26579) hydrogen bonds : bond 0.04076 ( 1030) hydrogen bonds : angle 5.15686 ( 3009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8373 (mmm) cc_final: 0.8046 (mmm) REVERT: B 73 ARG cc_start: 0.9102 (tpm170) cc_final: 0.8784 (tpp-160) REVERT: B 320 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8596 (pp) REVERT: B 401 MET cc_start: 0.8861 (ppp) cc_final: 0.8636 (ppp) REVERT: B 466 TYR cc_start: 0.8538 (t80) cc_final: 0.7829 (t80) REVERT: B 893 MET cc_start: 0.3516 (ppp) cc_final: 0.3231 (ppp) REVERT: A 408 MET cc_start: 0.9022 (pmm) cc_final: 0.8565 (pmm) REVERT: A 453 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8388 (ttp80) REVERT: A 736 LEU cc_start: 0.9342 (tp) cc_final: 0.9076 (tp) REVERT: C 75 MET cc_start: 0.8896 (tpt) cc_final: 0.8672 (tpp) REVERT: C 110 MET cc_start: 0.6290 (tpp) cc_final: 0.5909 (tpp) REVERT: C 120 MET cc_start: 0.9090 (mmp) cc_final: 0.8754 (mmp) outliers start: 38 outliers final: 14 residues processed: 144 average time/residue: 0.1390 time to fit residues: 31.7134 Evaluate side-chains 117 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 6 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 177 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 65 HIS B 439 HIS B 468 ASN B 885 ASN B 911 HIS A 509 HIS ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.073511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.052218 restraints weight = 129104.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.053213 restraints weight = 85873.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.053340 restraints weight = 51136.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.053410 restraints weight = 46642.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.053471 restraints weight = 39404.194| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19570 Z= 0.126 Angle : 0.646 12.351 26579 Z= 0.330 Chirality : 0.043 0.183 2927 Planarity : 0.005 0.062 3469 Dihedral : 6.426 82.090 2686 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.01 % Allowed : 15.57 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.22 (0.18), residues: 2409 helix: 0.80 (0.14), residues: 1366 sheet: -1.24 (0.43), residues: 169 loop : -1.38 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 792 TYR 0.017 0.001 TYR C 286 PHE 0.020 0.002 PHE B 673 TRP 0.019 0.002 TRP A1024 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00275 (19570) covalent geometry : angle 0.64553 (26579) hydrogen bonds : bond 0.03688 ( 1030) hydrogen bonds : angle 4.75483 ( 3009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8380 (mmm) cc_final: 0.8089 (mmm) REVERT: B 69 ARG cc_start: 0.8658 (mmp-170) cc_final: 0.8422 (mmp-170) REVERT: B 73 ARG cc_start: 0.9118 (tpm170) cc_final: 0.8796 (tpp-160) REVERT: B 320 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8631 (pp) REVERT: B 401 MET cc_start: 0.8887 (ppp) cc_final: 0.8617 (ppp) REVERT: B 466 TYR cc_start: 0.8515 (t80) cc_final: 0.7867 (t80) REVERT: B 633 ILE cc_start: 0.2226 (OUTLIER) cc_final: 0.1838 (mm) REVERT: B 851 TYR cc_start: 0.7090 (p90) cc_final: 0.6566 (p90) REVERT: A 406 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9195 (ptmt) REVERT: A 408 MET cc_start: 0.9035 (pmm) cc_final: 0.8595 (pmm) REVERT: A 453 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8418 (ttp80) REVERT: A 736 LEU cc_start: 0.9416 (tp) cc_final: 0.9118 (tp) REVERT: A 860 MET cc_start: 0.9020 (ttm) cc_final: 0.8576 (ttm) REVERT: A 861 TRP cc_start: 0.8228 (m-10) cc_final: 0.7713 (m-90) REVERT: A 946 MET cc_start: 0.8697 (ttt) cc_final: 0.8456 (ttm) REVERT: C 75 MET cc_start: 0.8860 (tpt) cc_final: 0.8655 (tpp) REVERT: C 120 MET cc_start: 0.9118 (mmp) cc_final: 0.8751 (mmp) outliers start: 41 outliers final: 12 residues processed: 150 average time/residue: 0.1480 time to fit residues: 34.8830 Evaluate side-chains 114 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 88 optimal weight: 30.0000 chunk 109 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 238 optimal weight: 40.0000 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN B 233 ASN B 930 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** C 288 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 = 0.3875 r_free = 0.3875 target = 0.071591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051122 restraints weight = 129450.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050529 restraints weight = 87081.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.050861 restraints weight = 59611.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051011 restraints weight = 49624.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051260 restraints weight = 44628.364| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19570 Z= 0.199 Angle : 0.680 11.372 26579 Z= 0.352 Chirality : 0.043 0.185 2927 Planarity : 0.005 0.064 3469 Dihedral : 6.441 81.539 2686 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.30 % Allowed : 17.38 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: -0.19 (0.18), residues: 2409 helix: 0.85 (0.14), residues: 1362 sheet: -1.21 (0.42), residues: 162 loop : -1.40 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 792 TYR 0.015 0.002 TYR B 513 PHE 0.022 0.002 PHE B 673 TRP 0.023 0.002 TRP A 874 HIS 0.008 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00427 (19570) covalent geometry : angle 0.68039 (26579) hydrogen bonds : bond 0.03874 ( 1030) hydrogen bonds : angle 4.88440 ( 3009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.740 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: B 45 MET cc_start: 0.8373 (mmm) cc_final: 0.8012 (mmm) REVERT: B 101 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: B 320 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8662 (pp) REVERT: B 401 MET cc_start: 0.8860 (ppp) cc_final: 0.8631 (ppp) REVERT: B 466 TYR cc_start: 0.8468 (t80) cc_final: 0.7871 (t80) REVERT: B 639 MET cc_start: 0.6129 (mpp) cc_final: 0.4751 (mpp) REVERT: B 934 MET cc_start: 0.5155 (ptt) cc_final: 0.4664 (ptm) REVERT: B 1023 MET cc_start: 0.5293 (tpp) cc_final: 0.4792 (tpp) REVERT: A 406 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9246 (ptmt) REVERT: A 453 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8146 (ttp80) REVERT: A 511 MET cc_start: 0.8653 (pmm) cc_final: 0.8417 (pmm) REVERT: A 736 LEU cc_start: 0.9369 (tp) cc_final: 0.9034 (tp) REVERT: A 860 MET cc_start: 0.8990 (ttm) cc_final: 0.8536 (ttm) REVERT: A 861 TRP cc_start: 0.8272 (m-10) cc_final: 0.7555 (m-90) REVERT: C 75 MET cc_start: 0.8838 (tpt) cc_final: 0.8588 (tpp) REVERT: C 120 MET cc_start: 0.9169 (mmp) cc_final: 0.8812 (mmp) outliers start: 47 outliers final: 27 residues processed: 141 average time/residue: 0.1362 time to fit residues: 31.0627 Evaluate side-chains 125 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 18 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 128 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 211 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 812 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.071970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.051421 restraints weight = 127811.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051168 restraints weight = 85430.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051456 restraints weight = 54964.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051585 restraints weight = 49075.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.051644 restraints weight = 42573.652| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19570 Z= 0.155 Angle : 0.649 11.225 26579 Z= 0.332 Chirality : 0.043 0.172 2927 Planarity : 0.005 0.064 3469 Dihedral : 6.281 82.365 2686 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.15 % Allowed : 18.56 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 2409 helix: 0.91 (0.14), residues: 1364 sheet: -1.32 (0.41), residues: 169 loop : -1.35 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 792 TYR 0.017 0.001 TYR C 286 PHE 0.020 0.001 PHE B 673 TRP 0.019 0.002 TRP A1024 HIS 0.006 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00339 (19570) covalent geometry : angle 0.64858 (26579) hydrogen bonds : bond 0.03615 ( 1030) hydrogen bonds : angle 4.71963 ( 3009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8508 (mmm) cc_final: 0.8141 (mmm) REVERT: B 101 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: B 224 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7844 (t80) REVERT: B 292 PHE cc_start: 0.7700 (t80) cc_final: 0.7154 (t80) REVERT: B 320 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 401 MET cc_start: 0.8922 (ppp) cc_final: 0.8683 (ppp) REVERT: B 466 TYR cc_start: 0.8514 (t80) cc_final: 0.7867 (t80) REVERT: B 486 MET cc_start: 0.3185 (tpp) cc_final: 0.2950 (tpp) REVERT: B 633 ILE cc_start: 0.3597 (OUTLIER) cc_final: 0.3226 (mm) REVERT: B 934 MET cc_start: 0.5000 (ptt) cc_final: 0.4486 (ptm) REVERT: B 1023 MET cc_start: 0.5232 (tpp) cc_final: 0.4844 (tpp) REVERT: A 406 LYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9245 (ptmt) REVERT: A 408 MET cc_start: 0.9021 (pmm) cc_final: 0.8747 (pmm) REVERT: A 453 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8360 (ttp80) REVERT: A 665 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7729 (p90) REVERT: A 736 LEU cc_start: 0.9409 (tp) cc_final: 0.9122 (tp) REVERT: A 756 MET cc_start: 0.7759 (mmm) cc_final: 0.7539 (mmm) REVERT: A 860 MET cc_start: 0.9048 (ttm) cc_final: 0.8539 (ttm) REVERT: A 861 TRP cc_start: 0.8287 (m-10) cc_final: 0.7722 (m-90) REVERT: A 983 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8526 (mm) REVERT: C 75 MET cc_start: 0.8856 (tpt) cc_final: 0.8613 (tpp) REVERT: C 120 MET cc_start: 0.9175 (mmp) cc_final: 0.8819 (mmp) outliers start: 44 outliers final: 27 residues processed: 135 average time/residue: 0.1342 time to fit residues: 29.5962 Evaluate side-chains 129 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 61 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** C 288 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 = 0.3907 r_free = 0.3907 target = 0.072783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051942 restraints weight = 129958.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052025 restraints weight = 86236.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052342 restraints weight = 54064.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052345 restraints weight = 49873.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.052502 restraints weight = 43587.472| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19570 Z= 0.119 Angle : 0.636 11.503 26579 Z= 0.321 Chirality : 0.042 0.170 2927 Planarity : 0.005 0.066 3469 Dihedral : 5.991 80.271 2686 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.06 % Allowed : 19.10 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 2409 helix: 1.06 (0.14), residues: 1366 sheet: -1.20 (0.41), residues: 169 loop : -1.27 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 792 TYR 0.017 0.001 TYR B 398 PHE 0.020 0.001 PHE B 673 TRP 0.021 0.002 TRP A1024 HIS 0.005 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00265 (19570) covalent geometry : angle 0.63616 (26579) hydrogen bonds : bond 0.03382 ( 1030) hydrogen bonds : angle 4.50238 ( 3009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8508 (mmm) cc_final: 0.8136 (mmm) REVERT: B 101 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: B 224 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7783 (t80) REVERT: B 292 PHE cc_start: 0.7770 (t80) cc_final: 0.7115 (t80) REVERT: B 401 MET cc_start: 0.8907 (ppp) cc_final: 0.8641 (ppp) REVERT: B 466 TYR cc_start: 0.8468 (t80) cc_final: 0.7867 (t80) REVERT: B 467 CYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5931 (p) REVERT: B 633 ILE cc_start: 0.3434 (OUTLIER) cc_final: 0.3147 (mm) REVERT: B 639 MET cc_start: 0.6137 (mpp) cc_final: 0.4683 (mpp) REVERT: B 934 MET cc_start: 0.5066 (ptt) cc_final: 0.4596 (ptm) REVERT: B 1023 MET cc_start: 0.5236 (tpp) cc_final: 0.4801 (tpp) REVERT: B 1036 MET cc_start: 0.0527 (mtp) cc_final: 0.0131 (mmm) REVERT: A 406 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9174 (ptmt) REVERT: A 453 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8381 (ttp80) REVERT: A 545 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6638 (p90) REVERT: A 736 LEU cc_start: 0.9438 (tp) cc_final: 0.9116 (tp) REVERT: A 756 MET cc_start: 0.7920 (mmm) cc_final: 0.7669 (mmm) REVERT: A 860 MET cc_start: 0.9052 (ttm) cc_final: 0.8503 (ttm) REVERT: A 861 TRP cc_start: 0.8213 (m-10) cc_final: 0.7651 (m-90) REVERT: A 955 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.9005 (t) REVERT: C 75 MET cc_start: 0.8848 (tpt) cc_final: 0.8611 (tpp) REVERT: C 110 MET cc_start: 0.5990 (tpp) cc_final: 0.5768 (tpp) REVERT: C 120 MET cc_start: 0.9173 (mmp) cc_final: 0.8816 (mmp) outliers start: 42 outliers final: 27 residues processed: 141 average time/residue: 0.1326 time to fit residues: 30.6341 Evaluate side-chains 133 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 73 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 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 = 0.3877 r_free = 0.3877 target = 0.071570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.051177 restraints weight = 128979.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051103 restraints weight = 78669.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051102 restraints weight = 54315.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.051183 restraints weight = 52458.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.052142 restraints weight = 44900.771| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19570 Z= 0.167 Angle : 0.664 13.009 26579 Z= 0.336 Chirality : 0.043 0.171 2927 Planarity : 0.005 0.064 3469 Dihedral : 6.037 79.565 2686 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.25 % Allowed : 19.20 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 2409 helix: 1.04 (0.14), residues: 1369 sheet: -1.21 (0.41), residues: 169 loop : -1.23 (0.23), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 792 TYR 0.014 0.001 TYR C 286 PHE 0.020 0.001 PHE B 673 TRP 0.020 0.002 TRP A 208 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00364 (19570) covalent geometry : angle 0.66415 (26579) hydrogen bonds : bond 0.03592 ( 1030) hydrogen bonds : angle 4.64210 ( 3009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8488 (mmm) cc_final: 0.8155 (mmm) REVERT: B 101 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: B 224 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 401 MET cc_start: 0.8919 (ppp) cc_final: 0.8570 (ppp) REVERT: B 466 TYR cc_start: 0.8481 (t80) cc_final: 0.7856 (t80) REVERT: B 467 CYS cc_start: 0.6621 (OUTLIER) cc_final: 0.5994 (p) REVERT: B 486 MET cc_start: 0.3242 (tpp) cc_final: 0.3031 (tpp) REVERT: B 633 ILE cc_start: 0.3659 (OUTLIER) cc_final: 0.3144 (mm) REVERT: B 639 MET cc_start: 0.6262 (mpp) cc_final: 0.4620 (mpp) REVERT: B 934 MET cc_start: 0.5000 (ptt) cc_final: 0.4510 (ptm) REVERT: B 1036 MET cc_start: 0.1071 (mtp) cc_final: -0.1975 (ttp) REVERT: A 406 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9203 (ptmt) REVERT: A 453 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8228 (ttp80) REVERT: A 545 HIS cc_start: 0.6992 (OUTLIER) cc_final: 0.6572 (p90) REVERT: A 574 MET cc_start: 0.8794 (ppp) cc_final: 0.8537 (ppp) REVERT: A 665 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7817 (p90) REVERT: A 756 MET cc_start: 0.7969 (mmm) cc_final: 0.7719 (mmm) REVERT: A 860 MET cc_start: 0.9035 (ttm) cc_final: 0.8817 (mtm) REVERT: C 75 MET cc_start: 0.8826 (tpt) cc_final: 0.8563 (tpp) REVERT: C 110 MET cc_start: 0.5760 (tpp) cc_final: 0.5478 (tpp) REVERT: C 120 MET cc_start: 0.9197 (mmp) cc_final: 0.8836 (mmp) outliers start: 46 outliers final: 28 residues processed: 133 average time/residue: 0.1313 time to fit residues: 29.2087 Evaluate side-chains 131 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 418 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 61 optimal weight: 30.0000 chunk 194 optimal weight: 0.1980 chunk 230 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 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 = 0.3900 r_free = 0.3900 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.052085 restraints weight = 128936.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.052043 restraints weight = 79292.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052022 restraints weight = 58358.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.052032 restraints weight = 56287.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.052634 restraints weight = 46487.267| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19570 Z= 0.122 Angle : 0.652 12.679 26579 Z= 0.326 Chirality : 0.043 0.380 2927 Planarity : 0.005 0.065 3469 Dihedral : 5.832 77.530 2684 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.06 % Allowed : 19.49 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.19 (0.18), residues: 2409 helix: 1.12 (0.14), residues: 1368 sheet: -1.17 (0.41), residues: 169 loop : -1.14 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 792 TYR 0.016 0.001 TYR C 286 PHE 0.019 0.001 PHE B 673 TRP 0.021 0.002 TRP A1024 HIS 0.006 0.001 HIS B 545 Details of bonding type rmsd covalent geometry : bond 0.00275 (19570) covalent geometry : angle 0.65154 (26579) hydrogen bonds : bond 0.03332 ( 1030) hydrogen bonds : angle 4.50147 ( 3009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8484 (mmm) cc_final: 0.8148 (mmm) REVERT: B 101 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: B 224 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7886 (t80) REVERT: B 401 MET cc_start: 0.8911 (ppp) cc_final: 0.8619 (ppp) REVERT: B 466 TYR cc_start: 0.8481 (t80) cc_final: 0.7868 (t80) REVERT: B 467 CYS cc_start: 0.6562 (OUTLIER) cc_final: 0.5937 (p) REVERT: B 633 ILE cc_start: 0.3275 (OUTLIER) cc_final: 0.2751 (mm) REVERT: B 639 MET cc_start: 0.6243 (mpp) cc_final: 0.4778 (mpp) REVERT: B 934 MET cc_start: 0.4973 (ptt) cc_final: 0.4519 (ptm) REVERT: A 224 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 406 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9145 (ptmt) REVERT: A 453 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8389 (ttp80) REVERT: A 545 HIS cc_start: 0.6966 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 574 MET cc_start: 0.8751 (ppp) cc_final: 0.8470 (ppp) REVERT: A 606 MET cc_start: 0.8176 (mmm) cc_final: 0.7922 (mmp) REVERT: A 665 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7721 (p90) REVERT: A 756 MET cc_start: 0.7911 (mmm) cc_final: 0.7645 (mmm) REVERT: A 860 MET cc_start: 0.9043 (ttm) cc_final: 0.8824 (mtm) REVERT: A 893 MET cc_start: 0.8067 (ppp) cc_final: 0.7763 (ppp) REVERT: C 75 MET cc_start: 0.8842 (tpt) cc_final: 0.8589 (tpp) REVERT: C 110 MET cc_start: 0.5980 (tpp) cc_final: 0.5741 (tpp) REVERT: C 120 MET cc_start: 0.9178 (mmp) cc_final: 0.8825 (mmp) outliers start: 42 outliers final: 27 residues processed: 135 average time/residue: 0.1374 time to fit residues: 30.2629 Evaluate side-chains 130 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 79 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 226 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 220 optimal weight: 0.0670 chunk 167 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 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 = 0.3901 r_free = 0.3901 target = 0.072509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052230 restraints weight = 129974.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052223 restraints weight = 78580.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052185 restraints weight = 54921.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.052265 restraints weight = 54801.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052757 restraints weight = 45429.615| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19570 Z= 0.124 Angle : 0.660 15.758 26579 Z= 0.327 Chirality : 0.042 0.206 2927 Planarity : 0.005 0.064 3469 Dihedral : 5.714 73.970 2684 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.81 % Allowed : 19.88 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.23 (0.18), residues: 2409 helix: 1.14 (0.14), residues: 1372 sheet: -1.19 (0.41), residues: 169 loop : -1.12 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 792 TYR 0.024 0.001 TYR B 296 PHE 0.021 0.001 PHE A 902 TRP 0.021 0.002 TRP A1024 HIS 0.005 0.001 HIS A 708 Details of bonding type rmsd covalent geometry : bond 0.00281 (19570) covalent geometry : angle 0.65984 (26579) hydrogen bonds : bond 0.03286 ( 1030) hydrogen bonds : angle 4.45825 ( 3009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4818 Ramachandran restraints generated. 2409 Oldfield, 0 Emsley, 2409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8455 (mmm) cc_final: 0.8042 (mmm) REVERT: B 101 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: B 224 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7902 (t80) REVERT: B 320 LEU cc_start: 0.8902 (tp) cc_final: 0.8573 (pp) REVERT: B 401 MET cc_start: 0.8898 (ppp) cc_final: 0.8561 (ppp) REVERT: B 466 TYR cc_start: 0.8440 (t80) cc_final: 0.7844 (t80) REVERT: B 467 CYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6002 (p) REVERT: B 633 ILE cc_start: 0.3415 (OUTLIER) cc_final: 0.2906 (mm) REVERT: B 639 MET cc_start: 0.6250 (mpp) cc_final: 0.4797 (mpp) REVERT: B 934 MET cc_start: 0.5118 (ptt) cc_final: 0.4666 (ptm) REVERT: B 1023 MET cc_start: 0.5626 (tpp) cc_final: 0.5364 (tpp) REVERT: A 224 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 406 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9144 (ptmt) REVERT: A 545 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6730 (p90) REVERT: A 574 MET cc_start: 0.8784 (ppp) cc_final: 0.8468 (ppp) REVERT: A 606 MET cc_start: 0.8254 (mmm) cc_final: 0.8006 (mmp) REVERT: A 665 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7704 (p90) REVERT: A 705 ILE cc_start: 0.8272 (tp) cc_final: 0.7976 (tp) REVERT: A 756 MET cc_start: 0.7925 (mmm) cc_final: 0.7654 (mmm) REVERT: A 860 MET cc_start: 0.9049 (ttm) cc_final: 0.8830 (mtm) REVERT: A 893 MET cc_start: 0.8013 (ppp) cc_final: 0.7689 (ppp) REVERT: A 943 MET cc_start: 0.7812 (ptm) cc_final: 0.7540 (ttt) REVERT: C 75 MET cc_start: 0.8793 (tpt) cc_final: 0.8562 (tpp) REVERT: C 110 MET cc_start: 0.5993 (tpp) cc_final: 0.5770 (tpp) REVERT: C 120 MET cc_start: 0.9171 (mmp) cc_final: 0.8825 (mmp) outliers start: 37 outliers final: 27 residues processed: 129 average time/residue: 0.1212 time to fit residues: 25.7830 Evaluate side-chains 127 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 545 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 665 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 218 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 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 = 0.3881 r_free = 0.3881 target = 0.071724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.051773 restraints weight = 129269.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051257 restraints weight = 85152.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051177 restraints weight = 70407.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051398 restraints weight = 58955.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051540 restraints weight = 47696.680| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19570 Z= 0.154 Angle : 0.662 13.310 26579 Z= 0.333 Chirality : 0.042 0.203 2927 Planarity : 0.005 0.062 3469 Dihedral : 5.758 72.183 2684 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.01 % Allowed : 19.39 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % 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: 0.20 (0.18), residues: 2409 helix: 1.13 (0.14), residues: 1375 sheet: -1.20 (0.41), residues: 169 loop : -1.15 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 792 TYR 0.021 0.001 TYR B 296 PHE 0.020 0.001 PHE B 673 TRP 0.019 0.002 TRP A 208 HIS 0.007 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00341 (19570) covalent geometry : angle 0.66227 (26579) hydrogen bonds : bond 0.03440 ( 1030) hydrogen bonds : angle 4.54401 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.74 seconds wall clock time: 62 minutes 35.43 seconds (3755.43 seconds total)