Starting phenix.real_space_refine on Sun Jul 5 02:07:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ub6_26436/07_2026/7ub6_26436.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.134 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15818 2.51 5 N 4068 2.21 5 O 4762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24762 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8151 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 50, 'TRANS': 991} Chain breaks: 6 Chain: "B" Number of atoms: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8028 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8079 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 49, 'TRANS': 985} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.49, per 1000 atoms: 0.22 Number of scatterers: 24762 At special positions: 0 Unit cell: (127.44, 138.24, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4762 8.00 N 4068 7.00 C 15818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 45 sheets defined 26.0% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.933A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.867A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.375A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.827A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.745A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.875A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.569A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.788A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.777A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.828A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.651A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.927A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.677A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.949A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.346A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 835 through 842 removed outlier: 3.585A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 857 removed outlier: 3.677A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.363A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.640A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.289A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.556A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.800A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.237A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 756 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.712A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.579A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 842 removed outlier: 4.218A pdb=" N LEU C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 837 through 842' Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.532A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.289A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.678A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.098A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.695A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.756A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.117A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.180A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.068A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.308A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.658A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.737A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.992A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.709A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.945A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.072A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.469A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 30 removed outlier: 3.691A pdb=" N THR B 23 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.168A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 310 through 319 removed outlier: 6.946A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.352A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.657A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.278A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.655A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.638A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.787A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.902A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.674A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.260A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.542A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.703A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.697A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2769 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: 6.58 Time building geometry restraints manager: 2.76 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: 7851 1.34 - 1.47: 6257 1.47 - 1.59: 11063 1.59 - 1.72: 0 1.72 - 1.84: 141 Bond restraints: 25312 Sorted by residual: bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.332 1.367 -0.035 1.12e-02 7.97e+03 9.88e+00 bond pdb=" N LEU C 517 " pdb=" CA LEU C 517 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.32e+00 bond pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.26e+00 bond pdb=" N LYS A 195 " pdb=" CA LYS A 195 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.26e-02 6.30e+03 7.10e+00 bond pdb=" N PHE C 392 " pdb=" CA PHE C 392 " ideal model delta sigma weight residual 1.452 1.486 -0.035 1.30e-02 5.92e+03 7.08e+00 ... (remaining 25307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 33723 2.08 - 4.16: 630 4.16 - 6.25: 49 6.25 - 8.33: 13 8.33 - 10.41: 6 Bond angle restraints: 34421 Sorted by residual: angle pdb=" C ASP B 848 " pdb=" N LEU B 849 " pdb=" CA LEU B 849 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C CYS C 480 " pdb=" N ASN C 481 " pdb=" CA ASN C 481 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N PRO A 621 " ideal model delta sigma weight residual 118.88 124.73 -5.85 1.54e+00 4.22e-01 1.44e+01 angle pdb=" N VAL A 620 " pdb=" CA VAL A 620 " pdb=" C VAL A 620 " ideal model delta sigma weight residual 108.88 116.72 -7.84 2.16e+00 2.14e-01 1.32e+01 angle pdb=" CA ALA C 522 " pdb=" C ALA C 522 " pdb=" O ALA C 522 " ideal model delta sigma weight residual 122.36 118.17 4.19 1.21e+00 6.83e-01 1.20e+01 ... (remaining 34416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 13407 17.44 - 34.88: 1155 34.88 - 52.32: 182 52.32 - 69.76: 32 69.76 - 87.20: 22 Dihedral angle restraints: 14798 sinusoidal: 5763 harmonic: 9035 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -170.91 84.91 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -169.25 83.25 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.83 78.83 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 14795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3531 0.085 - 0.170: 468 0.170 - 0.255: 20 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 4020 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4017 not shown) Planarity restraints: 4431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.025 2.00e-02 2.50e+03 2.12e-02 9.03e+00 pdb=" CG TYR A 453 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO C 295 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO A 295 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.033 5.00e-02 4.00e+02 ... (remaining 4428 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3658 2.76 - 3.30: 21218 3.30 - 3.83: 40525 3.83 - 4.37: 46028 4.37 - 4.90: 82986 Nonbonded interactions: 194415 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.229 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.309 3.040 nonbonded pdb=" O THR B1116 " pdb=" OG1 THR B1120 " model vdw 2.312 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.321 3.040 nonbonded pdb=" O THR C1116 " pdb=" OG1 THR C1120 " model vdw 2.331 3.040 ... (remaining 194410 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 24 through 68 or resid 81 through 137 or resid 166 through \ 210 or resid 215 through 243 or resid 263 through 475 or resid 479 through 674 \ or resid 691 through 1308)) selection = (chain 'B' and (resid 24 through 137 or resid 166 through 622 or resid 641 throu \ gh 1308)) selection = (chain 'C' and (resid 24 through 68 or resid 81 through 177 or resid 187 through \ 210 or resid 215 through 243 or resid 263 through 475 or resid 479 through 622 \ or resid 641 through 674 or resid 691 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 24.780 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25390 Z= 0.213 Angle : 0.683 13.684 34613 Z= 0.364 Chirality : 0.052 0.425 4020 Planarity : 0.005 0.061 4399 Dihedral : 13.117 87.197 8858 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3057 helix: 0.06 (0.17), residues: 689 sheet: 0.30 (0.19), residues: 679 loop : -1.17 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.052 0.001 TYR A 453 PHE 0.034 0.002 PHE A 559 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (25312) covalent geometry : angle 0.66616 / 0.36 (34421) SS BOND : bond 0.00273 / 0.17 ( 42) SS BOND : angle 0.88597 / 0.61 ( 84) hydrogen bonds : bond 0.08024 / 5.22 ( 1006) hydrogen bonds : angle 5.91771 / 4.08 ( 2769) link_BETA1-4 : bond 0.00423 / 0.21 ( 4) link_BETA1-4 : angle 1.30866 / 0.85 ( 12) link_NAG-ASN : bond 0.00385 / 0.25 ( 32) link_NAG-ASN : angle 2.84821 / 2.22 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.996 Fit side-chains REVERT: A 197 ILE cc_start: 0.8901 (mm) cc_final: 0.8420 (mm) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1473 time to fit residues: 14.2152 Evaluate side-chains 43 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 613 GLN B 188 ASN B 239 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 580 GLN C 613 GLN C 690 GLN C 779 GLN C 804 GLN C 901 GLN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.047123 restraints weight = 92301.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.047989 restraints weight = 56836.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048444 restraints weight = 39300.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048609 restraints weight = 37206.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.048700 restraints weight = 33647.426| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 25390 Z= 0.342 Angle : 0.672 10.910 34613 Z= 0.344 Chirality : 0.049 0.428 4020 Planarity : 0.004 0.041 4399 Dihedral : 4.578 20.825 3324 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.19 % Allowed : 5.04 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3057 helix: 1.20 (0.19), residues: 680 sheet: -0.03 (0.19), residues: 697 loop : -1.08 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.040 0.002 TYR C 756 PHE 0.030 0.002 PHE A 906 TRP 0.015 0.002 TRP A 886 HIS 0.008 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.34 (25312) covalent geometry : angle 0.65557 / 0.34 (34421) SS BOND : bond 0.00550 / 0.34 ( 42) SS BOND : angle 1.03859 / 0.71 ( 84) hydrogen bonds : bond 0.05808 / 3.77 ( 1006) hydrogen bonds : angle 5.43780 / 3.74 ( 2769) link_BETA1-4 : bond 0.00480 / 0.24 ( 4) link_BETA1-4 : angle 1.48079 / 1.07 ( 12) link_NAG-ASN : bond 0.00509 / 0.34 ( 32) link_NAG-ASN : angle 2.75067 / 2.10 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.975 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.1482 time to fit residues: 12.7114 Evaluate side-chains 46 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 489 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 267 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 120 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.065129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049031 restraints weight = 91004.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050371 restraints weight = 51943.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.050608 restraints weight = 33323.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051318 restraints weight = 33256.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051332 restraints weight = 28608.842| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25390 Z= 0.108 Angle : 0.483 10.573 34613 Z= 0.248 Chirality : 0.043 0.383 4020 Planarity : 0.003 0.037 4399 Dihedral : 4.095 18.373 3324 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.30 % Allowed : 6.49 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3057 helix: 2.01 (0.20), residues: 682 sheet: 0.21 (0.20), residues: 692 loop : -0.98 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1091 TYR 0.018 0.001 TYR C 837 PHE 0.011 0.001 PHE A 559 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (25312) covalent geometry : angle 0.46625 / 0.24 (34421) SS BOND : bond 0.00323 / 0.21 ( 42) SS BOND : angle 0.83025 / 0.57 ( 84) hydrogen bonds : bond 0.04178 / 2.70 ( 1006) hydrogen bonds : angle 4.98414 / 3.43 ( 2769) link_BETA1-4 : bond 0.00210 / 0.11 ( 4) link_BETA1-4 : angle 0.98416 / 0.72 ( 12) link_NAG-ASN : bond 0.00263 / 0.17 ( 32) link_NAG-ASN : angle 2.34871 / 1.80 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: C 523 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8203 (p) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.1565 time to fit residues: 15.2564 Evaluate side-chains 48 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 254 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 173 optimal weight: 0.0170 chunk 145 optimal weight: 0.5980 chunk 258 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048471 restraints weight = 90812.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049682 restraints weight = 53874.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050050 restraints weight = 35172.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051028 restraints weight = 34665.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051141 restraints weight = 28490.868| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25390 Z= 0.151 Angle : 0.492 10.419 34613 Z= 0.251 Chirality : 0.043 0.383 4020 Planarity : 0.003 0.034 4399 Dihedral : 3.994 16.676 3324 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.45 % Allowed : 8.35 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3057 helix: 2.18 (0.20), residues: 689 sheet: 0.19 (0.20), residues: 692 loop : -0.92 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.021 0.001 TYR C 756 PHE 0.013 0.001 PHE A1042 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (25312) covalent geometry : angle 0.47632 / 0.25 (34421) SS BOND : bond 0.00323 / 0.20 ( 42) SS BOND : angle 0.79900 / 0.51 ( 84) hydrogen bonds : bond 0.04266 / 2.76 ( 1006) hydrogen bonds : angle 4.90468 / 3.37 ( 2769) link_BETA1-4 : bond 0.00199 / 0.10 ( 4) link_BETA1-4 : angle 1.05483 / 0.79 ( 12) link_NAG-ASN : bond 0.00267 / 0.18 ( 32) link_NAG-ASN : angle 2.30883 / 1.79 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8838 (mtt) cc_final: 0.8185 (mtt) REVERT: B 1029 MET cc_start: 0.9460 (tpp) cc_final: 0.9128 (ttm) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.1449 time to fit residues: 14.6010 Evaluate side-chains 55 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 33 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.048074 restraints weight = 91198.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049260 restraints weight = 52924.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.049450 restraints weight = 35235.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.050286 restraints weight = 34755.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050320 restraints weight = 29956.946| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25390 Z= 0.186 Angle : 0.518 10.521 34613 Z= 0.264 Chirality : 0.044 0.382 4020 Planarity : 0.003 0.035 4399 Dihedral : 4.040 16.963 3324 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.67 % Allowed : 9.53 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3057 helix: 2.17 (0.20), residues: 693 sheet: 0.11 (0.20), residues: 694 loop : -0.92 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.027 0.001 TYR C 756 PHE 0.014 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (25312) covalent geometry : angle 0.50237 / 0.26 (34421) SS BOND : bond 0.00357 / 0.22 ( 42) SS BOND : angle 0.78334 / 0.52 ( 84) hydrogen bonds : bond 0.04526 / 2.93 ( 1006) hydrogen bonds : angle 4.96465 / 3.41 ( 2769) link_BETA1-4 : bond 0.00141 / 0.07 ( 4) link_BETA1-4 : angle 1.04319 / 0.75 ( 12) link_NAG-ASN : bond 0.00281 / 0.19 ( 32) link_NAG-ASN : angle 2.36571 / 1.84 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.9452 (tpp) cc_final: 0.9167 (ttm) REVERT: C 392 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: C 523 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8314 (p) REVERT: C 900 MET cc_start: 0.8679 (mtt) cc_final: 0.8379 (mtp) REVERT: C 1094 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8379 (m) outliers start: 18 outliers final: 12 residues processed: 62 average time/residue: 0.1439 time to fit residues: 16.5986 Evaluate side-chains 58 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 116 optimal weight: 8.9990 chunk 53 optimal weight: 0.0060 chunk 217 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 285 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.049122 restraints weight = 91289.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.050332 restraints weight = 54149.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050564 restraints weight = 35621.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051393 restraints weight = 34857.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051389 restraints weight = 30886.779| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25390 Z= 0.099 Angle : 0.457 10.304 34613 Z= 0.234 Chirality : 0.043 0.375 4020 Planarity : 0.003 0.035 4399 Dihedral : 3.819 16.289 3324 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.67 % Allowed : 9.72 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3057 helix: 2.45 (0.20), residues: 688 sheet: 0.27 (0.20), residues: 689 loop : -0.83 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.014 0.001 TYR B1067 PHE 0.010 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (25312) covalent geometry : angle 0.44167 / 0.23 (34421) SS BOND : bond 0.00275 / 0.16 ( 42) SS BOND : angle 0.84304 / 0.53 ( 84) hydrogen bonds : bond 0.03837 / 2.48 ( 1006) hydrogen bonds : angle 4.72811 / 3.25 ( 2769) link_BETA1-4 : bond 0.00122 / 0.06 ( 4) link_BETA1-4 : angle 0.87134 / 0.64 ( 12) link_NAG-ASN : bond 0.00257 / 0.17 ( 32) link_NAG-ASN : angle 2.17721 / 1.70 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8744 (mtt) cc_final: 0.7993 (mtt) REVERT: B 1029 MET cc_start: 0.9439 (tpp) cc_final: 0.9068 (ttm) REVERT: C 523 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8143 (p) REVERT: C 900 MET cc_start: 0.8552 (mtt) cc_final: 0.8247 (mtp) outliers start: 18 outliers final: 13 residues processed: 66 average time/residue: 0.1385 time to fit residues: 16.9966 Evaluate side-chains 59 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 157 optimal weight: 0.3980 chunk 162 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS B1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049466 restraints weight = 90910.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050639 restraints weight = 53694.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051002 restraints weight = 35636.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.051234 restraints weight = 33831.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.051361 restraints weight = 31863.128| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25390 Z= 0.098 Angle : 0.453 10.135 34613 Z= 0.229 Chirality : 0.042 0.370 4020 Planarity : 0.003 0.035 4399 Dihedral : 3.700 15.648 3324 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.63 % Allowed : 10.24 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3057 helix: 2.44 (0.20), residues: 696 sheet: 0.37 (0.20), residues: 704 loop : -0.78 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.013 0.001 TYR B1067 PHE 0.010 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (25312) covalent geometry : angle 0.43650 / 0.23 (34421) SS BOND : bond 0.00239 / 0.14 ( 42) SS BOND : angle 1.08218 / 0.66 ( 84) hydrogen bonds : bond 0.03677 / 2.37 ( 1006) hydrogen bonds : angle 4.62719 / 3.18 ( 2769) link_BETA1-4 : bond 0.00173 / 0.09 ( 4) link_BETA1-4 : angle 0.90276 / 0.69 ( 12) link_NAG-ASN : bond 0.00257 / 0.17 ( 32) link_NAG-ASN : angle 2.10696 / 1.65 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8816 (mtt) cc_final: 0.8147 (mtt) REVERT: B 1029 MET cc_start: 0.9459 (tpp) cc_final: 0.9008 (ttm) REVERT: C 392 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: C 523 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8072 (p) REVERT: C 900 MET cc_start: 0.8582 (mtt) cc_final: 0.8290 (mtp) outliers start: 17 outliers final: 12 residues processed: 60 average time/residue: 0.1310 time to fit residues: 13.8611 Evaluate side-chains 58 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 137 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 210 optimal weight: 0.0070 chunk 266 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.063724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.047693 restraints weight = 91673.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048628 restraints weight = 55854.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.049016 restraints weight = 37871.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049718 restraints weight = 35550.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.049762 restraints weight = 31672.154| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25390 Z= 0.242 Angle : 0.556 10.434 34613 Z= 0.282 Chirality : 0.045 0.372 4020 Planarity : 0.003 0.032 4399 Dihedral : 3.998 16.739 3324 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.96 % Allowed : 10.20 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3057 helix: 2.18 (0.20), residues: 696 sheet: 0.18 (0.19), residues: 713 loop : -0.85 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.025 0.001 TYR C 756 PHE 0.016 0.001 PHE A1042 TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (25312) covalent geometry : angle 0.53943 / 0.28 (34421) SS BOND : bond 0.00367 / 0.22 ( 42) SS BOND : angle 1.15574 / 0.73 ( 84) hydrogen bonds : bond 0.04671 / 3.03 ( 1006) hydrogen bonds : angle 4.95068 / 3.40 ( 2769) link_BETA1-4 : bond 0.00234 / 0.11 ( 4) link_BETA1-4 : angle 1.13657 / 0.81 ( 12) link_NAG-ASN : bond 0.00338 / 0.23 ( 32) link_NAG-ASN : angle 2.37710 / 1.85 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 1029 MET cc_start: 0.9465 (tpp) cc_final: 0.9174 (ttm) REVERT: C 392 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: C 523 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8326 (p) REVERT: C 900 MET cc_start: 0.8685 (mtt) cc_final: 0.8372 (mtp) outliers start: 26 outliers final: 18 residues processed: 64 average time/residue: 0.1387 time to fit residues: 16.4638 Evaluate side-chains 65 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 276 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 957 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 = 0.3334 r_free = 0.3334 target = 0.064601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048591 restraints weight = 90764.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049798 restraints weight = 53646.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050099 restraints weight = 35225.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050753 restraints weight = 34346.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050785 restraints weight = 30758.580| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25390 Z= 0.132 Angle : 0.481 10.309 34613 Z= 0.244 Chirality : 0.043 0.371 4020 Planarity : 0.003 0.034 4399 Dihedral : 3.849 16.322 3324 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.70 % Allowed : 10.61 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3057 helix: 2.35 (0.20), residues: 697 sheet: 0.25 (0.20), residues: 701 loop : -0.82 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.016 0.001 TYR C 756 PHE 0.011 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (25312) covalent geometry : angle 0.46445 / 0.24 (34421) SS BOND : bond 0.00270 / 0.16 ( 42) SS BOND : angle 0.97160 / 0.61 ( 84) hydrogen bonds : bond 0.04070 / 2.63 ( 1006) hydrogen bonds : angle 4.78588 / 3.29 ( 2769) link_BETA1-4 : bond 0.00089 / 0.05 ( 4) link_BETA1-4 : angle 0.92626 / 0.68 ( 12) link_NAG-ASN : bond 0.00245 / 0.17 ( 32) link_NAG-ASN : angle 2.23532 / 1.74 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7789 (t80) REVERT: A 900 MET cc_start: 0.8821 (mtt) cc_final: 0.8112 (mtt) REVERT: B 1029 MET cc_start: 0.9448 (tpp) cc_final: 0.9107 (ttm) REVERT: C 392 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: C 523 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 900 MET cc_start: 0.8592 (mtt) cc_final: 0.8293 (mtp) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.1389 time to fit residues: 15.5446 Evaluate side-chains 63 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 833 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 232 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 125 optimal weight: 0.0980 chunk 124 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 200 optimal weight: 7.9990 chunk 145 optimal weight: 0.0670 chunk 233 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050556 restraints weight = 90943.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051620 restraints weight = 50291.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052118 restraints weight = 34690.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.052319 restraints weight = 33150.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052400 restraints weight = 29097.245| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25390 Z= 0.079 Angle : 0.437 9.937 34613 Z= 0.222 Chirality : 0.042 0.367 4020 Planarity : 0.003 0.036 4399 Dihedral : 3.560 15.668 3324 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.48 % Allowed : 10.94 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3057 helix: 2.61 (0.20), residues: 690 sheet: 0.38 (0.20), residues: 703 loop : -0.72 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.013 0.001 TYR B1067 PHE 0.010 0.001 PHE A 92 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 (25312) covalent geometry : angle 0.42388 / 0.22 (34421) SS BOND : bond 0.00198 / 0.11 ( 42) SS BOND : angle 0.77887 / 0.49 ( 84) hydrogen bonds : bond 0.03332 / 2.15 ( 1006) hydrogen bonds : angle 4.52020 / 3.11 ( 2769) link_BETA1-4 : bond 0.00196 / 0.10 ( 4) link_BETA1-4 : angle 0.77850 / 0.60 ( 12) link_NAG-ASN : bond 0.00295 / 0.19 ( 32) link_NAG-ASN : angle 1.99408 / 1.56 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 987 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8449 (m) REVERT: B 1029 MET cc_start: 0.9440 (tpp) cc_final: 0.8943 (ttm) REVERT: C 392 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: C 523 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (p) REVERT: C 900 MET cc_start: 0.8431 (mtt) cc_final: 0.8145 (mtp) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.1393 time to fit residues: 14.3470 Evaluate side-chains 56 residues out of total 2696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 833 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 251 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 145 optimal weight: 0.0020 chunk 28 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 913 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048293 restraints weight = 90816.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.049746 restraints weight = 51357.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050242 restraints weight = 32538.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050480 restraints weight = 32954.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.050431 restraints weight = 27991.993| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25390 Z= 0.174 Angle : 0.499 11.390 34613 Z= 0.252 Chirality : 0.044 0.363 4020 Planarity : 0.003 0.034 4399 Dihedral : 3.753 15.799 3324 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.59 % Allowed : 10.83 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3057 helix: 2.40 (0.20), residues: 696 sheet: 0.32 (0.20), residues: 699 loop : -0.73 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.019 0.001 TYR C 756 PHE 0.012 0.001 PHE B1121 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (25312) covalent geometry : angle 0.48377 / 0.25 (34421) SS BOND : bond 0.00298 / 0.18 ( 42) SS BOND : angle 0.94284 / 0.60 ( 84) hydrogen bonds : bond 0.04191 / 2.71 ( 1006) hydrogen bonds : angle 4.74591 / 3.26 ( 2769) link_BETA1-4 : bond 0.00147 / 0.07 ( 4) link_BETA1-4 : angle 1.03702 / 0.76 ( 12) link_NAG-ASN : bond 0.00281 / 0.20 ( 32) link_NAG-ASN : angle 2.19191 / 1.71 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.72 seconds wall clock time: 55 minutes 28.86 seconds (3328.86 seconds total)