Starting phenix.real_space_refine on Sat Jul 4 20:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.map" model { file = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wz0_32900/07_2026/7wz0_32900.cif" } resolution = 3.0 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 26 5.49 5 Mg 6 5.21 5 S 118 5.16 5 C 14690 2.51 5 N 3514 2.21 5 O 4334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 22688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 490 Unusual residues: {' MG': 3, 'CLR': 2, 'OBN': 1, 'PCW': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: C, D, E, K, L, M, N Time building chain proxies: 9.90, per 1000 atoms: 0.44 Number of scatterers: 22688 At special positions: 0 Unit cell: (218.428, 181.844, 102.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 26 15.00 Mg 6 11.99 O 4334 8.00 N 3514 7.00 C 14690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.02 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 752.2 milliseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 22 sheets defined 49.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.577A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.536A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.665A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.640A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.840A pdb=" N VAL A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.547A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.684A pdb=" N SER A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.859A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.624A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.645A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.750A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.670A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.226A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 3.538A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.564A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.702A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.527A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 29 through 61 removed outlier: 3.815A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.549A pdb=" N SER B 98 " --> pdb=" O ASN B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.613A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.605A pdb=" N ARG B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.711A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.109A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.578A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.536A pdb=" N ARG C 264 " --> pdb=" O THR C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 313 Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.665A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.640A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.841A pdb=" N VAL C 364 " --> pdb=" O LEU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.547A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.685A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.858A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.623A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 707 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.646A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.750A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 772 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 797 Proline residue: C 789 - end of helix Processing helix chain 'C' and resid 803 through 812 Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.670A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.225A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 3.539A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.565A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.701A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.527A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1022 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 29 through 61 removed outlier: 3.815A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.549A pdb=" N SER D 98 " --> pdb=" O ASN D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.614A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.605A pdb=" N ARG D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.711A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 254 removed outlier: 4.108A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.673A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226 removed outlier: 4.086A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.717A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.814A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.617A pdb=" N ILE A 492 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU A 479 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 490 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.570A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.058A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.530A pdb=" N ASP B 19 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 24 " --> pdb=" O ASP B 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.714A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 228 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.673A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.085A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.717A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB7, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.814A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.618A pdb=" N ILE C 492 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU C 479 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU C 490 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.057A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AC1, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.531A pdb=" N ASP D 19 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.713A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 228 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AC4, first strand: chain 'D' and resid 124 through 125 988 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.46 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: 6729 1.34 - 1.46: 5112 1.46 - 1.59: 11039 1.59 - 1.71: 64 1.71 - 1.83: 172 Bond restraints: 23116 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.507 0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C39 PCW G 103 " pdb=" C40 PCW G 103 " ideal model delta sigma weight residual 1.333 1.546 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C39 PCW E 103 " pdb=" C40 PCW E 103 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C19 PCW A1112 " pdb=" C20 PCW A1112 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 28364 2.39 - 4.78: 2236 4.78 - 7.16: 445 7.16 - 9.55: 147 9.55 - 11.94: 18 Bond angle restraints: 31210 Sorted by residual: angle pdb=" C ALA C 187 " pdb=" N GLY C 188 " pdb=" CA GLY C 188 " ideal model delta sigma weight residual 123.44 116.05 7.39 1.19e+00 7.06e-01 3.85e+01 angle pdb=" C ALA A 187 " pdb=" N GLY A 188 " pdb=" CA GLY A 188 " ideal model delta sigma weight residual 123.44 116.09 7.35 1.19e+00 7.06e-01 3.82e+01 angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 111.04 120.33 -9.29 1.55e+00 4.16e-01 3.59e+01 angle pdb=" N LYS B 158 " pdb=" CA LYS B 158 " pdb=" C LYS B 158 " ideal model delta sigma weight residual 111.04 120.30 -9.26 1.55e+00 4.16e-01 3.57e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 109.15 101.20 7.95 1.44e+00 4.82e-01 3.05e+01 ... (remaining 31205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 12992 35.82 - 71.63: 680 71.63 - 107.45: 32 107.45 - 143.26: 24 143.26 - 179.08: 2 Dihedral angle restraints: 13730 sinusoidal: 6074 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual -168.17 10.91 -179.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual -168.17 10.89 -179.06 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual -168.17 -29.97 -138.20 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 13727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3030 0.090 - 0.180: 442 0.180 - 0.269: 40 0.269 - 0.359: 28 0.359 - 0.449: 2 Chirality restraints: 3542 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.37e+01 ... (remaining 3539 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.091 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 123 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.091 5.00e-02 4.00e+02 1.42e-01 3.21e+01 pdb=" N PRO D 123 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO C 125 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.058 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 86 2.44 - 3.06: 14458 3.06 - 3.67: 30607 3.67 - 4.29: 48729 4.29 - 4.90: 79463 Nonbonded interactions: 173343 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.828 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.829 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1204 " model vdw 1.969 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1204 " model vdw 1.976 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 2.010 2.170 ... (remaining 173338 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.170 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.012 0.309 23160 Z= 0.578 Angle : 1.528 17.090 31336 Z= 0.775 Chirality : 0.069 0.449 3542 Planarity : 0.010 0.142 3806 Dihedral : 18.945 179.078 8800 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.76 % Favored : 90.44 % Rotamer: Outliers : 10.52 % Allowed : 9.50 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -3.72 (0.14), residues: 2636 helix: -2.11 (0.12), residues: 1190 sheet: -2.18 (0.29), residues: 252 loop : -2.85 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 596 TYR 0.055 0.003 TYR D 40 PHE 0.032 0.003 PHE D 297 TRP 0.025 0.003 TRP B 156 HIS 0.019 0.003 HIS A 919 Details of bonding type rmsd/Z covalent geometry : bond 0.01165 / 0.58 (23116) covalent geometry : angle 1.50066 / 0.77 (31210) SS BOND : bond 0.00653 / 0.35 ( 6) SS BOND : angle 2.62183 / 1.41 ( 12) hydrogen bonds : bond 0.17508 / 11.58 ( 988) hydrogen bonds : angle 7.62600 / 5.34 ( 2880) link_ALPHA1-3 : bond 0.00922 / 0.47 ( 6) link_ALPHA1-3 : angle 3.22010 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00878 / 0.43 ( 4) link_ALPHA1-6 : angle 1.26954 / 0.71 ( 12) link_BETA1-2 : bond 0.01011 / 0.51 ( 2) link_BETA1-2 : angle 5.53042 / 2.63 ( 6) link_BETA1-4 : bond 0.01182 / 0.68 ( 14) link_BETA1-4 : angle 6.60541 / 4.14 ( 42) link_BETA1-6 : bond 0.00555 / 0.28 ( 4) link_BETA1-6 : angle 1.83241 / 1.18 ( 12) link_NAG-ASN : bond 0.02278 / 1.12 ( 8) link_NAG-ASN : angle 4.87350 / 2.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 492 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8114 (t80) cc_final: 0.7577 (t80) REVERT: A 250 VAL cc_start: 0.8112 (t) cc_final: 0.7908 (m) REVERT: A 481 PRO cc_start: 0.6045 (Cg_exo) cc_final: 0.5776 (Cg_endo) REVERT: A 488 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5984 (p90) REVERT: A 493 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7427 (m-70) REVERT: A 517 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6850 (mmt-90) REVERT: A 583 LEU cc_start: 0.6732 (mt) cc_final: 0.6399 (mt) REVERT: A 1000 LEU cc_start: 0.8414 (mp) cc_final: 0.8102 (mp) REVERT: A 1011 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8017 (mmm-85) REVERT: B 26 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (tp) REVERT: B 95 ASN cc_start: 0.7066 (t0) cc_final: 0.6848 (t0) REVERT: C 149 TYR cc_start: 0.8045 (t80) cc_final: 0.7502 (t80) REVERT: C 396 GLN cc_start: 0.6933 (tt0) cc_final: 0.6632 (tt0) REVERT: C 486 ASN cc_start: 0.7348 (m110) cc_final: 0.7146 (m-40) REVERT: C 504 LEU cc_start: 0.7165 (tp) cc_final: 0.6931 (tp) REVERT: C 513 ARG cc_start: 0.6299 (mmt-90) cc_final: 0.5927 (mmt90) REVERT: C 517 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6820 (mmt-90) REVERT: C 837 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8562 (ptt90) REVERT: C 846 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7854 (p0) REVERT: C 1000 LEU cc_start: 0.8429 (mp) cc_final: 0.8129 (mp) REVERT: D 196 THR cc_start: 0.7448 (OUTLIER) cc_final: 0.7246 (p) outliers start: 238 outliers final: 32 residues processed: 661 average time/residue: 0.5612 time to fit residues: 424.8931 Evaluate side-chains 257 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 7 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 486 ASN A 489 GLN A 683 HIS A 696 GLN A 904 GLN B 56 GLN B 70 GLN B 205 ASN B 258 GLN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 118 GLN C 474 ASN C 486 ASN C 683 HIS C 904 GLN D 56 GLN D 70 GLN D 95 ASN D 107 HIS D 205 ASN D 258 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105161 restraints weight = 32946.414| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.33 r_work: 0.3136 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23160 Z= 0.149 Angle : 0.724 11.342 31336 Z= 0.351 Chirality : 0.046 0.429 3542 Planarity : 0.006 0.073 3806 Dihedral : 15.240 174.190 3923 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.26 % Allowed : 17.68 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.58 (0.15), residues: 2636 helix: -0.01 (0.15), residues: 1222 sheet: -2.02 (0.27), residues: 252 loop : -1.93 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 61 TYR 0.027 0.002 TYR A 684 PHE 0.028 0.002 PHE A 184 TRP 0.018 0.001 TRP B 156 HIS 0.009 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (23116) covalent geometry : angle 0.70174 / 0.35 (31210) SS BOND : bond 0.00101 / 0.06 ( 6) SS BOND : angle 1.43351 / 0.69 ( 12) hydrogen bonds : bond 0.05997 / 4.01 ( 988) hydrogen bonds : angle 5.20577 / 3.63 ( 2880) link_ALPHA1-3 : bond 0.00947 / 0.52 ( 6) link_ALPHA1-3 : angle 2.92909 / 1.66 ( 18) link_ALPHA1-6 : bond 0.00722 / 0.35 ( 4) link_ALPHA1-6 : angle 1.52994 / 0.94 ( 12) link_BETA1-2 : bond 0.01109 / 0.56 ( 2) link_BETA1-2 : angle 4.01669 / 1.98 ( 6) link_BETA1-4 : bond 0.01022 / 0.61 ( 14) link_BETA1-4 : angle 3.74013 / 2.54 ( 42) link_BETA1-6 : bond 0.00758 / 0.37 ( 4) link_BETA1-6 : angle 1.50275 / 0.92 ( 12) link_NAG-ASN : bond 0.00786 / 0.39 ( 8) link_NAG-ASN : angle 2.26806 / 1.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 247 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8106 (tp) cc_final: 0.7876 (pt) REVERT: A 51 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7786 (tm) REVERT: A 149 TYR cc_start: 0.8638 (t80) cc_final: 0.8095 (t80) REVERT: A 221 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 250 VAL cc_start: 0.8020 (t) cc_final: 0.7766 (m) REVERT: A 423 ARG cc_start: 0.8009 (tmm-80) cc_final: 0.7803 (tmm-80) REVERT: A 486 ASN cc_start: 0.7750 (m110) cc_final: 0.7132 (m-40) REVERT: A 551 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7095 (tpp80) REVERT: A 671 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8370 (ttpp) REVERT: A 672 ASP cc_start: 0.8039 (m-30) cc_final: 0.7828 (p0) REVERT: A 834 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7844 (ptp-170) REVERT: A 1011 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8456 (mmm-85) REVERT: B 97 LYS cc_start: 0.8886 (mppt) cc_final: 0.8668 (mtmm) REVERT: C 51 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7811 (tm) REVERT: C 149 TYR cc_start: 0.8632 (t80) cc_final: 0.8047 (t80) REVERT: C 223 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: C 391 MET cc_start: 0.8064 (mtm) cc_final: 0.7570 (mtm) REVERT: C 396 GLN cc_start: 0.6940 (tt0) cc_final: 0.6490 (tt0) REVERT: C 423 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7358 (ppp80) REVERT: C 424 ILE cc_start: 0.7855 (mt) cc_final: 0.7624 (mt) REVERT: C 488 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5733 (p90) REVERT: C 795 ILE cc_start: 0.8855 (mm) cc_final: 0.8491 (mt) REVERT: D 26 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (tp) REVERT: D 160 CYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8287 (m) REVERT: D 196 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.7121 (p) REVERT: D 300 LYS cc_start: 0.8931 (mttt) cc_final: 0.8702 (mtpt) outliers start: 119 outliers final: 24 residues processed: 344 average time/residue: 0.4965 time to fit residues: 198.4672 Evaluate side-chains 221 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 423 ARG Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 127 ASN A 683 HIS A 904 GLN B 70 GLN B 95 ASN B 271 ASN C 52 HIS C 127 ASN C 683 HIS C 904 GLN D 70 GLN D 95 ASN D 271 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089500 restraints weight = 32548.289| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.13 r_work: 0.2825 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23160 Z= 0.198 Angle : 0.719 10.549 31336 Z= 0.353 Chirality : 0.047 0.386 3542 Planarity : 0.006 0.051 3806 Dihedral : 13.910 164.895 3869 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.47 % Allowed : 18.26 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.58 (0.16), residues: 2636 helix: 0.68 (0.15), residues: 1214 sheet: -1.38 (0.28), residues: 264 loop : -1.24 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 61 TYR 0.027 0.002 TYR D 248 PHE 0.030 0.003 PHE C 793 TRP 0.031 0.002 TRP C 894 HIS 0.010 0.002 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (23116) covalent geometry : angle 0.70127 / 0.35 (31210) SS BOND : bond 0.00472 / 0.24 ( 6) SS BOND : angle 2.24368 / 1.14 ( 12) hydrogen bonds : bond 0.07310 / 4.93 ( 988) hydrogen bonds : angle 4.71272 / 3.28 ( 2880) link_ALPHA1-3 : bond 0.00884 / 0.47 ( 6) link_ALPHA1-3 : angle 2.60675 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00841 / 0.41 ( 4) link_ALPHA1-6 : angle 1.46098 / 0.89 ( 12) link_BETA1-2 : bond 0.00787 / 0.39 ( 2) link_BETA1-2 : angle 3.44242 / 1.67 ( 6) link_BETA1-4 : bond 0.00969 / 0.58 ( 14) link_BETA1-4 : angle 3.38984 / 2.30 ( 42) link_BETA1-6 : bond 0.00440 / 0.21 ( 4) link_BETA1-6 : angle 1.32188 / 0.80 ( 12) link_NAG-ASN : bond 0.01040 / 0.44 ( 8) link_NAG-ASN : angle 1.85831 / 1.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 217 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7623 (mptm) REVERT: A 51 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7618 (tm) REVERT: A 149 TYR cc_start: 0.8813 (t80) cc_final: 0.8374 (t80) REVERT: A 181 ASN cc_start: 0.7764 (m-40) cc_final: 0.7545 (t0) REVERT: A 221 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: A 391 MET cc_start: 0.8224 (mtm) cc_final: 0.7657 (mtm) REVERT: A 404 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 423 ARG cc_start: 0.7962 (tmm-80) cc_final: 0.7741 (tmm-80) REVERT: A 488 TYR cc_start: 0.6676 (p90) cc_final: 0.5891 (p90) REVERT: A 504 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6709 (tm) REVERT: A 513 ARG cc_start: 0.6311 (mmt90) cc_final: 0.5635 (mtt180) REVERT: A 523 LEU cc_start: 0.7596 (tt) cc_final: 0.7118 (mp) REVERT: A 531 LYS cc_start: 0.6409 (pmmt) cc_final: 0.6167 (ttpp) REVERT: A 551 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7367 (tpp80) REVERT: A 670 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 847 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: A 889 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7860 (mmp80) REVERT: B 294 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8597 (tmm-80) REVERT: B 300 LYS cc_start: 0.9028 (mttt) cc_final: 0.8656 (mttp) REVERT: C 96 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8411 (mp) REVERT: C 149 TYR cc_start: 0.8833 (t80) cc_final: 0.8384 (t80) REVERT: C 221 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: C 267 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8317 (tmt) REVERT: C 391 MET cc_start: 0.8144 (mtm) cc_final: 0.7660 (mtm) REVERT: C 396 GLN cc_start: 0.6649 (tt0) cc_final: 0.6255 (tt0) REVERT: C 423 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7155 (mtp85) REVERT: C 486 ASN cc_start: 0.7390 (m-40) cc_final: 0.7058 (m-40) REVERT: C 488 TYR cc_start: 0.6522 (p90) cc_final: 0.6098 (p90) REVERT: C 551 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7027 (tpp80) REVERT: C 832 MET cc_start: 0.9213 (tpt) cc_final: 0.9004 (tpt) REVERT: C 834 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7943 (ptp-170) REVERT: C 889 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7901 (mmp80) REVERT: D 26 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8729 (tp) REVERT: D 196 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7138 (p) REVERT: D 294 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8452 (ttm-80) REVERT: D 300 LYS cc_start: 0.8986 (mttt) cc_final: 0.8729 (mtpt) outliers start: 101 outliers final: 29 residues processed: 296 average time/residue: 0.5061 time to fit residues: 173.5667 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 834 ARG Chi-restraints excluded: chain C residue 889 ARG Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 294 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 186 optimal weight: 8.9990 chunk 224 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 226 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 557 HIS A 683 HIS B 95 ASN C 52 HIS C 683 HIS D 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091295 restraints weight = 32367.035| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.15 r_work: 0.2866 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23160 Z= 0.135 Angle : 0.601 9.906 31336 Z= 0.290 Chirality : 0.043 0.402 3542 Planarity : 0.004 0.054 3806 Dihedral : 13.007 162.140 3855 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.76 % Allowed : 19.45 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.06 (0.16), residues: 2636 helix: 1.10 (0.15), residues: 1214 sheet: -1.03 (0.28), residues: 282 loop : -0.98 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 61 TYR 0.015 0.001 TYR A 869 PHE 0.022 0.002 PHE A 793 TRP 0.022 0.001 TRP C 894 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (23116) covalent geometry : angle 0.58247 / 0.29 (31210) SS BOND : bond 0.00264 / 0.14 ( 6) SS BOND : angle 1.49808 / 0.80 ( 12) hydrogen bonds : bond 0.05692 / 3.82 ( 988) hydrogen bonds : angle 4.42416 / 3.08 ( 2880) link_ALPHA1-3 : bond 0.00713 / 0.38 ( 6) link_ALPHA1-3 : angle 2.66236 / 1.55 ( 18) link_ALPHA1-6 : bond 0.00713 / 0.35 ( 4) link_ALPHA1-6 : angle 1.37780 / 0.87 ( 12) link_BETA1-2 : bond 0.00649 / 0.33 ( 2) link_BETA1-2 : angle 3.84426 / 1.90 ( 6) link_BETA1-4 : bond 0.00751 / 0.45 ( 14) link_BETA1-4 : angle 3.11838 / 2.12 ( 42) link_BETA1-6 : bond 0.00242 / 0.12 ( 4) link_BETA1-6 : angle 1.32179 / 0.82 ( 12) link_NAG-ASN : bond 0.00611 / 0.28 ( 8) link_NAG-ASN : angle 1.43462 / 0.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 205 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8833 (t80) cc_final: 0.8361 (t80) REVERT: A 159 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6619 (t0) REVERT: A 184 PHE cc_start: 0.8104 (m-80) cc_final: 0.7846 (m-80) REVERT: A 221 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: A 391 MET cc_start: 0.8181 (mtm) cc_final: 0.7619 (mtm) REVERT: A 404 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: A 462 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 488 TYR cc_start: 0.6707 (p90) cc_final: 0.5901 (p90) REVERT: A 504 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6573 (tm) REVERT: A 523 LEU cc_start: 0.7523 (tt) cc_final: 0.7093 (mp) REVERT: A 551 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7393 (tpp80) REVERT: A 847 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: A 960 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: B 294 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8536 (tmm-80) REVERT: B 300 LYS cc_start: 0.9031 (mttt) cc_final: 0.8706 (mttp) REVERT: C 149 TYR cc_start: 0.8815 (t80) cc_final: 0.8351 (t80) REVERT: C 183 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 221 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: C 267 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8235 (tmt) REVERT: C 391 MET cc_start: 0.8130 (mtm) cc_final: 0.7598 (mtm) REVERT: C 396 GLN cc_start: 0.6698 (tt0) cc_final: 0.6302 (tt0) REVERT: C 423 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7027 (mtp85) REVERT: C 427 LEU cc_start: 0.8090 (tp) cc_final: 0.7712 (tp) REVERT: C 462 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8456 (tt) REVERT: C 486 ASN cc_start: 0.7457 (m-40) cc_final: 0.7090 (t0) REVERT: C 488 TYR cc_start: 0.6558 (p90) cc_final: 0.5981 (p90) REVERT: C 551 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7228 (tpp80) REVERT: C 670 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8557 (tp) REVERT: C 847 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: C 960 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 125 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: D 196 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7161 (p) REVERT: D 294 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8462 (ttm-80) REVERT: D 300 LYS cc_start: 0.9001 (mttt) cc_final: 0.8694 (mtpt) outliers start: 85 outliers final: 32 residues processed: 265 average time/residue: 0.4706 time to fit residues: 146.1247 Evaluate side-chains 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 GLN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 164 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 181 ASN A 683 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN C 683 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089080 restraints weight = 31872.758| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.13 r_work: 0.2824 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23160 Z= 0.165 Angle : 0.631 10.361 31336 Z= 0.305 Chirality : 0.044 0.395 3542 Planarity : 0.005 0.058 3806 Dihedral : 12.544 153.606 3855 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.42 % Allowed : 18.74 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2636 helix: 1.20 (0.15), residues: 1212 sheet: -0.71 (0.29), residues: 260 loop : -0.84 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 61 TYR 0.020 0.002 TYR B 44 PHE 0.030 0.002 PHE C 433 TRP 0.028 0.001 TRP C 894 HIS 0.009 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (23116) covalent geometry : angle 0.61450 / 0.30 (31210) SS BOND : bond 0.00299 / 0.15 ( 6) SS BOND : angle 1.46068 / 0.75 ( 12) hydrogen bonds : bond 0.06373 / 4.29 ( 988) hydrogen bonds : angle 4.40000 / 3.06 ( 2880) link_ALPHA1-3 : bond 0.00680 / 0.37 ( 6) link_ALPHA1-3 : angle 2.60051 / 1.53 ( 18) link_ALPHA1-6 : bond 0.00691 / 0.34 ( 4) link_ALPHA1-6 : angle 1.36370 / 0.88 ( 12) link_BETA1-2 : bond 0.00663 / 0.33 ( 2) link_BETA1-2 : angle 3.72265 / 1.84 ( 6) link_BETA1-4 : bond 0.00701 / 0.42 ( 14) link_BETA1-4 : angle 2.92278 / 1.98 ( 42) link_BETA1-6 : bond 0.00216 / 0.11 ( 4) link_BETA1-6 : angle 1.35514 / 0.84 ( 12) link_NAG-ASN : bond 0.00501 / 0.23 ( 8) link_NAG-ASN : angle 1.44643 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 189 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8833 (t80) cc_final: 0.8445 (t80) REVERT: A 184 PHE cc_start: 0.8239 (m-80) cc_final: 0.7908 (m-80) REVERT: A 221 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: A 391 MET cc_start: 0.8067 (mtm) cc_final: 0.7621 (mtm) REVERT: A 404 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: A 462 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8347 (tt) REVERT: A 488 TYR cc_start: 0.6605 (p90) cc_final: 0.5964 (p90) REVERT: A 523 LEU cc_start: 0.7435 (tt) cc_final: 0.6973 (mp) REVERT: A 670 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 847 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: A 889 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8076 (mmp80) REVERT: B 294 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8664 (tmm-80) REVERT: B 300 LYS cc_start: 0.9039 (mttt) cc_final: 0.8697 (mtmm) REVERT: C 149 TYR cc_start: 0.8848 (t80) cc_final: 0.8493 (t80) REVERT: C 183 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 221 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 267 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8402 (tmt) REVERT: C 391 MET cc_start: 0.8038 (mtm) cc_final: 0.7677 (mtm) REVERT: C 396 GLN cc_start: 0.6719 (tt0) cc_final: 0.6279 (tt0) REVERT: C 423 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7119 (mtp85) REVERT: C 462 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8404 (tt) REVERT: C 486 ASN cc_start: 0.7511 (m-40) cc_final: 0.7138 (t0) REVERT: C 523 LEU cc_start: 0.7547 (tt) cc_final: 0.7154 (mp) REVERT: C 551 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7371 (tpp80) REVERT: C 670 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8604 (tp) REVERT: C 847 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: C 889 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8074 (mmp80) REVERT: C 960 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: D 196 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7192 (p) REVERT: D 294 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8446 (ttm-80) REVERT: D 300 LYS cc_start: 0.9023 (mttt) cc_final: 0.8689 (mtpt) outliers start: 100 outliers final: 44 residues processed: 265 average time/residue: 0.5147 time to fit residues: 157.9219 Evaluate side-chains 235 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 GLN Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 889 ARG Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 HIS B 95 ASN C 168 GLN C 683 HIS D 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088886 restraints weight = 32127.014| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.15 r_work: 0.2824 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 23160 Z= 0.163 Angle : 0.623 9.230 31336 Z= 0.302 Chirality : 0.044 0.397 3542 Planarity : 0.005 0.058 3806 Dihedral : 12.178 147.039 3855 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.67 % Allowed : 19.85 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.24 (0.16), residues: 2636 helix: 1.26 (0.15), residues: 1206 sheet: -0.42 (0.28), residues: 280 loop : -0.85 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 61 TYR 0.019 0.002 TYR D 44 PHE 0.026 0.002 PHE A 793 TRP 0.028 0.001 TRP C 894 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (23116) covalent geometry : angle 0.60737 / 0.30 (31210) SS BOND : bond 0.00301 / 0.16 ( 6) SS BOND : angle 1.40286 / 0.72 ( 12) hydrogen bonds : bond 0.06193 / 4.17 ( 988) hydrogen bonds : angle 4.35389 / 3.03 ( 2880) link_ALPHA1-3 : bond 0.00636 / 0.34 ( 6) link_ALPHA1-3 : angle 2.57493 / 1.50 ( 18) link_ALPHA1-6 : bond 0.00678 / 0.33 ( 4) link_ALPHA1-6 : angle 1.38498 / 0.90 ( 12) link_BETA1-2 : bond 0.00650 / 0.33 ( 2) link_BETA1-2 : angle 3.68400 / 1.82 ( 6) link_BETA1-4 : bond 0.00662 / 0.40 ( 14) link_BETA1-4 : angle 2.79343 / 1.90 ( 42) link_BETA1-6 : bond 0.00172 / 0.08 ( 4) link_BETA1-6 : angle 1.29190 / 0.81 ( 12) link_NAG-ASN : bond 0.00489 / 0.22 ( 8) link_NAG-ASN : angle 1.42208 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 186 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8802 (t80) cc_final: 0.8427 (t80) REVERT: A 184 PHE cc_start: 0.8287 (m-80) cc_final: 0.7935 (m-80) REVERT: A 221 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: A 391 MET cc_start: 0.8071 (mtm) cc_final: 0.7635 (mtm) REVERT: A 404 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 442 ILE cc_start: 0.8374 (mt) cc_final: 0.8042 (tp) REVERT: A 462 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8361 (tt) REVERT: A 488 TYR cc_start: 0.6564 (p90) cc_final: 0.5994 (p90) REVERT: A 523 LEU cc_start: 0.7477 (tt) cc_final: 0.6985 (mm) REVERT: A 847 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 889 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8082 (mmp80) REVERT: A 960 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: B 294 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (tmm-80) REVERT: B 300 LYS cc_start: 0.9009 (mttt) cc_final: 0.8687 (mtmm) REVERT: C 41 MET cc_start: 0.7217 (ppp) cc_final: 0.7008 (pp-130) REVERT: C 149 TYR cc_start: 0.8830 (t80) cc_final: 0.8507 (t80) REVERT: C 183 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 221 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: C 391 MET cc_start: 0.8025 (mtm) cc_final: 0.7660 (mtm) REVERT: C 396 GLN cc_start: 0.6688 (tt0) cc_final: 0.6263 (tt0) REVERT: C 423 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7136 (mtp85) REVERT: C 427 LEU cc_start: 0.7902 (tp) cc_final: 0.7579 (tp) REVERT: C 445 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7364 (ptp-170) REVERT: C 462 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (tt) REVERT: C 486 ASN cc_start: 0.7580 (m-40) cc_final: 0.7171 (t0) REVERT: C 523 LEU cc_start: 0.7477 (tt) cc_final: 0.7089 (mp) REVERT: C 670 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8579 (tp) REVERT: C 847 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: C 889 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8101 (mmp80) REVERT: C 960 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: D 196 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.7087 (p) REVERT: D 294 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8447 (ttm-80) REVERT: D 300 LYS cc_start: 0.8950 (mttt) cc_final: 0.8606 (mtpt) outliers start: 83 outliers final: 42 residues processed: 254 average time/residue: 0.4823 time to fit residues: 143.5532 Evaluate side-chains 232 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 GLN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 889 ARG Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 HIS B 95 ASN C 168 GLN C 683 HIS D 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088351 restraints weight = 31978.521| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.07 r_work: 0.2810 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23160 Z= 0.173 Angle : 0.640 9.431 31336 Z= 0.310 Chirality : 0.045 0.391 3542 Planarity : 0.005 0.063 3806 Dihedral : 12.079 139.487 3855 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.16 % Allowed : 19.58 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.29 (0.16), residues: 2636 helix: 1.27 (0.15), residues: 1216 sheet: -0.46 (0.30), residues: 246 loop : -0.78 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 61 TYR 0.019 0.002 TYR B 44 PHE 0.028 0.002 PHE A 793 TRP 0.029 0.001 TRP C 894 HIS 0.008 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (23116) covalent geometry : angle 0.62614 / 0.31 (31210) SS BOND : bond 0.00285 / 0.15 ( 6) SS BOND : angle 1.38298 / 0.71 ( 12) hydrogen bonds : bond 0.06461 / 4.35 ( 988) hydrogen bonds : angle 4.35571 / 3.04 ( 2880) link_ALPHA1-3 : bond 0.00616 / 0.33 ( 6) link_ALPHA1-3 : angle 2.54522 / 1.50 ( 18) link_ALPHA1-6 : bond 0.00667 / 0.33 ( 4) link_ALPHA1-6 : angle 1.37823 / 0.90 ( 12) link_BETA1-2 : bond 0.00648 / 0.33 ( 2) link_BETA1-2 : angle 3.62915 / 1.79 ( 6) link_BETA1-4 : bond 0.00626 / 0.38 ( 14) link_BETA1-4 : angle 2.70610 / 1.83 ( 42) link_BETA1-6 : bond 0.00159 / 0.08 ( 4) link_BETA1-6 : angle 1.33926 / 0.84 ( 12) link_NAG-ASN : bond 0.00448 / 0.20 ( 8) link_NAG-ASN : angle 1.39558 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 177 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8821 (t80) cc_final: 0.8461 (t80) REVERT: A 184 PHE cc_start: 0.8233 (m-80) cc_final: 0.7893 (m-80) REVERT: A 221 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: A 391 MET cc_start: 0.8084 (mtm) cc_final: 0.7658 (mtm) REVERT: A 442 ILE cc_start: 0.8332 (mt) cc_final: 0.8068 (tp) REVERT: A 462 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8375 (tt) REVERT: A 488 TYR cc_start: 0.6410 (p90) cc_final: 0.5906 (p90) REVERT: A 523 LEU cc_start: 0.7568 (tt) cc_final: 0.7058 (mm) REVERT: A 847 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: A 889 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8073 (mmp80) REVERT: A 960 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: B 294 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8661 (tmm-80) REVERT: B 300 LYS cc_start: 0.9011 (mttt) cc_final: 0.8693 (mtmm) REVERT: C 149 TYR cc_start: 0.8843 (t80) cc_final: 0.8532 (t80) REVERT: C 168 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6948 (tp40) REVERT: C 221 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: C 391 MET cc_start: 0.8067 (mtm) cc_final: 0.7722 (mtm) REVERT: C 396 GLN cc_start: 0.6539 (tt0) cc_final: 0.6200 (tt0) REVERT: C 423 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7090 (mtp85) REVERT: C 427 LEU cc_start: 0.7978 (tp) cc_final: 0.7625 (tp) REVERT: C 486 ASN cc_start: 0.7605 (m-40) cc_final: 0.7127 (t0) REVERT: C 523 LEU cc_start: 0.7559 (tt) cc_final: 0.7099 (mp) REVERT: C 670 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 847 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: C 889 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8097 (mmp80) REVERT: C 960 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: D 158 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8692 (mmmt) REVERT: D 294 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8454 (ttm-80) REVERT: D 300 LYS cc_start: 0.8979 (mttt) cc_final: 0.8658 (mtpt) outliers start: 94 outliers final: 54 residues processed: 259 average time/residue: 0.4983 time to fit residues: 150.8712 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 889 ARG Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 294 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 9 optimal weight: 0.4980 chunk 23 optimal weight: 10.0000 chunk 232 optimal weight: 0.0030 chunk 198 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 202 optimal weight: 0.0570 chunk 206 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 HIS ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 208 GLN B 243 GLN C 683 HIS ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.139635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093646 restraints weight = 32083.306| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.07 r_work: 0.2911 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23160 Z= 0.110 Angle : 0.576 11.459 31336 Z= 0.276 Chirality : 0.042 0.403 3542 Planarity : 0.004 0.055 3806 Dihedral : 11.114 134.380 3854 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.17 % Allowed : 21.26 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.63 (0.16), residues: 2636 helix: 1.63 (0.15), residues: 1210 sheet: -0.25 (0.32), residues: 226 loop : -0.69 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 61 TYR 0.017 0.001 TYR B 209 PHE 0.023 0.001 PHE C 538 TRP 0.022 0.001 TRP C 894 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (23116) covalent geometry : angle 0.56087 / 0.27 (31210) SS BOND : bond 0.00129 / 0.07 ( 6) SS BOND : angle 0.93101 / 0.47 ( 12) hydrogen bonds : bond 0.04493 / 3.00 ( 988) hydrogen bonds : angle 4.12280 / 2.87 ( 2880) link_ALPHA1-3 : bond 0.00664 / 0.37 ( 6) link_ALPHA1-3 : angle 2.51212 / 1.48 ( 18) link_ALPHA1-6 : bond 0.00615 / 0.30 ( 4) link_ALPHA1-6 : angle 1.37104 / 0.89 ( 12) link_BETA1-2 : bond 0.00599 / 0.30 ( 2) link_BETA1-2 : angle 3.82202 / 1.87 ( 6) link_BETA1-4 : bond 0.00634 / 0.40 ( 14) link_BETA1-4 : angle 2.58282 / 1.77 ( 42) link_BETA1-6 : bond 0.00174 / 0.09 ( 4) link_BETA1-6 : angle 1.35251 / 0.85 ( 12) link_NAG-ASN : bond 0.00495 / 0.23 ( 8) link_NAG-ASN : angle 1.16071 / 0.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8861 (t80) cc_final: 0.8449 (t80) REVERT: A 184 PHE cc_start: 0.8291 (m-80) cc_final: 0.7985 (m-80) REVERT: A 221 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: A 391 MET cc_start: 0.8040 (mtm) cc_final: 0.7597 (mtm) REVERT: A 427 LEU cc_start: 0.8060 (tp) cc_final: 0.7710 (tp) REVERT: A 442 ILE cc_start: 0.8386 (mt) cc_final: 0.8127 (tp) REVERT: A 462 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (tt) REVERT: A 488 TYR cc_start: 0.6483 (p90) cc_final: 0.6020 (p90) REVERT: A 523 LEU cc_start: 0.7705 (tt) cc_final: 0.7230 (mm) REVERT: A 847 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: B 201 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: B 300 LYS cc_start: 0.8991 (mttt) cc_final: 0.8661 (mtpt) REVERT: C 149 TYR cc_start: 0.8850 (t80) cc_final: 0.8484 (t80) REVERT: C 156 ARG cc_start: 0.6109 (mtt180) cc_final: 0.5868 (mtt180) REVERT: C 168 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6986 (tp40) REVERT: C 183 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 184 PHE cc_start: 0.8170 (m-80) cc_final: 0.7889 (m-80) REVERT: C 221 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: C 391 MET cc_start: 0.8002 (mtm) cc_final: 0.7613 (mtm) REVERT: C 396 GLN cc_start: 0.6560 (tt0) cc_final: 0.6117 (tt0) REVERT: C 423 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7112 (mtp85) REVERT: C 427 LEU cc_start: 0.8011 (tp) cc_final: 0.7709 (tp) REVERT: C 445 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7252 (pmm-80) REVERT: C 486 ASN cc_start: 0.7646 (m-40) cc_final: 0.7423 (t0) REVERT: C 488 TYR cc_start: 0.6443 (p90) cc_final: 0.5810 (p90) REVERT: C 523 LEU cc_start: 0.7615 (tt) cc_final: 0.7159 (mp) REVERT: C 847 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: D 201 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: D 300 LYS cc_start: 0.8997 (mttt) cc_final: 0.8687 (mtpt) REVERT: D 302 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8349 (tp30) outliers start: 49 outliers final: 15 residues processed: 244 average time/residue: 0.5731 time to fit residues: 160.9761 Evaluate side-chains 209 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 302 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 138 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 ASN A 683 HIS B 95 ASN B 243 GLN C 168 GLN C 683 HIS D 95 ASN D 208 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088766 restraints weight = 32172.220| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.20 r_work: 0.2823 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 23160 Z= 0.175 Angle : 0.646 11.150 31336 Z= 0.310 Chirality : 0.045 0.391 3542 Planarity : 0.005 0.061 3806 Dihedral : 11.296 126.086 3850 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 21.66 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.55 (0.16), residues: 2636 helix: 1.46 (0.15), residues: 1222 sheet: -0.14 (0.29), residues: 280 loop : -0.68 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 61 TYR 0.020 0.002 TYR A 869 PHE 0.030 0.002 PHE A 793 TRP 0.029 0.001 TRP C 894 HIS 0.006 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.17 (23116) covalent geometry : angle 0.63250 / 0.31 (31210) SS BOND : bond 0.00300 / 0.16 ( 6) SS BOND : angle 1.34527 / 0.69 ( 12) hydrogen bonds : bond 0.06229 / 4.20 ( 988) hydrogen bonds : angle 4.26956 / 2.97 ( 2880) link_ALPHA1-3 : bond 0.00589 / 0.31 ( 6) link_ALPHA1-3 : angle 2.45882 / 1.45 ( 18) link_ALPHA1-6 : bond 0.00671 / 0.33 ( 4) link_ALPHA1-6 : angle 1.37117 / 0.90 ( 12) link_BETA1-2 : bond 0.00640 / 0.32 ( 2) link_BETA1-2 : angle 3.60080 / 1.78 ( 6) link_BETA1-4 : bond 0.00590 / 0.36 ( 14) link_BETA1-4 : angle 2.57977 / 1.74 ( 42) link_BETA1-6 : bond 0.00127 / 0.06 ( 4) link_BETA1-6 : angle 1.34758 / 0.84 ( 12) link_NAG-ASN : bond 0.00390 / 0.17 ( 8) link_NAG-ASN : angle 1.27513 / 0.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 TYR cc_start: 0.8816 (t80) cc_final: 0.8451 (t80) REVERT: A 156 ARG cc_start: 0.6353 (mtt180) cc_final: 0.6065 (mtt180) REVERT: A 184 PHE cc_start: 0.8345 (m-80) cc_final: 0.8029 (m-80) REVERT: A 221 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: A 391 MET cc_start: 0.8077 (mtm) cc_final: 0.7610 (mtm) REVERT: A 427 LEU cc_start: 0.8091 (tp) cc_final: 0.7732 (tp) REVERT: A 442 ILE cc_start: 0.8382 (mt) cc_final: 0.8138 (tp) REVERT: A 462 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 488 TYR cc_start: 0.6447 (p90) cc_final: 0.5986 (p90) REVERT: A 523 LEU cc_start: 0.7586 (tt) cc_final: 0.7083 (mm) REVERT: A 544 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 847 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: B 294 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8553 (tmm-80) REVERT: B 300 LYS cc_start: 0.8991 (mttt) cc_final: 0.8639 (mtpt) REVERT: C 149 TYR cc_start: 0.8847 (t80) cc_final: 0.8541 (t80) REVERT: C 156 ARG cc_start: 0.6264 (mtt180) cc_final: 0.5932 (mtt180) REVERT: C 183 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7402 (mm-30) REVERT: C 184 PHE cc_start: 0.8146 (m-80) cc_final: 0.7847 (m-80) REVERT: C 221 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: C 391 MET cc_start: 0.8026 (mtm) cc_final: 0.7695 (mtm) REVERT: C 396 GLN cc_start: 0.6473 (tt0) cc_final: 0.6049 (tt0) REVERT: C 423 ARG cc_start: 0.7753 (ttp-170) cc_final: 0.7121 (mtp85) REVERT: C 427 LEU cc_start: 0.8070 (tp) cc_final: 0.7757 (tp) REVERT: C 445 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7221 (pmm-80) REVERT: C 486 ASN cc_start: 0.7785 (m-40) cc_final: 0.7504 (t0) REVERT: C 488 TYR cc_start: 0.6349 (p90) cc_final: 0.5728 (p90) REVERT: C 523 LEU cc_start: 0.7570 (tt) cc_final: 0.7074 (mm) REVERT: C 847 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: D 300 LYS cc_start: 0.8978 (mttt) cc_final: 0.8666 (mtpt) REVERT: D 302 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8304 (tp30) outliers start: 42 outliers final: 19 residues processed: 225 average time/residue: 0.5892 time to fit residues: 152.2552 Evaluate side-chains 207 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 302 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 683 HIS B 95 ASN C 683 HIS D 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088772 restraints weight = 32109.134| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.09 r_work: 0.2826 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23160 Z= 0.168 Angle : 0.648 13.658 31336 Z= 0.311 Chirality : 0.044 0.389 3542 Planarity : 0.005 0.060 3806 Dihedral : 11.240 116.975 3850 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.68 % Allowed : 22.02 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.50 (0.16), residues: 2636 helix: 1.43 (0.15), residues: 1210 sheet: -0.20 (0.28), residues: 292 loop : -0.68 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 61 TYR 0.019 0.002 TYR A 869 PHE 0.026 0.002 PHE A 793 TRP 0.031 0.001 TRP A 894 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (23116) covalent geometry : angle 0.63476 / 0.31 (31210) SS BOND : bond 0.00333 / 0.17 ( 6) SS BOND : angle 1.38842 / 0.70 ( 12) hydrogen bonds : bond 0.06154 / 4.15 ( 988) hydrogen bonds : angle 4.28241 / 2.97 ( 2880) link_ALPHA1-3 : bond 0.00544 / 0.30 ( 6) link_ALPHA1-3 : angle 2.46063 / 1.44 ( 18) link_ALPHA1-6 : bond 0.00647 / 0.32 ( 4) link_ALPHA1-6 : angle 1.37532 / 0.90 ( 12) link_BETA1-2 : bond 0.00608 / 0.31 ( 2) link_BETA1-2 : angle 3.55186 / 1.75 ( 6) link_BETA1-4 : bond 0.00600 / 0.36 ( 14) link_BETA1-4 : angle 2.54804 / 1.72 ( 42) link_BETA1-6 : bond 0.00070 / 0.03 ( 4) link_BETA1-6 : angle 1.34275 / 0.84 ( 12) link_NAG-ASN : bond 0.00422 / 0.19 ( 8) link_NAG-ASN : angle 1.25818 / 0.78 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.7198 (ppp) cc_final: 0.6993 (pp-130) REVERT: A 149 TYR cc_start: 0.8813 (t80) cc_final: 0.8485 (t80) REVERT: A 156 ARG cc_start: 0.6352 (mtt180) cc_final: 0.6059 (mtt180) REVERT: A 184 PHE cc_start: 0.8358 (m-80) cc_final: 0.8096 (m-80) REVERT: A 221 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: A 391 MET cc_start: 0.8078 (mtm) cc_final: 0.7651 (mtm) REVERT: A 427 LEU cc_start: 0.8135 (tp) cc_final: 0.7772 (tp) REVERT: A 442 ILE cc_start: 0.8403 (mt) cc_final: 0.8167 (tp) REVERT: A 462 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 488 TYR cc_start: 0.6326 (p90) cc_final: 0.5852 (p90) REVERT: A 523 LEU cc_start: 0.7597 (tt) cc_final: 0.7069 (mm) REVERT: A 544 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 847 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: A 960 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: B 294 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8509 (tmm-80) REVERT: B 300 LYS cc_start: 0.9007 (mttt) cc_final: 0.8654 (mtpt) REVERT: C 149 TYR cc_start: 0.8836 (t80) cc_final: 0.8565 (t80) REVERT: C 156 ARG cc_start: 0.6298 (mtt180) cc_final: 0.6073 (mtt180) REVERT: C 184 PHE cc_start: 0.8191 (m-80) cc_final: 0.7871 (m-80) REVERT: C 221 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: C 391 MET cc_start: 0.8057 (mtm) cc_final: 0.7723 (mtm) REVERT: C 396 GLN cc_start: 0.6532 (tt0) cc_final: 0.6216 (tt0) REVERT: C 423 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7141 (mtp85) REVERT: C 427 LEU cc_start: 0.8130 (tp) cc_final: 0.7825 (tp) REVERT: C 445 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7238 (pmm-80) REVERT: C 486 ASN cc_start: 0.7865 (m-40) cc_final: 0.7429 (t0) REVERT: C 523 LEU cc_start: 0.7589 (tt) cc_final: 0.7064 (mm) REVERT: C 847 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: C 960 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: D 300 LYS cc_start: 0.8974 (mttt) cc_final: 0.8647 (mtpt) REVERT: D 302 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8382 (tp30) outliers start: 38 outliers final: 22 residues processed: 217 average time/residue: 0.5624 time to fit residues: 141.0782 Evaluate side-chains 213 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 960 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 302 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 178 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 HIS B 95 ASN C 683 HIS D 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090954 restraints weight = 32091.075| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.07 r_work: 0.2858 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23160 Z= 0.127 Angle : 0.609 12.654 31336 Z= 0.290 Chirality : 0.043 0.390 3542 Planarity : 0.004 0.058 3806 Dihedral : 10.701 106.939 3850 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.50 % Allowed : 22.28 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.67 (0.16), residues: 2636 helix: 1.64 (0.15), residues: 1202 sheet: -0.17 (0.28), residues: 292 loop : -0.65 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 61 TYR 0.017 0.001 TYR A 869 PHE 0.022 0.001 PHE A 793 TRP 0.026 0.001 TRP A 894 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (23116) covalent geometry : angle 0.59544 / 0.29 (31210) SS BOND : bond 0.00167 / 0.09 ( 6) SS BOND : angle 1.08990 / 0.56 ( 12) hydrogen bonds : bond 0.05242 / 3.52 ( 988) hydrogen bonds : angle 4.15834 / 2.89 ( 2880) link_ALPHA1-3 : bond 0.00660 / 0.37 ( 6) link_ALPHA1-3 : angle 2.43176 / 1.44 ( 18) link_ALPHA1-6 : bond 0.00631 / 0.31 ( 4) link_ALPHA1-6 : angle 1.36485 / 0.89 ( 12) link_BETA1-2 : bond 0.00626 / 0.31 ( 2) link_BETA1-2 : angle 3.65726 / 1.80 ( 6) link_BETA1-4 : bond 0.00581 / 0.36 ( 14) link_BETA1-4 : angle 2.48888 / 1.69 ( 42) link_BETA1-6 : bond 0.00150 / 0.07 ( 4) link_BETA1-6 : angle 1.31681 / 0.83 ( 12) link_NAG-ASN : bond 0.00410 / 0.19 ( 8) link_NAG-ASN : angle 1.17943 / 0.74 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7594.14 seconds wall clock time: 129 minutes 51.83 seconds (7791.83 seconds total)