Starting phenix.real_space_refine on Tue Jun 17 01:07:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yeh_33773/06_2025/7yeh_33773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yeh_33773/06_2025/7yeh_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_33773/06_2025/7yeh_33773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yeh_33773/06_2025/7yeh_33773.map" model { file = "/net/cci-nas-00/data/ceres_data/7yeh_33773/06_2025/7yeh_33773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yeh_33773/06_2025/7yeh_33773.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.84, per 1000 atoms: 0.57 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: 4.41 Conformation dependent library (CDL) restraints added in 2.2 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: 2.18 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: 6.43 Time building geometry restraints manager: 5.24 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 41.400 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (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 TRP 0.071 0.005 TRP A 861 HIS 0.008 0.002 HIS B 629 PHE 0.015 0.002 PHE C 133 TYR 0.021 0.002 TYR B 398 ARG 0.016 0.001 ARG A 877 Details of bonding type rmsd hydrogen bonds : bond 0.14433 ( 1030) hydrogen bonds : angle 7.06962 ( 3009) covalent geometry : bond 0.00583 (19570) covalent geometry : angle 1.00425 (26579) *********************** 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 : 2.070 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: 0.7770 (mm-30) REVERT: B 320 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8332 (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: 0.7828 (t80) REVERT: B 606 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.5209 (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 1036 MET cc_start: -0.0531 (OUTLIER) cc_final: -0.2499 (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: 0.7711 (mmt) REVERT: A 756 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: A 861 TRP cc_start: 0.8022 (m-90) cc_final: 0.7475 (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: 0.3867 time to fit residues: 116.5934 Evaluate side-chains 122 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 203 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.073380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051880 restraints weight = 127475.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.052648 restraints weight = 78585.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052916 restraints weight = 48641.914| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19570 Z= 0.167 Angle : 0.731 14.301 26579 Z= 0.381 Chirality : 0.046 0.193 2927 Planarity : 0.005 0.051 3469 Dihedral : 8.775 114.420 2743 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.62 % Allowed : 10.04 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2409 helix: 0.46 (0.14), residues: 1365 sheet: -1.46 (0.38), residues: 201 loop : -1.57 (0.24), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 48 HIS 0.004 0.001 HIS B 930 PHE 0.031 0.002 PHE B 292 TYR 0.024 0.002 TYR B 851 ARG 0.006 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 1030) hydrogen bonds : angle 5.46704 ( 3009) covalent geometry : bond 0.00363 (19570) covalent geometry : angle 0.73113 (26579) *********************** 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 156 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7399 (pt0) REVERT: B 320 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8533 (pp) REVERT: B 466 TYR cc_start: 0.8580 (t80) cc_final: 0.7923 (t80) REVERT: B 851 TYR cc_start: 0.6990 (p90) cc_final: 0.6517 (p90) REVERT: B 877 ARG cc_start: 0.4352 (OUTLIER) cc_final: 0.3426 (ptm160) REVERT: B 893 MET cc_start: 0.3528 (ppp) cc_final: 0.3214 (ppp) REVERT: B 1023 MET cc_start: 0.6952 (mpp) cc_final: 0.6452 (mtt) REVERT: A 408 MET cc_start: 0.9135 (pmm) cc_final: 0.8655 (pmm) REVERT: A 736 LEU cc_start: 0.9320 (tp) cc_final: 0.9101 (tp) REVERT: A 792 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: A 861 TRP cc_start: 0.8328 (m-90) cc_final: 0.7652 (m-90) REVERT: C 75 MET cc_start: 0.8971 (tpt) cc_final: 0.8765 (tpp) REVERT: C 120 MET cc_start: 0.9104 (mmp) cc_final: 0.8805 (mmp) outliers start: 33 outliers final: 8 residues processed: 145 average time/residue: 0.3436 time to fit residues: 76.5170 Evaluate side-chains 114 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 213 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 0.0030 chunk 119 optimal weight: 3.9990 overall best weight: 3.3796 ------------------------------------------------------------------------------- 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 264 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS B 708 HIS ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 891 GLN B 897 GLN B 911 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.072123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051168 restraints weight = 127973.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051114 restraints weight = 89597.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051384 restraints weight = 57116.426| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19570 Z= 0.189 Angle : 0.690 12.147 26579 Z= 0.359 Chirality : 0.044 0.164 2927 Planarity : 0.005 0.059 3469 Dihedral : 6.956 82.050 2696 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.86 % Allowed : 13.91 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2409 helix: 0.62 (0.14), residues: 1361 sheet: -1.47 (0.43), residues: 168 loop : -1.38 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 874 HIS 0.007 0.001 HIS A 439 PHE 0.024 0.002 PHE B 673 TYR 0.033 0.002 TYR B1020 ARG 0.007 0.001 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 1030) hydrogen bonds : angle 5.15133 ( 3009) covalent geometry : bond 0.00408 (19570) covalent geometry : angle 0.69017 (26579) *********************** 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 148 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 2.293 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: 0.8329 (mmm) cc_final: 0.7955 (mmm) REVERT: B 46 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7518 (mm-40) REVERT: B 292 PHE cc_start: 0.7359 (t80) cc_final: 0.7073 (t80) REVERT: B 320 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (pp) REVERT: B 401 MET cc_start: 0.8904 (ppp) cc_final: 0.8636 (ppp) REVERT: B 466 TYR cc_start: 0.8567 (t80) cc_final: 0.7884 (t80) REVERT: B 893 MET cc_start: 0.3529 (ppp) cc_final: 0.3212 (ppp) REVERT: A 408 MET cc_start: 0.9021 (pmm) cc_final: 0.8561 (pmm) REVERT: A 453 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8374 (ttp80) REVERT: A 736 LEU cc_start: 0.9377 (tp) cc_final: 0.9140 (tp) REVERT: C 75 MET cc_start: 0.8941 (tpt) cc_final: 0.8722 (tpp) REVERT: C 110 MET cc_start: 0.6331 (tpp) cc_final: 0.5934 (tpp) REVERT: C 120 MET cc_start: 0.9119 (mmp) cc_final: 0.8795 (mmp) outliers start: 38 outliers final: 16 residues processed: 141 average time/residue: 0.2999 time to fit residues: 68.7524 Evaluate side-chains 118 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 VAL 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 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 830 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 34 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 204 GLN B 439 HIS B 468 ASN ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.072834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051952 restraints weight = 129363.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.051933 restraints weight = 87026.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052129 restraints weight = 54788.960| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19570 Z= 0.141 Angle : 0.641 12.082 26579 Z= 0.330 Chirality : 0.043 0.273 2927 Planarity : 0.005 0.063 3469 Dihedral : 6.525 82.132 2688 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.06 % Allowed : 15.96 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2409 helix: 0.87 (0.14), residues: 1362 sheet: -1.22 (0.43), residues: 162 loop : -1.39 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1024 HIS 0.006 0.001 HIS A 439 PHE 0.021 0.001 PHE A 902 TYR 0.033 0.001 TYR B1020 ARG 0.005 0.000 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 1030) hydrogen bonds : angle 4.82877 ( 3009) covalent geometry : bond 0.00310 (19570) covalent geometry : angle 0.64114 (26579) *********************** 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 150 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 1.998 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: 0.8300 (mmm) cc_final: 0.7944 (mmm) REVERT: B 73 ARG cc_start: 0.9119 (tpm170) cc_final: 0.8795 (tpp-160) REVERT: B 292 PHE cc_start: 0.7451 (t80) cc_final: 0.7086 (t80) REVERT: B 320 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8669 (pp) REVERT: B 401 MET cc_start: 0.8889 (ppp) cc_final: 0.8651 (ppp) REVERT: B 466 TYR cc_start: 0.8480 (t80) cc_final: 0.7804 (t80) REVERT: B 1014 MET cc_start: 0.6791 (mmt) cc_final: 0.6475 (mpp) REVERT: B 1023 MET cc_start: 0.4610 (mmt) cc_final: 0.4387 (tpp) REVERT: B 1036 MET cc_start: -0.0664 (mtp) cc_final: -0.3495 (ttp) REVERT: A 406 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9224 (ptmt) REVERT: A 408 MET cc_start: 0.9007 (pmm) cc_final: 0.8569 (pmm) REVERT: A 453 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8400 (ttp80) REVERT: A 736 LEU cc_start: 0.9412 (tp) cc_final: 0.9090 (tp) REVERT: A 860 MET cc_start: 0.9056 (ttm) cc_final: 0.8663 (ttm) REVERT: A 861 TRP cc_start: 0.8258 (m-10) cc_final: 0.7517 (m-90) REVERT: C 75 MET cc_start: 0.8847 (tpt) cc_final: 0.8629 (tpp) REVERT: C 110 MET cc_start: 0.6216 (tpp) cc_final: 0.5812 (tpp) REVERT: C 120 MET cc_start: 0.9126 (mmp) cc_final: 0.8793 (mmp) outliers start: 42 outliers final: 17 residues processed: 146 average time/residue: 0.3156 time to fit residues: 73.0472 Evaluate side-chains 115 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 630 GLN Chi-restraints excluded: chain B residue 688 VAL 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 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 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 185 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 95 optimal weight: 40.0000 chunk 123 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 930 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.072022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.051526 restraints weight = 129495.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.051285 restraints weight = 79123.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051305 restraints weight = 56812.072| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19570 Z= 0.166 Angle : 0.644 11.255 26579 Z= 0.333 Chirality : 0.043 0.156 2927 Planarity : 0.005 0.063 3469 Dihedral : 6.412 81.656 2688 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.55 % Allowed : 16.99 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2409 helix: 0.91 (0.14), residues: 1363 sheet: -1.20 (0.43), residues: 162 loop : -1.35 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 874 HIS 0.007 0.001 HIS A 439 PHE 0.022 0.002 PHE B 673 TYR 0.029 0.002 TYR B1020 ARG 0.005 0.001 ARG B 973 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 1030) hydrogen bonds : angle 4.77252 ( 3009) covalent geometry : bond 0.00362 (19570) covalent geometry : angle 0.64423 (26579) *********************** 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 149 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 2.335 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: 0.8368 (mmm) cc_final: 0.8048 (mmm) REVERT: B 320 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (pp) REVERT: B 401 MET cc_start: 0.8866 (ppp) cc_final: 0.8632 (ppp) REVERT: B 466 TYR cc_start: 0.8445 (t80) cc_final: 0.7826 (t80) REVERT: B 633 ILE cc_start: 0.3841 (OUTLIER) cc_final: 0.3476 (mm) REVERT: B 1023 MET cc_start: 0.4452 (mmt) cc_final: 0.3898 (tpp) REVERT: A 406 LYS cc_start: 0.9605 (OUTLIER) cc_final: 0.9220 (ptmt) REVERT: A 453 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8233 (ttp80) REVERT: A 736 LEU cc_start: 0.9376 (tp) cc_final: 0.9074 (tp) REVERT: A 756 MET cc_start: 0.7854 (mmm) cc_final: 0.7632 (mmm) REVERT: A 860 MET cc_start: 0.8999 (ttm) cc_final: 0.8539 (ttm) REVERT: A 861 TRP cc_start: 0.8272 (m-10) cc_final: 0.7567 (m-90) REVERT: C 75 MET cc_start: 0.8829 (tpt) cc_final: 0.8579 (tpp) REVERT: C 110 MET cc_start: 0.6094 (tpp) cc_final: 0.5697 (tpp) REVERT: C 120 MET cc_start: 0.9144 (mmp) cc_final: 0.8809 (mmp) outliers start: 52 outliers final: 27 residues processed: 144 average time/residue: 0.2963 time to fit residues: 70.5019 Evaluate side-chains 124 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 207 ILE 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 633 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1037 ILE 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 561 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 688 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 229 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 928 ASN ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051843 restraints weight = 130611.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051987 restraints weight = 80931.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051925 restraints weight = 57291.485| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19570 Z= 0.135 Angle : 0.627 11.240 26579 Z= 0.321 Chirality : 0.042 0.171 2927 Planarity : 0.005 0.065 3469 Dihedral : 6.178 81.360 2688 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.96 % Allowed : 18.02 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2409 helix: 1.01 (0.14), residues: 1368 sheet: -1.23 (0.42), residues: 169 loop : -1.30 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1024 HIS 0.005 0.001 HIS A 439 PHE 0.020 0.001 PHE B 673 TYR 0.025 0.001 TYR B1020 ARG 0.004 0.000 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 1030) hydrogen bonds : angle 4.56881 ( 3009) covalent geometry : bond 0.00300 (19570) covalent geometry : angle 0.62730 (26579) *********************** 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 140 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8399 (mmm) cc_final: 0.8114 (mmm) REVERT: B 73 ARG cc_start: 0.9088 (tpm170) cc_final: 0.8782 (tpp-160) REVERT: B 224 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 320 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (pp) REVERT: B 401 MET cc_start: 0.8905 (ppp) cc_final: 0.8639 (ppp) REVERT: B 466 TYR cc_start: 0.8458 (t80) cc_final: 0.7784 (t80) REVERT: B 486 MET cc_start: 0.3299 (tpp) cc_final: 0.3006 (tpp) REVERT: B 633 ILE cc_start: 0.3624 (OUTLIER) cc_final: 0.3355 (mm) REVERT: B 797 ILE cc_start: 0.6991 (tp) cc_final: 0.6548 (pt) REVERT: B 1014 MET cc_start: 0.6602 (mmt) cc_final: 0.6301 (mpp) REVERT: B 1023 MET cc_start: 0.4473 (mmt) cc_final: 0.4148 (tpp) REVERT: A 406 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9197 (ptmt) REVERT: A 453 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8363 (ttp80) REVERT: A 511 MET cc_start: 0.8722 (pmm) cc_final: 0.8433 (pmm) REVERT: A 545 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6724 (p90) REVERT: A 736 LEU cc_start: 0.9442 (tp) cc_final: 0.9121 (tp) REVERT: A 756 MET cc_start: 0.7924 (mmm) cc_final: 0.7677 (mmm) REVERT: A 860 MET cc_start: 0.9082 (ttm) cc_final: 0.8588 (ttm) REVERT: A 861 TRP cc_start: 0.8218 (m-10) cc_final: 0.7482 (m-90) REVERT: C 75 MET cc_start: 0.8860 (tpt) cc_final: 0.8620 (tpp) REVERT: C 90 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 110 MET cc_start: 0.6073 (tpp) cc_final: 0.5643 (tpp) REVERT: C 120 MET cc_start: 0.9168 (mmp) cc_final: 0.8829 (mmp) outliers start: 40 outliers final: 21 residues processed: 135 average time/residue: 0.2955 time to fit residues: 64.7976 Evaluate side-chains 124 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 224 PHE 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 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 990 LEU Chi-restraints excluded: chain B residue 1037 ILE 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 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 990 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 430 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.072572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.052062 restraints weight = 128422.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052130 restraints weight = 78527.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052091 restraints weight = 55029.548| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3624 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= 0.128 Angle : 0.625 11.155 26579 Z= 0.319 Chirality : 0.042 0.161 2927 Planarity : 0.005 0.065 3469 Dihedral : 6.023 80.050 2688 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.01 % Allowed : 18.46 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.18), residues: 2409 helix: 1.08 (0.14), residues: 1368 sheet: -1.22 (0.42), residues: 169 loop : -1.25 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1024 HIS 0.008 0.001 HIS B 545 PHE 0.021 0.001 PHE A 902 TYR 0.023 0.001 TYR B1020 ARG 0.004 0.000 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 1030) hydrogen bonds : angle 4.50061 ( 3009) covalent geometry : bond 0.00285 (19570) covalent geometry : angle 0.62498 (26579) *********************** 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 140 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8398 (mmm) cc_final: 0.8096 (mmm) REVERT: B 73 ARG cc_start: 0.9096 (tpm170) cc_final: 0.8789 (tpp-160) REVERT: B 224 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 401 MET cc_start: 0.8912 (ppp) cc_final: 0.8637 (ppp) REVERT: B 466 TYR cc_start: 0.8454 (t80) cc_final: 0.7784 (t80) REVERT: B 486 MET cc_start: 0.3236 (tpp) cc_final: 0.2991 (tpp) REVERT: B 633 ILE cc_start: 0.3215 (OUTLIER) cc_final: 0.2863 (mm) REVERT: B 797 ILE cc_start: 0.7062 (tp) cc_final: 0.6769 (pt) REVERT: B 934 MET cc_start: 0.4580 (ppp) cc_final: 0.3983 (ppp) REVERT: B 1023 MET cc_start: 0.4477 (mmt) cc_final: 0.3904 (tpp) REVERT: A 406 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9192 (ptmt) REVERT: A 453 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8357 (ttp80) REVERT: A 545 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.6642 (p90) REVERT: A 665 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7653 (p90) REVERT: A 756 MET cc_start: 0.7964 (mmm) cc_final: 0.7718 (mmm) REVERT: A 860 MET cc_start: 0.9079 (ttm) cc_final: 0.8555 (ttm) REVERT: A 861 TRP cc_start: 0.8230 (m-10) cc_final: 0.7478 (m-90) REVERT: C 75 MET cc_start: 0.8841 (tpt) cc_final: 0.8604 (tpp) REVERT: C 90 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 110 MET cc_start: 0.6116 (tpp) cc_final: 0.5694 (tpp) REVERT: C 120 MET cc_start: 0.9168 (mmp) cc_final: 0.8821 (mmp) outliers start: 41 outliers final: 27 residues processed: 134 average time/residue: 0.2912 time to fit residues: 63.4082 Evaluate side-chains 132 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 320 LEU Chi-restraints excluded: chain B residue 398 TYR 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 27 LEU 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 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 A residue 990 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 90 LEU 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 Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 22 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** 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 794 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 = 0.3871 r_free = 0.3871 target = 0.071464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.050566 restraints weight = 128710.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050771 restraints weight = 82892.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050651 restraints weight = 57953.868| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19570 Z= 0.183 Angle : 0.665 15.069 26579 Z= 0.341 Chirality : 0.043 0.160 2927 Planarity : 0.005 0.063 3469 Dihedral : 6.076 79.850 2686 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.30 % Allowed : 18.76 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2409 helix: 1.01 (0.14), residues: 1377 sheet: -1.26 (0.41), residues: 169 loop : -1.30 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 874 HIS 0.008 0.001 HIS B 545 PHE 0.025 0.001 PHE A 902 TYR 0.023 0.002 TYR B1020 ARG 0.014 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1030) hydrogen bonds : angle 4.68612 ( 3009) covalent geometry : bond 0.00397 (19570) covalent geometry : angle 0.66517 (26579) *********************** 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 144 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8396 (mmm) cc_final: 0.8085 (mmm) REVERT: B 73 ARG cc_start: 0.9116 (tpm170) cc_final: 0.8784 (tpp-160) REVERT: B 224 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 398 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: B 401 MET cc_start: 0.8928 (ppp) cc_final: 0.8670 (ppp) REVERT: B 466 TYR cc_start: 0.8474 (t80) cc_final: 0.7788 (t80) REVERT: B 486 MET cc_start: 0.3326 (tpp) cc_final: 0.3079 (tpp) REVERT: B 639 MET cc_start: 0.6449 (mpp) cc_final: 0.4991 (mpp) REVERT: B 797 ILE cc_start: 0.7095 (tp) cc_final: 0.6661 (pt) REVERT: B 934 MET cc_start: 0.4764 (ppp) cc_final: 0.4141 (ppp) REVERT: B 1023 MET cc_start: 0.4395 (mmt) cc_final: 0.3859 (tpp) REVERT: A 406 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9218 (ptmt) REVERT: A 453 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8320 (ttp80) REVERT: A 545 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6658 (p90) REVERT: A 606 MET cc_start: 0.8780 (mmp) cc_final: 0.8474 (mmm) REVERT: A 665 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7768 (p90) REVERT: A 756 MET cc_start: 0.8028 (mmm) cc_final: 0.7782 (mmm) REVERT: A 860 MET cc_start: 0.9098 (ttm) cc_final: 0.8803 (mtm) REVERT: A 861 TRP cc_start: 0.8281 (m-10) cc_final: 0.7542 (m-90) REVERT: C 75 MET cc_start: 0.8875 (tpt) cc_final: 0.8615 (tpp) REVERT: C 90 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8514 (mp) REVERT: C 110 MET cc_start: 0.5930 (tpp) cc_final: 0.5194 (tpp) REVERT: C 120 MET cc_start: 0.9197 (mmp) cc_final: 0.8842 (mmp) outliers start: 47 outliers final: 31 residues processed: 136 average time/residue: 0.2739 time to fit residues: 61.3674 Evaluate side-chains 135 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ILE 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 398 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 588 VAL 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 57 VAL Chi-restraints excluded: chain A residue 101 GLU 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 537 VAL 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 90 LEU 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 Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 111 optimal weight: 9.9990 chunk 54 optimal weight: 40.0000 chunk 192 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 545 HIS ** 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 640 ASN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3903 r_free = 0.3903 target = 0.072748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.052157 restraints weight = 128533.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.052251 restraints weight = 87120.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.052327 restraints weight = 59415.746| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19570 Z= 0.117 Angle : 0.635 15.868 26579 Z= 0.320 Chirality : 0.042 0.200 2927 Planarity : 0.005 0.065 3469 Dihedral : 5.812 77.775 2684 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.11 % Allowed : 18.85 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2409 helix: 1.13 (0.14), residues: 1370 sheet: -1.15 (0.41), residues: 169 loop : -1.21 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1024 HIS 0.006 0.001 HIS B 545 PHE 0.020 0.001 PHE A 902 TYR 0.022 0.001 TYR B1020 ARG 0.004 0.000 ARG A 954 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1030) hydrogen bonds : angle 4.44945 ( 3009) covalent geometry : bond 0.00265 (19570) covalent geometry : angle 0.63479 (26579) *********************** 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 145 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8391 (mmm) cc_final: 0.8061 (mmm) REVERT: B 73 ARG cc_start: 0.9075 (tpm170) cc_final: 0.8760 (tpp-160) REVERT: B 224 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7858 (t80) REVERT: B 401 MET cc_start: 0.8907 (ppp) cc_final: 0.8638 (ppp) REVERT: B 466 TYR cc_start: 0.8434 (t80) cc_final: 0.7825 (t80) REVERT: B 467 CYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5954 (p) REVERT: B 639 MET cc_start: 0.6539 (mpp) cc_final: 0.5094 (mpp) REVERT: B 797 ILE cc_start: 0.7204 (tp) cc_final: 0.6719 (pt) REVERT: B 934 MET cc_start: 0.4659 (ppp) cc_final: 0.4052 (ppp) REVERT: B 1023 MET cc_start: 0.4386 (mmt) cc_final: 0.3857 (tpp) REVERT: A 224 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 406 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9157 (ptmt) REVERT: A 453 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8436 (ttp80) REVERT: A 606 MET cc_start: 0.8727 (mmp) cc_final: 0.8443 (mmm) REVERT: A 665 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7614 (p90) REVERT: A 756 MET cc_start: 0.7984 (mmm) cc_final: 0.7738 (mmm) REVERT: A 860 MET cc_start: 0.9078 (ttm) cc_final: 0.8794 (mtm) REVERT: A 861 TRP cc_start: 0.8194 (m-10) cc_final: 0.7430 (m-90) REVERT: C 75 MET cc_start: 0.8807 (tpt) cc_final: 0.8552 (tpp) REVERT: C 90 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8479 (mp) REVERT: C 110 MET cc_start: 0.6041 (tpp) cc_final: 0.5433 (tpp) REVERT: C 120 MET cc_start: 0.9159 (mmp) cc_final: 0.8800 (mmp) outliers start: 43 outliers final: 29 residues processed: 139 average time/residue: 0.2947 time to fit residues: 67.0891 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 : 2.053 ------------------------------------------------------------------------------- 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 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 588 VAL 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 57 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 224 PHE 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 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 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 90 LEU 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 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 48 optimal weight: 0.0770 chunk 146 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 238 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 545 HIS ** 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 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.073248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.053211 restraints weight = 128737.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052986 restraints weight = 78251.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052936 restraints weight = 56946.474| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4162 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= 0.113 Angle : 0.643 14.277 26579 Z= 0.321 Chirality : 0.042 0.211 2927 Planarity : 0.005 0.064 3469 Dihedral : 5.595 73.451 2684 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.76 % Allowed : 19.20 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2409 helix: 1.15 (0.14), residues: 1374 sheet: -1.12 (0.41), residues: 169 loop : -1.17 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1024 HIS 0.006 0.001 HIS A 629 PHE 0.020 0.001 PHE B 673 TYR 0.021 0.001 TYR B1020 ARG 0.004 0.000 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 1030) hydrogen bonds : angle 4.33376 ( 3009) covalent geometry : bond 0.00254 (19570) covalent geometry : angle 0.64268 (26579) ********************** 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 140 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8400 (mmm) cc_final: 0.8040 (mmm) REVERT: B 224 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 320 LEU cc_start: 0.8827 (tp) cc_final: 0.8544 (pp) REVERT: B 401 MET cc_start: 0.8926 (ppp) cc_final: 0.8622 (ppp) REVERT: B 466 TYR cc_start: 0.8535 (t80) cc_final: 0.7880 (t80) REVERT: B 467 CYS cc_start: 0.6597 (OUTLIER) cc_final: 0.5978 (p) REVERT: B 633 ILE cc_start: 0.2957 (OUTLIER) cc_final: 0.2602 (mm) REVERT: B 639 MET cc_start: 0.6463 (mpp) cc_final: 0.5218 (mpp) REVERT: B 797 ILE cc_start: 0.7065 (tp) cc_final: 0.6721 (pt) REVERT: B 934 MET cc_start: 0.4262 (ppp) cc_final: 0.3658 (ppp) REVERT: B 1023 MET cc_start: 0.4412 (mmt) cc_final: 0.3873 (tpp) REVERT: A 406 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9160 (ptmt) REVERT: A 545 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6727 (p90) REVERT: A 606 MET cc_start: 0.8744 (mmp) cc_final: 0.8448 (mmm) REVERT: A 665 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7591 (p90) REVERT: A 705 ILE cc_start: 0.8186 (tp) cc_final: 0.7865 (tp) REVERT: A 756 MET cc_start: 0.7927 (mmm) cc_final: 0.7662 (mmm) REVERT: A 860 MET cc_start: 0.9065 (ttm) cc_final: 0.8809 (mtm) REVERT: A 861 TRP cc_start: 0.8162 (m-10) cc_final: 0.7407 (m-90) REVERT: A 893 MET cc_start: 0.7954 (ppp) cc_final: 0.7616 (ppp) REVERT: C 75 MET cc_start: 0.8834 (tpt) cc_final: 0.8611 (tpp) REVERT: C 90 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 110 MET cc_start: 0.6215 (tpp) cc_final: 0.5933 (mmm) REVERT: C 120 MET cc_start: 0.9141 (mmp) cc_final: 0.8805 (mmp) outliers start: 36 outliers final: 25 residues processed: 135 average time/residue: 0.2950 time to fit residues: 65.1663 Evaluate side-chains 126 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 2.112 ------------------------------------------------------------------------------- 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 201 PHE Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 515 LEU 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 326 HIS Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 406 LYS Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 VAL 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 90 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 432 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 214 optimal weight: 8.9990 chunk 236 optimal weight: 0.0570 chunk 90 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 189 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- 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 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 794 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 = 0.3911 r_free = 0.3911 target = 0.072923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052660 restraints weight = 130076.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.052910 restraints weight = 76151.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.052456 restraints weight = 61806.601| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4272 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= 0.118 Angle : 0.656 15.213 26579 Z= 0.327 Chirality : 0.042 0.295 2927 Planarity : 0.005 0.064 3469 Dihedral : 5.517 71.357 2684 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.96 % Allowed : 19.29 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2409 helix: 1.21 (0.14), residues: 1374 sheet: -1.21 (0.41), residues: 169 loop : -1.16 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1024 HIS 0.005 0.001 HIS B 545 PHE 0.020 0.001 PHE B 673 TYR 0.021 0.001 TYR B1020 ARG 0.004 0.000 ARG B 70 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1030) hydrogen bonds : angle 4.32776 ( 3009) covalent geometry : bond 0.00269 (19570) covalent geometry : angle 0.65600 (26579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6971.86 seconds wall clock time: 124 minutes 55.47 seconds (7495.47 seconds total)