Starting phenix.real_space_refine on Sat Jul 4 19:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyw_32896/07_2026/7wyw_32896.map" } resolution = 3.8 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= 0.001 sd= 0.004 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 14632 2.51 5 N 3514 2.21 5 O 4310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 22606 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 477 Unusual residues: {' MG': 3, 'CLR': 3, '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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 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: 10.39, per 1000 atoms: 0.46 Number of scatterers: 22606 At special positions: 0 Unit cell: (216.276, 180.768, 103.296, 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 4310 8.00 N 3514 7.00 C 14632 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=2.03 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=2.03 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: 2.05 Conformation dependent library (CDL) restraints added in 842.0 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 20 sheets defined 49.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 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 89 through 97 removed outlier: 3.831A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (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: 3.530A 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: 3.676A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.378A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.928A 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: 3.504A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.690A 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: 3.853A 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: 3.657A 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: 3.641A 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: 3.752A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.942A 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: 3.667A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.634A 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: 4.240A 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: 3.512A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.043A 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: 3.553A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.761A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.519A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.473A 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 62 removed outlier: 3.897A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.515A 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: 3.576A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.003A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.563A pdb=" N ARG B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.749A 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 '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 89 through 97 removed outlier: 3.832A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (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: 3.530A 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: 3.677A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 354 removed outlier: 4.378A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.928A 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: 3.504A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.690A 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: 3.854A 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: 3.657A 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: 3.640A 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: 3.752A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.668A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.240A 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: 3.511A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.552A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.761A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.518A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.473A 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 62 removed outlier: 3.897A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.514A 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: 3.577A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.004A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.563A pdb=" N ARG D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.749A 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 '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 177 through 181 removed outlier: 11.684A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.719A 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: 4.102A 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: 6.713A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.186A 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: 3.852A 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: 6.599A pdb=" N ILE A 492 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 479 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 490 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.062A 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: 3.791A pdb=" N GLU B 24 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.562A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.816A 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 'C' and resid 177 through 181 removed outlier: 11.683A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.106A 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: 6.855A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.103A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.713A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.852A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.599A pdb=" N ILE C 492 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU C 479 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU C 490 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.063A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.792A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.563A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 88 through 91 982 hydrogen bonds defined for protein. 2862 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: 4.45 Time building geometry restraints manager: 2.66 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: 6617 1.34 - 1.46: 4989 1.46 - 1.58: 11190 1.58 - 1.71: 56 1.71 - 1.83: 172 Bond restraints: 23024 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C39 PCW G 103 " pdb=" C40 PCW G 103 " ideal model delta sigma weight residual 1.333 1.544 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C39 PCW E 103 " pdb=" C40 PCW E 103 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C19 PCW C1114 " pdb=" C20 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 28593 2.46 - 4.93: 1944 4.93 - 7.39: 383 7.39 - 9.85: 116 9.85 - 12.32: 22 Bond angle restraints: 31058 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 104.67 8.45 1.25e+00 6.40e-01 4.57e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.29 10.38 1.55e+00 4.16e-01 4.49e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 98.33 10.34 1.55e+00 4.16e-01 4.45e+01 angle pdb=" N LEU B 202 " pdb=" CA LEU B 202 " pdb=" C LEU B 202 " ideal model delta sigma weight residual 112.38 118.76 -6.38 1.22e+00 6.72e-01 2.74e+01 ... (remaining 31053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 12763 35.88 - 71.76: 675 71.76 - 107.64: 34 107.64 - 143.52: 24 143.52 - 179.41: 2 Dihedral angle restraints: 13498 sinusoidal: 5842 harmonic: 7656 Sorted by residual: 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 11.24 -179.41 1 3.00e+01 1.11e-03 2.13e+01 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 11.23 -179.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW C1112 " pdb=" C31 PCW C1112 " pdb=" C32 PCW C1112 " pdb=" O2 PCW C1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.80 -138.37 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 13495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2807 0.075 - 0.150: 592 0.150 - 0.224: 65 0.224 - 0.299: 31 0.299 - 0.374: 17 Chirality restraints: 3512 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 -2.23 -0.17 2.00e-02 2.50e+03 7.30e+01 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 -2.23 -0.17 2.00e-02 2.50e+03 6.93e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.05e+01 ... (remaining 3509 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO C 125 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 125 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 569 " 0.059 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO C 570 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 570 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 570 " 0.049 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 104 2.47 - 3.08: 15040 3.08 - 3.68: 30720 3.68 - 4.29: 48098 4.29 - 4.90: 78369 Nonbonded interactions: 172331 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.861 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.861 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1204 " model vdw 1.990 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1204 " model vdw 1.995 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 1.998 2.170 ... (remaining 172326 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.011 0.307 23068 Z= 0.561 Angle : 1.472 17.386 31184 Z= 0.749 Chirality : 0.067 0.374 3512 Planarity : 0.009 0.096 3804 Dihedral : 19.076 179.406 8568 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.30 % Allowed : 9.24 % Favored : 80.46 % 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: -3.47 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1194 sheet: -2.32 (0.29), residues: 260 loop : -2.69 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 596 TYR 0.039 0.002 TYR D 40 PHE 0.030 0.002 PHE B 297 TRP 0.033 0.003 TRP D 33 HIS 0.012 0.002 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.01117 / 0.56 (23024) covalent geometry : angle 1.44791 / 0.74 (31058) SS BOND : bond 0.00390 / 0.22 ( 6) SS BOND : angle 2.19286 / 1.26 ( 12) hydrogen bonds : bond 0.16845 / 11.15 ( 982) hydrogen bonds : angle 7.44814 / 5.18 ( 2862) link_ALPHA1-3 : bond 0.00834 / 0.42 ( 6) link_ALPHA1-3 : angle 3.18198 / 1.64 ( 18) link_ALPHA1-6 : bond 0.00735 / 0.36 ( 4) link_ALPHA1-6 : angle 1.31400 / 0.74 ( 12) link_BETA1-2 : bond 0.00900 / 0.45 ( 2) link_BETA1-2 : angle 5.43796 / 2.59 ( 6) link_BETA1-4 : bond 0.00989 / 0.58 ( 14) link_BETA1-4 : angle 6.25410 / 3.61 ( 42) link_BETA1-6 : bond 0.00348 / 0.18 ( 4) link_BETA1-6 : angle 1.33886 / 0.86 ( 12) link_NAG-ASN : bond 0.01813 / 0.89 ( 8) link_NAG-ASN : angle 4.01258 / 2.07 ( 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 545 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 312 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5856 (tp) REVERT: A 127 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.5915 (p0) REVERT: A 158 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7646 (tmm) REVERT: A 231 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 460 ILE cc_start: 0.8630 (mm) cc_final: 0.8306 (mt) REVERT: A 493 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: A 708 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: A 933 ASP cc_start: 0.8789 (t70) cc_final: 0.8466 (t0) REVERT: A 1002 ASP cc_start: 0.8152 (t0) cc_final: 0.7932 (t0) REVERT: A 1011 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7436 (tpt90) REVERT: A 1016 TRP cc_start: 0.8497 (t60) cc_final: 0.8236 (t60) REVERT: B 20 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7380 (m) REVERT: B 137 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7469 (mtt180) REVERT: B 266 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7926 (p) REVERT: G 13 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 63 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5933 (tp) REVERT: C 64 THR cc_start: 0.6942 (OUTLIER) cc_final: 0.6682 (t) REVERT: C 127 ASN cc_start: 0.6447 (OUTLIER) cc_final: 0.5984 (p0) REVERT: C 158 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: C 231 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8166 (t80) REVERT: C 267 MET cc_start: 0.8448 (ppp) cc_final: 0.8074 (ppp) REVERT: C 460 ILE cc_start: 0.8685 (mm) cc_final: 0.8342 (tp) REVERT: C 708 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: C 837 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7337 (ptt-90) REVERT: C 852 MET cc_start: 0.6667 (mmm) cc_final: 0.6367 (mmm) REVERT: C 933 ASP cc_start: 0.8887 (t70) cc_final: 0.8579 (t0) REVERT: D 20 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7833 (m) REVERT: D 266 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7499 (p) REVERT: E 13 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8202 (p) outliers start: 233 outliers final: 34 residues processed: 502 average time/residue: 0.1871 time to fit residues: 135.8484 Evaluate side-chains 197 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 167 GLN A 360 ASN A 486 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A1019 GLN B 56 GLN B 107 HIS B 203 GLN B 258 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 167 GLN C 360 ASN C 474 ASN C 486 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN D 56 GLN D 107 HIS D 203 GLN D 258 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069954 restraints weight = 66573.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071975 restraints weight = 38043.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072574 restraints weight = 26025.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072884 restraints weight = 22856.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073058 restraints weight = 22012.541| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23068 Z= 0.173 Angle : 0.710 11.675 31184 Z= 0.349 Chirality : 0.045 0.416 3512 Planarity : 0.006 0.051 3804 Dihedral : 16.204 171.189 3713 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.36 % Allowed : 12.02 % Favored : 84.62 % 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: -1.64 (0.15), residues: 2636 helix: -0.00 (0.15), residues: 1182 sheet: -1.92 (0.27), residues: 276 loop : -1.99 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 281 TYR 0.020 0.001 TYR C 569 PHE 0.020 0.002 PHE C 793 TRP 0.027 0.002 TRP D 156 HIS 0.007 0.002 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (23024) covalent geometry : angle 0.68596 / 0.34 (31058) SS BOND : bond 0.00203 / 0.09 ( 6) SS BOND : angle 1.03329 / 0.48 ( 12) hydrogen bonds : bond 0.06159 / 4.08 ( 982) hydrogen bonds : angle 5.31871 / 3.72 ( 2862) link_ALPHA1-3 : bond 0.00797 / 0.46 ( 6) link_ALPHA1-3 : angle 3.02468 / 1.71 ( 18) link_ALPHA1-6 : bond 0.00689 / 0.34 ( 4) link_ALPHA1-6 : angle 1.46765 / 0.96 ( 12) link_BETA1-2 : bond 0.00886 / 0.45 ( 2) link_BETA1-2 : angle 4.54805 / 2.22 ( 6) link_BETA1-4 : bond 0.00955 / 0.57 ( 14) link_BETA1-4 : angle 3.80859 / 2.22 ( 42) link_BETA1-6 : bond 0.00210 / 0.10 ( 4) link_BETA1-6 : angle 1.51433 / 0.94 ( 12) link_NAG-ASN : bond 0.00689 / 0.33 ( 8) link_NAG-ASN : angle 2.45294 / 1.38 ( 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 216 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 140 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 HIS cc_start: 0.8090 (m-70) cc_final: 0.7715 (m-70) REVERT: A 127 ASN cc_start: 0.6291 (OUTLIER) cc_final: 0.5710 (p0) REVERT: A 158 MET cc_start: 0.8350 (mmp) cc_final: 0.7721 (tmm) REVERT: A 231 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 351 MET cc_start: 0.8250 (mmm) cc_final: 0.7867 (mtt) REVERT: A 424 ILE cc_start: 0.7877 (mt) cc_final: 0.7649 (mt) REVERT: A 967 PHE cc_start: 0.7767 (t80) cc_final: 0.7364 (t80) REVERT: B 20 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7820 (m) REVERT: B 85 ILE cc_start: 0.7518 (mt) cc_final: 0.6088 (mm) REVERT: G 13 THR cc_start: 0.8430 (m) cc_final: 0.8004 (p) REVERT: C 127 ASN cc_start: 0.6533 (OUTLIER) cc_final: 0.5961 (p0) REVERT: C 158 MET cc_start: 0.8321 (mmp) cc_final: 0.7740 (tmm) REVERT: C 231 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8127 (t80) REVERT: C 351 MET cc_start: 0.8160 (mmm) cc_final: 0.7936 (mtt) REVERT: C 507 MET cc_start: 0.8055 (ttp) cc_final: 0.7682 (tmm) REVERT: C 837 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7940 (ptt180) REVERT: C 967 PHE cc_start: 0.7833 (t80) cc_final: 0.7468 (t80) REVERT: D 20 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.8011 (m) REVERT: D 85 ILE cc_start: 0.7490 (mt) cc_final: 0.6080 (mm) REVERT: E 13 THR cc_start: 0.8497 (m) cc_final: 0.8145 (p) outliers start: 76 outliers final: 33 residues processed: 206 average time/residue: 0.1543 time to fit residues: 50.4047 Evaluate side-chains 148 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 142 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 263 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 0.2980 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN A1019 GLN B 243 GLN C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.090923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067911 restraints weight = 67225.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067860 restraints weight = 49732.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068532 restraints weight = 38816.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068922 restraints weight = 31802.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069016 restraints weight = 28894.163| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23068 Z= 0.175 Angle : 0.660 11.999 31184 Z= 0.317 Chirality : 0.044 0.390 3512 Planarity : 0.005 0.041 3804 Dihedral : 14.113 158.161 3654 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.87 % Allowed : 12.91 % Favored : 84.22 % 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: -0.73 (0.16), residues: 2636 helix: 0.67 (0.15), residues: 1190 sheet: -1.53 (0.27), residues: 286 loop : -1.41 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 281 TYR 0.023 0.002 TYR A 569 PHE 0.019 0.002 PHE C 793 TRP 0.027 0.002 TRP A 894 HIS 0.008 0.002 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (23024) covalent geometry : angle 0.64163 / 0.31 (31058) SS BOND : bond 0.00110 / 0.05 ( 6) SS BOND : angle 1.42269 / 0.72 ( 12) hydrogen bonds : bond 0.05343 / 3.57 ( 982) hydrogen bonds : angle 4.69564 / 3.30 ( 2862) link_ALPHA1-3 : bond 0.00711 / 0.36 ( 6) link_ALPHA1-3 : angle 2.56265 / 1.52 ( 18) link_ALPHA1-6 : bond 0.00910 / 0.44 ( 4) link_ALPHA1-6 : angle 1.42744 / 0.90 ( 12) link_BETA1-2 : bond 0.00655 / 0.33 ( 2) link_BETA1-2 : angle 3.65494 / 1.81 ( 6) link_BETA1-4 : bond 0.00733 / 0.44 ( 14) link_BETA1-4 : angle 3.27721 / 1.87 ( 42) link_BETA1-6 : bond 0.00289 / 0.15 ( 4) link_BETA1-6 : angle 1.49043 / 0.88 ( 12) link_NAG-ASN : bond 0.00388 / 0.18 ( 8) link_NAG-ASN : angle 1.79595 / 1.05 ( 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 184 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 119 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8222 (mmp) cc_final: 0.7722 (tmm) REVERT: A 231 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8254 (t80) REVERT: A 404 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: A 413 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6224 (ptpp) REVERT: B 20 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8069 (m) REVERT: G 10 GLU cc_start: 0.8127 (pm20) cc_final: 0.7796 (pm20) REVERT: G 13 THR cc_start: 0.8604 (m) cc_final: 0.8246 (p) REVERT: C 158 MET cc_start: 0.8237 (mmp) cc_final: 0.7815 (tmm) REVERT: C 231 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8217 (t80) REVERT: C 404 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: C 413 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6262 (ptpp) REVERT: D 20 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8204 (m) REVERT: E 10 GLU cc_start: 0.8138 (pm20) cc_final: 0.7770 (pm20) REVERT: E 13 THR cc_start: 0.8582 (m) cc_final: 0.8268 (p) outliers start: 65 outliers final: 39 residues processed: 176 average time/residue: 0.1396 time to fit residues: 40.5120 Evaluate side-chains 154 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 251 optimal weight: 0.0370 chunk 159 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066048 restraints weight = 67208.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.066042 restraints weight = 51806.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066838 restraints weight = 37408.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067093 restraints weight = 30957.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067229 restraints weight = 29014.922| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23068 Z= 0.187 Angle : 0.639 10.349 31184 Z= 0.307 Chirality : 0.044 0.399 3512 Planarity : 0.004 0.038 3804 Dihedral : 13.257 148.704 3634 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.05 % Allowed : 13.04 % Favored : 83.91 % 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: -0.41 (0.16), residues: 2636 helix: 0.84 (0.15), residues: 1206 sheet: -1.03 (0.28), residues: 266 loop : -1.24 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 TYR 0.017 0.002 TYR A 569 PHE 0.023 0.002 PHE C 793 TRP 0.053 0.003 TRP A 894 HIS 0.007 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (23024) covalent geometry : angle 0.62038 / 0.30 (31058) SS BOND : bond 0.00125 / 0.06 ( 6) SS BOND : angle 1.15821 / 0.72 ( 12) hydrogen bonds : bond 0.05218 / 3.49 ( 982) hydrogen bonds : angle 4.51046 / 3.18 ( 2862) link_ALPHA1-3 : bond 0.00622 / 0.33 ( 6) link_ALPHA1-3 : angle 2.56583 / 1.52 ( 18) link_ALPHA1-6 : bond 0.00668 / 0.33 ( 4) link_ALPHA1-6 : angle 1.58792 / 0.99 ( 12) link_BETA1-2 : bond 0.00622 / 0.31 ( 2) link_BETA1-2 : angle 4.16982 / 2.06 ( 6) link_BETA1-4 : bond 0.00665 / 0.40 ( 14) link_BETA1-4 : angle 3.16232 / 1.81 ( 42) link_BETA1-6 : bond 0.00125 / 0.06 ( 4) link_BETA1-6 : angle 1.57368 / 0.96 ( 12) link_NAG-ASN : bond 0.00416 / 0.20 ( 8) link_NAG-ASN : angle 1.75143 / 1.00 ( 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 181 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 112 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8287 (mmp) cc_final: 0.7850 (tmm) REVERT: A 404 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: A 413 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6280 (ptpp) REVERT: G 10 GLU cc_start: 0.8192 (pm20) cc_final: 0.7886 (pm20) REVERT: G 13 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8538 (p) REVERT: C 158 MET cc_start: 0.8292 (mmp) cc_final: 0.7908 (tmm) REVERT: C 404 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 413 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6300 (ptpp) REVERT: E 10 GLU cc_start: 0.8167 (pm20) cc_final: 0.7807 (pm20) REVERT: E 13 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8568 (p) outliers start: 69 outliers final: 43 residues processed: 170 average time/residue: 0.1335 time to fit residues: 37.7465 Evaluate side-chains 144 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 95 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 63 optimal weight: 20.0000 chunk 247 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 110 optimal weight: 0.0670 chunk 248 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 946 GLN B 146 GLN C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.090438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067608 restraints weight = 66584.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068230 restraints weight = 46251.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068677 restraints weight = 36321.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068983 restraints weight = 30644.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069070 restraints weight = 28140.547| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23068 Z= 0.115 Angle : 0.562 11.057 31184 Z= 0.268 Chirality : 0.042 0.393 3512 Planarity : 0.004 0.038 3804 Dihedral : 12.278 139.641 3624 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.43 % Allowed : 14.19 % Favored : 83.38 % 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: 0.04 (0.16), residues: 2636 helix: 1.13 (0.15), residues: 1220 sheet: -0.52 (0.31), residues: 246 loop : -1.02 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.011 0.001 TYR A 569 PHE 0.020 0.001 PHE C 793 TRP 0.073 0.002 TRP A 894 HIS 0.012 0.001 HIS A 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (23024) covalent geometry : angle 0.54352 / 0.26 (31058) SS BOND : bond 0.00063 / 0.03 ( 6) SS BOND : angle 0.66593 / 0.35 ( 12) hydrogen bonds : bond 0.04411 / 2.96 ( 982) hydrogen bonds : angle 4.27912 / 3.01 ( 2862) link_ALPHA1-3 : bond 0.00754 / 0.42 ( 6) link_ALPHA1-3 : angle 2.51445 / 1.48 ( 18) link_ALPHA1-6 : bond 0.00727 / 0.35 ( 4) link_ALPHA1-6 : angle 1.50664 / 0.91 ( 12) link_BETA1-2 : bond 0.00665 / 0.33 ( 2) link_BETA1-2 : angle 3.92505 / 1.93 ( 6) link_BETA1-4 : bond 0.00697 / 0.42 ( 14) link_BETA1-4 : angle 2.82083 / 1.59 ( 42) link_BETA1-6 : bond 0.00123 / 0.06 ( 4) link_BETA1-6 : angle 1.45000 / 0.90 ( 12) link_NAG-ASN : bond 0.00459 / 0.22 ( 8) link_NAG-ASN : angle 1.59510 / 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 169 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7863 (tmm) REVERT: A 267 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8137 (tmm) REVERT: A 404 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: A 488 TYR cc_start: 0.7697 (p90) cc_final: 0.7242 (p90) REVERT: G 10 GLU cc_start: 0.8140 (pm20) cc_final: 0.7828 (pm20) REVERT: G 13 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 158 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (tmm) REVERT: C 267 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8116 (tmm) REVERT: C 404 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: C 571 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.5187 (p90) outliers start: 55 outliers final: 35 residues processed: 158 average time/residue: 0.1492 time to fit residues: 38.9166 Evaluate side-chains 142 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 50 optimal weight: 0.0970 chunk 213 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 206 optimal weight: 0.1980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067244 restraints weight = 66812.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067616 restraints weight = 47817.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068287 restraints weight = 36475.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068521 restraints weight = 30597.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068606 restraints weight = 28706.786| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23068 Z= 0.121 Angle : 0.566 11.894 31184 Z= 0.267 Chirality : 0.042 0.393 3512 Planarity : 0.003 0.039 3804 Dihedral : 11.573 128.229 3618 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.92 % Allowed : 14.37 % Favored : 82.71 % 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: 0.20 (0.16), residues: 2636 helix: 1.23 (0.15), residues: 1226 sheet: -0.35 (0.32), residues: 246 loop : -0.92 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.014 0.001 TYR A 488 PHE 0.021 0.001 PHE C 793 TRP 0.079 0.002 TRP A 894 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (23024) covalent geometry : angle 0.54907 / 0.26 (31058) SS BOND : bond 0.00131 / 0.07 ( 6) SS BOND : angle 0.62030 / 0.30 ( 12) hydrogen bonds : bond 0.04297 / 2.88 ( 982) hydrogen bonds : angle 4.25840 / 3.00 ( 2862) link_ALPHA1-3 : bond 0.00706 / 0.40 ( 6) link_ALPHA1-3 : angle 2.44480 / 1.45 ( 18) link_ALPHA1-6 : bond 0.00658 / 0.32 ( 4) link_ALPHA1-6 : angle 1.48095 / 0.90 ( 12) link_BETA1-2 : bond 0.00644 / 0.32 ( 2) link_BETA1-2 : angle 3.97677 / 1.97 ( 6) link_BETA1-4 : bond 0.00657 / 0.40 ( 14) link_BETA1-4 : angle 2.61950 / 1.49 ( 42) link_BETA1-6 : bond 0.00093 / 0.05 ( 4) link_BETA1-6 : angle 1.46101 / 0.91 ( 12) link_NAG-ASN : bond 0.00641 / 0.29 ( 8) link_NAG-ASN : angle 1.75276 / 1.10 ( 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 176 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7863 (tmm) REVERT: A 164 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5574 (ptp) REVERT: A 267 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8090 (tmm) REVERT: A 404 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: A 413 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6310 (ptpp) REVERT: A 473 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6536 (mtm110) REVERT: A 488 TYR cc_start: 0.7629 (p90) cc_final: 0.7196 (p90) REVERT: A 507 MET cc_start: 0.7754 (tpp) cc_final: 0.6742 (tpp) REVERT: B 266 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7894 (p) REVERT: G 10 GLU cc_start: 0.8147 (pm20) cc_final: 0.7808 (pm20) REVERT: G 13 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8550 (p) REVERT: C 158 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7915 (tmm) REVERT: C 267 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8174 (tmm) REVERT: C 404 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: C 413 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6309 (ptpp) REVERT: C 488 TYR cc_start: 0.7743 (p90) cc_final: 0.7165 (p90) REVERT: D 266 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7814 (p) REVERT: E 13 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8581 (p) outliers start: 66 outliers final: 41 residues processed: 165 average time/residue: 0.1453 time to fit residues: 39.0420 Evaluate side-chains 156 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 75 optimal weight: 0.0670 chunk 234 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 0.3980 chunk 202 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS C 52 HIS ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.090662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068025 restraints weight = 67102.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067952 restraints weight = 49311.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068692 restraints weight = 37660.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068976 restraints weight = 31581.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069072 restraints weight = 28878.622| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 23068 Z= 0.104 Angle : 0.546 12.372 31184 Z= 0.256 Chirality : 0.041 0.392 3512 Planarity : 0.003 0.038 3804 Dihedral : 10.899 113.462 3618 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.39 % Allowed : 15.12 % Favored : 82.49 % 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: 0.44 (0.16), residues: 2636 helix: 1.40 (0.15), residues: 1226 sheet: -0.10 (0.32), residues: 246 loop : -0.80 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.020 0.001 TYR A 684 PHE 0.020 0.001 PHE C 793 TRP 0.093 0.002 TRP A 894 HIS 0.007 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (23024) covalent geometry : angle 0.52935 / 0.25 (31058) SS BOND : bond 0.00106 / 0.06 ( 6) SS BOND : angle 0.48634 / 0.25 ( 12) hydrogen bonds : bond 0.03974 / 2.67 ( 982) hydrogen bonds : angle 4.15961 / 2.94 ( 2862) link_ALPHA1-3 : bond 0.00716 / 0.41 ( 6) link_ALPHA1-3 : angle 2.43617 / 1.44 ( 18) link_ALPHA1-6 : bond 0.00604 / 0.29 ( 4) link_ALPHA1-6 : angle 1.45392 / 0.89 ( 12) link_BETA1-2 : bond 0.00636 / 0.32 ( 2) link_BETA1-2 : angle 3.95065 / 1.94 ( 6) link_BETA1-4 : bond 0.00651 / 0.40 ( 14) link_BETA1-4 : angle 2.55399 / 1.43 ( 42) link_BETA1-6 : bond 0.00100 / 0.05 ( 4) link_BETA1-6 : angle 1.40014 / 0.87 ( 12) link_NAG-ASN : bond 0.00556 / 0.25 ( 8) link_NAG-ASN : angle 1.62427 / 1.02 ( 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 161 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 107 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7862 (tmm) REVERT: A 164 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5634 (ptp) REVERT: A 267 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8033 (tmm) REVERT: A 404 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: A 488 TYR cc_start: 0.7680 (p90) cc_final: 0.7170 (p90) REVERT: A 507 MET cc_start: 0.7413 (tpp) cc_final: 0.6763 (tpp) REVERT: G 13 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 267 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: C 404 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: D 266 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7744 (p) REVERT: D 272 MET cc_start: 0.7341 (ptm) cc_final: 0.6934 (ttp) REVERT: E 13 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (p) outliers start: 54 outliers final: 38 residues processed: 150 average time/residue: 0.1511 time to fit residues: 37.4839 Evaluate side-chains 146 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 219 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 240 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 248 ASN B 107 HIS C 52 HIS C 248 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063847 restraints weight = 67179.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064840 restraints weight = 49894.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065214 restraints weight = 36182.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065497 restraints weight = 32180.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065807 restraints weight = 29779.770| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 23068 Z= 0.206 Angle : 0.655 12.936 31184 Z= 0.311 Chirality : 0.044 0.380 3512 Planarity : 0.004 0.041 3804 Dihedral : 11.334 105.970 3618 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 15.12 % Favored : 81.96 % 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: 0.19 (0.16), residues: 2636 helix: 1.10 (0.15), residues: 1224 sheet: -0.14 (0.33), residues: 246 loop : -0.83 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 223 TYR 0.016 0.002 TYR A 994 PHE 0.025 0.002 PHE C 793 TRP 0.091 0.003 TRP A 894 HIS 0.007 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (23024) covalent geometry : angle 0.63979 / 0.31 (31058) SS BOND : bond 0.00169 / 0.09 ( 6) SS BOND : angle 0.88705 / 0.44 ( 12) hydrogen bonds : bond 0.05215 / 3.49 ( 982) hydrogen bonds : angle 4.38851 / 3.09 ( 2862) link_ALPHA1-3 : bond 0.00719 / 0.42 ( 6) link_ALPHA1-3 : angle 2.32606 / 1.37 ( 18) link_ALPHA1-6 : bond 0.00620 / 0.30 ( 4) link_ALPHA1-6 : angle 1.51755 / 0.92 ( 12) link_BETA1-2 : bond 0.00675 / 0.34 ( 2) link_BETA1-2 : angle 4.04066 / 2.03 ( 6) link_BETA1-4 : bond 0.00591 / 0.36 ( 14) link_BETA1-4 : angle 2.72802 / 1.57 ( 42) link_BETA1-6 : bond 0.00172 / 0.09 ( 4) link_BETA1-6 : angle 1.61886 / 1.00 ( 12) link_NAG-ASN : bond 0.00509 / 0.24 ( 8) link_NAG-ASN : angle 1.75428 / 1.10 ( 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 166 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 100 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8154 (mmp) cc_final: 0.7837 (tmm) REVERT: A 267 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8203 (tmm) REVERT: A 404 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: A 413 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6421 (ptpp) REVERT: A 473 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6478 (mtm180) REVERT: A 488 TYR cc_start: 0.7772 (p90) cc_final: 0.7271 (p90) REVERT: A 507 MET cc_start: 0.7510 (tpp) cc_final: 0.7043 (tpp) REVERT: B 266 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.7990 (p) REVERT: G 13 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 52 HIS cc_start: 0.7840 (m90) cc_final: 0.7417 (m-70) REVERT: C 267 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8181 (tmm) REVERT: C 404 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: C 413 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6422 (ptpp) REVERT: D 266 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 13 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (p) outliers start: 66 outliers final: 48 residues processed: 159 average time/residue: 0.1526 time to fit residues: 39.9171 Evaluate side-chains 153 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 95 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 2 optimal weight: 8.9990 chunk 246 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.088588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065054 restraints weight = 66997.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065820 restraints weight = 55466.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066489 restraints weight = 37704.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066752 restraints weight = 30677.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066843 restraints weight = 29328.485| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23068 Z= 0.140 Angle : 0.590 13.729 31184 Z= 0.278 Chirality : 0.042 0.384 3512 Planarity : 0.003 0.038 3804 Dihedral : 11.107 95.011 3618 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.52 % Allowed : 15.61 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2636 helix: 1.30 (0.15), residues: 1224 sheet: 0.24 (0.31), residues: 266 loop : -0.80 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 223 TYR 0.022 0.001 TYR A 684 PHE 0.020 0.001 PHE C 793 TRP 0.075 0.002 TRP A 894 HIS 0.006 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23024) covalent geometry : angle 0.57505 / 0.27 (31058) SS BOND : bond 0.00156 / 0.09 ( 6) SS BOND : angle 0.66551 / 0.33 ( 12) hydrogen bonds : bond 0.04525 / 3.05 ( 982) hydrogen bonds : angle 4.22798 / 2.98 ( 2862) link_ALPHA1-3 : bond 0.00730 / 0.42 ( 6) link_ALPHA1-3 : angle 2.39469 / 1.41 ( 18) link_ALPHA1-6 : bond 0.00615 / 0.30 ( 4) link_ALPHA1-6 : angle 1.47018 / 0.88 ( 12) link_BETA1-2 : bond 0.00656 / 0.33 ( 2) link_BETA1-2 : angle 3.95389 / 1.94 ( 6) link_BETA1-4 : bond 0.00614 / 0.38 ( 14) link_BETA1-4 : angle 2.55332 / 1.43 ( 42) link_BETA1-6 : bond 0.00127 / 0.07 ( 4) link_BETA1-6 : angle 1.48811 / 0.92 ( 12) link_NAG-ASN : bond 0.00560 / 0.25 ( 8) link_NAG-ASN : angle 1.64028 / 1.02 ( 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 165 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8101 (mmp) cc_final: 0.7838 (tmm) REVERT: A 267 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (tmm) REVERT: A 404 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: A 413 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6439 (ptpp) REVERT: A 473 ARG cc_start: 0.6837 (mtt180) cc_final: 0.6497 (mtm180) REVERT: A 488 TYR cc_start: 0.7835 (p90) cc_final: 0.7289 (p90) REVERT: A 507 MET cc_start: 0.7761 (tpp) cc_final: 0.7179 (tpp) REVERT: B 266 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7829 (p) REVERT: G 13 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8708 (p) REVERT: C 267 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8009 (tmm) REVERT: C 404 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: C 413 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6437 (ptpp) REVERT: D 266 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7796 (p) REVERT: E 13 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8716 (p) outliers start: 57 outliers final: 44 residues processed: 157 average time/residue: 0.1543 time to fit residues: 40.0896 Evaluate side-chains 156 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 901 SER Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 255 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 208 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 HIS ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.089820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066926 restraints weight = 67100.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067928 restraints weight = 54463.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068471 restraints weight = 37646.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068703 restraints weight = 29769.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068775 restraints weight = 28472.594| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23068 Z= 0.106 Angle : 0.570 13.899 31184 Z= 0.265 Chirality : 0.041 0.384 3512 Planarity : 0.003 0.038 3804 Dihedral : 10.518 86.014 3618 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 15.92 % Favored : 81.87 % 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: 0.61 (0.16), residues: 2636 helix: 1.50 (0.15), residues: 1224 sheet: 0.18 (0.30), residues: 280 loop : -0.72 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 223 TYR 0.024 0.001 TYR A 684 PHE 0.020 0.001 PHE C 793 TRP 0.051 0.002 TRP A 894 HIS 0.012 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (23024) covalent geometry : angle 0.55493 / 0.26 (31058) SS BOND : bond 0.00143 / 0.08 ( 6) SS BOND : angle 0.53281 / 0.26 ( 12) hydrogen bonds : bond 0.03961 / 2.67 ( 982) hydrogen bonds : angle 4.13723 / 2.91 ( 2862) link_ALPHA1-3 : bond 0.00748 / 0.43 ( 6) link_ALPHA1-3 : angle 2.34558 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00605 / 0.30 ( 4) link_ALPHA1-6 : angle 1.39464 / 0.85 ( 12) link_BETA1-2 : bond 0.00653 / 0.33 ( 2) link_BETA1-2 : angle 3.92392 / 1.93 ( 6) link_BETA1-4 : bond 0.00624 / 0.38 ( 14) link_BETA1-4 : angle 2.47612 / 1.37 ( 42) link_BETA1-6 : bond 0.00086 / 0.04 ( 4) link_BETA1-6 : angle 1.40174 / 0.88 ( 12) link_NAG-ASN : bond 0.00592 / 0.27 ( 8) link_NAG-ASN : angle 1.51993 / 0.96 ( 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 159 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8028 (tmm) REVERT: A 404 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: A 413 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6477 (ptpp) REVERT: A 488 TYR cc_start: 0.7795 (p90) cc_final: 0.7223 (p90) REVERT: A 507 MET cc_start: 0.7758 (tpp) cc_final: 0.7105 (tpp) REVERT: A 578 PHE cc_start: 0.7026 (m-80) cc_final: 0.6719 (m-80) REVERT: B 266 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7749 (p) REVERT: G 13 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8676 (p) REVERT: C 267 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8028 (tmm) REVERT: C 404 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: C 413 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6402 (ptpp) REVERT: C 488 TYR cc_start: 0.7693 (p90) cc_final: 0.7162 (p90) REVERT: C 507 MET cc_start: 0.7610 (mmm) cc_final: 0.6695 (tpp) REVERT: D 266 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 272 MET cc_start: 0.7410 (ptm) cc_final: 0.6989 (ttp) REVERT: E 13 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8669 (p) outliers start: 50 outliers final: 37 residues processed: 151 average time/residue: 0.1596 time to fit residues: 39.2198 Evaluate side-chains 149 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.087944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065299 restraints weight = 66938.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065143 restraints weight = 53833.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065841 restraints weight = 39812.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066081 restraints weight = 34211.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066219 restraints weight = 31337.013| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 23068 Z= 0.156 Angle : 0.610 13.784 31184 Z= 0.286 Chirality : 0.042 0.374 3512 Planarity : 0.004 0.038 3804 Dihedral : 10.399 82.255 3618 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.30 % Allowed : 16.22 % Favored : 81.48 % 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: 0.50 (0.16), residues: 2636 helix: 1.36 (0.15), residues: 1226 sheet: -0.02 (0.32), residues: 246 loop : -0.66 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 223 TYR 0.022 0.001 TYR A 684 PHE 0.023 0.001 PHE A 793 TRP 0.056 0.002 TRP A 894 HIS 0.005 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (23024) covalent geometry : angle 0.59552 / 0.28 (31058) SS BOND : bond 0.00146 / 0.08 ( 6) SS BOND : angle 0.67488 / 0.33 ( 12) hydrogen bonds : bond 0.04578 / 3.08 ( 982) hydrogen bonds : angle 4.21922 / 2.96 ( 2862) link_ALPHA1-3 : bond 0.00736 / 0.43 ( 6) link_ALPHA1-3 : angle 2.27946 / 1.33 ( 18) link_ALPHA1-6 : bond 0.00586 / 0.29 ( 4) link_ALPHA1-6 : angle 1.42377 / 0.86 ( 12) link_BETA1-2 : bond 0.00684 / 0.34 ( 2) link_BETA1-2 : angle 3.97848 / 1.97 ( 6) link_BETA1-4 : bond 0.00570 / 0.35 ( 14) link_BETA1-4 : angle 2.52776 / 1.43 ( 42) link_BETA1-6 : bond 0.00149 / 0.08 ( 4) link_BETA1-6 : angle 1.54356 / 0.96 ( 12) link_NAG-ASN : bond 0.00467 / 0.21 ( 8) link_NAG-ASN : angle 1.60486 / 1.02 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.06 seconds wall clock time: 54 minutes 17.01 seconds (3257.01 seconds total)