Starting phenix.real_space_refine on Sat Jul 4 20:29:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wyy_32898/07_2026/7wyy_32898.cif" } resolution = 3.9 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 14674 2.51 5 N 3518 2.21 5 O 4314 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: 22656 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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 447 Unusual residues: {' MG': 3, '7Q2': 1, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CLR': 1, 'PCW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: C, D, E, K, L, M, N Time building chain proxies: 10.61, per 1000 atoms: 0.47 Number of scatterers: 22656 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 4314 8.00 N 3518 7.00 C 14674 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: 2.18 Conformation dependent library (CDL) restraints added in 963.5 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: 114 helices and 22 sheets defined 50.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.558A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 removed outlier: 3.543A 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 removed outlier: 3.587A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.684A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.109A pdb=" N ALA A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.921A 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: 3.502A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.691A 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: 3.933A 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: 3.637A 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: 3.773A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 797 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: 3.671A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.248A 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: 3.515A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.557A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.760A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.513A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.487A 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: 4.119A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.523A 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: 3.580A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.006A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.572A pdb=" N ARG B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.738A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.146A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.558A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 removed outlier: 3.544A 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 removed outlier: 3.586A pdb=" N ILE C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.684A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.109A pdb=" N ALA C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.920A 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: 3.503A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.691A 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: 3.932A 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: 3.637A 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: 3.773A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 786 Processing helix chain 'C' and resid 787 through 797 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: 3.671A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.634A 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: 4.249A 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: 3.515A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.557A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.760A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.514A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.486A 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: 4.119A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.524A 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: 3.580A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 4.007A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 removed outlier: 3.570A pdb=" N ARG D 223 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.738A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.147A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.615A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.106A 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: 6.719A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.992A 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: 7.911A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.515A 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: 6.177A 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: 3.836A 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: 6.470A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.078A 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: 3.792A 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: 3.669A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.695A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 225 through 227 removed outlier: 4.614A pdb=" N CYS C 211 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.719A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB7, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.838A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.470A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.077A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AC1, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.791A pdb=" N GLU D 24 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.669A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AC4, first strand: chain 'D' and resid 124 through 125 994 hydrogen bonds defined for protein. 2886 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: 4.78 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6847 1.35 - 1.47: 5211 1.47 - 1.59: 10792 1.59 - 1.71: 60 1.71 - 1.83: 172 Bond restraints: 23082 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 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=" C39 PCW G1304 " pdb=" C40 PCW G1304 " ideal model delta sigma weight residual 1.333 1.546 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C39 PCW E1304 " pdb=" C40 PCW E1304 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C19 PCW C1109 " pdb=" C20 PCW C1109 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 23077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 28473 2.40 - 4.80: 2096 4.80 - 7.21: 422 7.21 - 9.61: 125 9.61 - 12.01: 32 Bond angle restraints: 31148 Sorted by residual: angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 98.44 10.23 1.55e+00 4.16e-01 4.36e+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 98.45 10.22 1.55e+00 4.16e-01 4.34e+01 angle pdb=" N SER D 32 " pdb=" CA SER D 32 " pdb=" C SER D 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.94e+01 angle pdb=" N THR C 57 " pdb=" CA THR C 57 " pdb=" C THR C 57 " ideal model delta sigma weight residual 108.46 116.64 -8.18 1.51e+00 4.39e-01 2.93e+01 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 111.14 116.99 -5.85 1.08e+00 8.57e-01 2.93e+01 ... (remaining 31143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12783 35.90 - 71.80: 685 71.80 - 107.70: 32 107.70 - 143.61: 24 143.61 - 179.51: 2 Dihedral angle restraints: 13526 sinusoidal: 5870 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW E1303 " pdb=" C31 PCW E1303 " pdb=" C32 PCW E1303 " pdb=" O2 PCW E1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.34 -179.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW G1303 " pdb=" C31 PCW G1303 " pdb=" C32 PCW G1303 " pdb=" O2 PCW G1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.21 -179.38 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1112 " pdb=" C31 PCW A1112 " pdb=" C32 PCW A1112 " pdb=" O2 PCW A1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.89 -138.28 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 13523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2871 0.079 - 0.158: 549 0.158 - 0.237: 61 0.237 - 0.316: 23 0.316 - 0.395: 20 Chirality restraints: 3524 Sorted by residual: 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 7.54e+01 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 7.45e+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 9.70e+00 ... (remaining 3521 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.093 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO D 123 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.093 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO B 123 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.065 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 125 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.052 5.00e-02 4.00e+02 ... (remaining 3815 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 108 2.47 - 3.08: 15030 3.08 - 3.68: 30696 3.68 - 4.29: 47987 4.29 - 4.90: 78168 Nonbonded interactions: 171989 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.860 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.860 2.170 nonbonded pdb=" OD2 ASP A 811 " pdb="MG MG A1103 " model vdw 1.969 2.170 nonbonded pdb=" OD2 ASP C 811 " pdb="MG MG C1103 " model vdw 1.970 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 1.991 2.170 ... (remaining 171984 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.380 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.308 23126 Z= 0.582 Angle : 1.494 17.198 31274 Z= 0.759 Chirality : 0.069 0.395 3524 Planarity : 0.009 0.146 3810 Dihedral : 19.106 179.507 8596 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.71 % Rotamer: Outliers : 10.61 % Allowed : 8.97 % Favored : 80.42 % 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: -3.53 (0.14), residues: 2636 helix: -1.87 (0.13), residues: 1186 sheet: -2.42 (0.29), residues: 250 loop : -2.77 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 596 TYR 0.038 0.002 TYR B 206 PHE 0.031 0.003 PHE B 297 TRP 0.037 0.003 TRP D 33 HIS 0.010 0.002 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.58 (23082) covalent geometry : angle 1.46977 / 0.75 (31148) SS BOND : bond 0.00426 / 0.23 ( 6) SS BOND : angle 2.20050 / 1.26 ( 12) hydrogen bonds : bond 0.17498 / 11.73 ( 994) hydrogen bonds : angle 7.49451 / 5.20 ( 2886) link_ALPHA1-3 : bond 0.00839 / 0.43 ( 6) link_ALPHA1-3 : angle 3.15551 / 1.58 ( 18) link_ALPHA1-6 : bond 0.00762 / 0.38 ( 4) link_ALPHA1-6 : angle 1.25286 / 0.71 ( 12) link_BETA1-2 : bond 0.00896 / 0.45 ( 2) link_BETA1-2 : angle 5.50601 / 2.62 ( 6) link_BETA1-4 : bond 0.01023 / 0.60 ( 14) link_BETA1-4 : angle 6.27841 / 3.63 ( 42) link_BETA1-6 : bond 0.00313 / 0.16 ( 4) link_BETA1-6 : angle 1.39389 / 0.92 ( 12) link_NAG-ASN : bond 0.01897 / 0.94 ( 8) link_NAG-ASN : angle 4.18387 / 2.18 ( 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 794 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 554 time to evaluate : 0.817 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5017 (m-40) REVERT: A 71 ILE cc_start: 0.7036 (mt) cc_final: 0.6594 (mm) REVERT: A 127 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6048 (p0) REVERT: A 158 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7827 (tpp) REVERT: A 351 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7568 (mtm) REVERT: A 488 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6286 (p90) REVERT: A 504 LEU cc_start: 0.6747 (tp) cc_final: 0.6304 (pp) REVERT: A 721 ASP cc_start: 0.8784 (m-30) cc_final: 0.8157 (m-30) REVERT: A 810 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (mt) REVERT: A 852 MET cc_start: 0.7518 (mmm) cc_final: 0.7282 (mmp) REVERT: B 242 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8667 (mt) REVERT: G 13 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (p) REVERT: C 65 ASN cc_start: 0.5457 (OUTLIER) cc_final: 0.4673 (m-40) REVERT: C 71 ILE cc_start: 0.7226 (mt) cc_final: 0.6726 (mm) REVERT: C 158 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7842 (tpp) REVERT: C 351 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7590 (mtp) REVERT: C 488 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6317 (p90) REVERT: C 504 LEU cc_start: 0.6590 (tp) cc_final: 0.6263 (pp) REVERT: C 708 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: C 721 ASP cc_start: 0.8742 (m-30) cc_final: 0.8126 (m-30) REVERT: C 753 ASP cc_start: 0.7863 (m-30) cc_final: 0.7067 (t70) REVERT: C 815 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6902 (t0) REVERT: C 852 MET cc_start: 0.7304 (mmm) cc_final: 0.7073 (mmp) REVERT: D 106 MET cc_start: 0.8179 (mmm) cc_final: 0.7908 (mtt) REVERT: D 287 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7782 (m-80) outliers start: 240 outliers final: 46 residues processed: 722 average time/residue: 0.1893 time to fit residues: 201.6320 Evaluate side-chains 295 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP 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 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 815 ASP Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP 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 94 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 287 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 209 HIS A 434 GLN A 474 ASN A 486 ASN A 620 HIS A 683 HIS A 744 GLN A 826 GLN A 904 GLN A1019 GLN B 56 GLN B 203 GLN B 258 GLN C 52 HIS C 474 ASN C 486 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 566 ASN C 620 HIS C 683 HIS C 744 GLN C 826 GLN C 904 GLN C1019 GLN D 56 GLN D 146 GLN D 258 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104006 restraints weight = 42449.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103908 restraints weight = 41087.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105335 restraints weight = 34414.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.105541 restraints weight = 27519.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105789 restraints weight = 26045.008| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23126 Z= 0.157 Angle : 0.720 11.432 31274 Z= 0.352 Chirality : 0.045 0.421 3524 Planarity : 0.006 0.072 3810 Dihedral : 15.952 171.309 3756 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.60 % Allowed : 15.16 % Favored : 80.24 % 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: -1.56 (0.15), residues: 2636 helix: 0.04 (0.15), residues: 1204 sheet: -1.76 (0.28), residues: 256 loop : -2.01 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 471 TYR 0.018 0.001 TYR B 40 PHE 0.019 0.002 PHE B 25 TRP 0.019 0.002 TRP C 392 HIS 0.013 0.002 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (23082) covalent geometry : angle 0.69774 / 0.35 (31148) SS BOND : bond 0.00124 / 0.06 ( 6) SS BOND : angle 0.95899 / 0.49 ( 12) hydrogen bonds : bond 0.05994 / 4.01 ( 994) hydrogen bonds : angle 5.15745 / 3.52 ( 2886) link_ALPHA1-3 : bond 0.00858 / 0.48 ( 6) link_ALPHA1-3 : angle 3.05095 / 1.72 ( 18) link_ALPHA1-6 : bond 0.00628 / 0.31 ( 4) link_ALPHA1-6 : angle 1.45018 / 0.92 ( 12) link_BETA1-2 : bond 0.01010 / 0.51 ( 2) link_BETA1-2 : angle 4.42061 / 2.13 ( 6) link_BETA1-4 : bond 0.00920 / 0.57 ( 14) link_BETA1-4 : angle 3.67325 / 2.14 ( 42) link_BETA1-6 : bond 0.00418 / 0.21 ( 4) link_BETA1-6 : angle 1.42084 / 0.91 ( 12) link_NAG-ASN : bond 0.00768 / 0.40 ( 8) link_NAG-ASN : angle 2.21873 / 1.26 ( 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 361 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 257 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.7070 (mt) cc_final: 0.6658 (mm) REVERT: A 308 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 351 MET cc_start: 0.8082 (mmm) cc_final: 0.7651 (mtp) REVERT: B 20 SER cc_start: 0.5825 (OUTLIER) cc_final: 0.5074 (p) REVERT: B 142 ASP cc_start: 0.5961 (t0) cc_final: 0.5299 (t0) REVERT: C 71 ILE cc_start: 0.7136 (mt) cc_final: 0.6676 (mm) REVERT: C 287 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6820 (mp0) REVERT: C 313 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7881 (tt) REVERT: C 351 MET cc_start: 0.8156 (mmm) cc_final: 0.7866 (mtp) REVERT: C 470 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7143 (mpp) REVERT: C 721 ASP cc_start: 0.8730 (m-30) cc_final: 0.8141 (m-30) REVERT: D 20 SER cc_start: 0.6229 (OUTLIER) cc_final: 0.5479 (p) REVERT: D 142 ASP cc_start: 0.5681 (t0) cc_final: 0.5303 (t0) REVERT: E 4 GLU cc_start: 0.4648 (pm20) cc_final: 0.4364 (pp20) outliers start: 104 outliers final: 62 residues processed: 342 average time/residue: 0.1481 time to fit residues: 82.6255 Evaluate side-chains 248 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE 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 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 98 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 242 optimal weight: 0.0020 chunk 171 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 ASN A 489 GLN A 557 HIS A 826 GLN B 243 GLN C 486 ASN C 744 GLN C1019 GLN D 243 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096269 restraints weight = 42560.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096232 restraints weight = 43600.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097421 restraints weight = 35947.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097830 restraints weight = 29391.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098101 restraints weight = 27750.826| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23126 Z= 0.164 Angle : 0.668 11.292 31274 Z= 0.322 Chirality : 0.044 0.396 3524 Planarity : 0.005 0.056 3810 Dihedral : 13.725 153.556 3687 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.11 % Allowed : 16.14 % Favored : 79.75 % 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: -0.57 (0.16), residues: 2636 helix: 0.81 (0.15), residues: 1198 sheet: -1.41 (0.28), residues: 268 loop : -1.36 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 473 TYR 0.017 0.002 TYR C 488 PHE 0.021 0.002 PHE C 100 TRP 0.012 0.002 TRP A 890 HIS 0.008 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (23082) covalent geometry : angle 0.64861 / 0.32 (31148) SS BOND : bond 0.00218 / 0.12 ( 6) SS BOND : angle 1.93609 / 1.02 ( 12) hydrogen bonds : bond 0.05532 / 3.69 ( 994) hydrogen bonds : angle 4.54155 / 3.10 ( 2886) link_ALPHA1-3 : bond 0.00929 / 0.51 ( 6) link_ALPHA1-3 : angle 2.58104 / 1.51 ( 18) link_ALPHA1-6 : bond 0.00595 / 0.29 ( 4) link_ALPHA1-6 : angle 1.48923 / 0.92 ( 12) link_BETA1-2 : bond 0.00738 / 0.37 ( 2) link_BETA1-2 : angle 3.46252 / 1.71 ( 6) link_BETA1-4 : bond 0.01042 / 0.61 ( 14) link_BETA1-4 : angle 3.34383 / 1.85 ( 42) link_BETA1-6 : bond 0.00125 / 0.06 ( 4) link_BETA1-6 : angle 1.31297 / 0.86 ( 12) link_NAG-ASN : bond 0.01278 / 0.57 ( 8) link_NAG-ASN : angle 2.10323 / 1.32 ( 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 324 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 231 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7053 (tp) cc_final: 0.6177 (tp) REVERT: A 100 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7786 (m-10) REVERT: A 158 MET cc_start: 0.8002 (tpp) cc_final: 0.7310 (tpt) REVERT: A 351 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: A 466 SER cc_start: 0.7675 (t) cc_final: 0.7457 (p) REVERT: A 719 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8792 (t) REVERT: A 721 ASP cc_start: 0.8747 (m-30) cc_final: 0.8296 (m-30) REVERT: B 20 SER cc_start: 0.6157 (OUTLIER) cc_final: 0.5276 (p) REVERT: B 94 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8518 (p) REVERT: B 111 ASP cc_start: 0.7806 (t70) cc_final: 0.6907 (t0) REVERT: B 203 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7391 (mt0) REVERT: C 48 LEU cc_start: 0.7130 (tp) cc_final: 0.6589 (tp) REVERT: C 71 ILE cc_start: 0.7185 (mt) cc_final: 0.6976 (mm) REVERT: C 287 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6818 (mm-30) REVERT: C 351 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7836 (mtp) REVERT: C 466 SER cc_start: 0.7557 (t) cc_final: 0.6880 (p) REVERT: C 470 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: C 719 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8843 (t) REVERT: C 721 ASP cc_start: 0.8801 (m-30) cc_final: 0.8338 (m-30) REVERT: D 20 SER cc_start: 0.6751 (OUTLIER) cc_final: 0.6075 (p) REVERT: D 142 ASP cc_start: 0.6201 (t0) cc_final: 0.5603 (t0) outliers start: 93 outliers final: 57 residues processed: 303 average time/residue: 0.1428 time to fit residues: 71.7298 Evaluate side-chains 257 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 191 optimal weight: 0.0370 chunk 92 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 489 GLN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN C 685 HIS C 744 GLN D 270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088273 restraints weight = 42688.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087980 restraints weight = 37577.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089303 restraints weight = 33142.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089296 restraints weight = 25932.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089477 restraints weight = 24440.486| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23126 Z= 0.204 Angle : 0.677 10.595 31274 Z= 0.326 Chirality : 0.045 0.379 3524 Planarity : 0.005 0.049 3810 Dihedral : 13.157 152.277 3671 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.51 % Allowed : 17.20 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2636 helix: 1.00 (0.15), residues: 1186 sheet: -1.10 (0.31), residues: 258 loop : -1.18 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 473 TYR 0.016 0.002 TYR A 869 PHE 0.023 0.002 PHE A 578 TRP 0.013 0.002 TRP A 890 HIS 0.007 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (23082) covalent geometry : angle 0.65976 / 0.32 (31148) SS BOND : bond 0.00126 / 0.07 ( 6) SS BOND : angle 1.64750 / 1.09 ( 12) hydrogen bonds : bond 0.05864 / 3.90 ( 994) hydrogen bonds : angle 4.47842 / 3.09 ( 2886) link_ALPHA1-3 : bond 0.01215 / 0.74 ( 6) link_ALPHA1-3 : angle 2.54734 / 1.60 ( 18) link_ALPHA1-6 : bond 0.00423 / 0.21 ( 4) link_ALPHA1-6 : angle 1.48762 / 0.98 ( 12) link_BETA1-2 : bond 0.00681 / 0.34 ( 2) link_BETA1-2 : angle 3.85177 / 1.88 ( 6) link_BETA1-4 : bond 0.00565 / 0.34 ( 14) link_BETA1-4 : angle 2.99953 / 1.68 ( 42) link_BETA1-6 : bond 0.00166 / 0.09 ( 4) link_BETA1-6 : angle 1.53274 / 1.03 ( 12) link_NAG-ASN : bond 0.00378 / 0.18 ( 8) link_NAG-ASN : angle 1.93146 / 1.14 ( 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 292 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 190 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7058 (tp) cc_final: 0.6364 (tp) REVERT: A 100 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7459 (m-10) REVERT: A 351 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: A 391 MET cc_start: 0.7235 (mtm) cc_final: 0.6960 (mtm) REVERT: A 507 MET cc_start: 0.8437 (tpp) cc_final: 0.8086 (tpp) REVERT: A 675 THR cc_start: 0.8708 (p) cc_final: 0.8286 (t) REVERT: A 847 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: B 20 SER cc_start: 0.6592 (OUTLIER) cc_final: 0.5577 (p) REVERT: B 111 ASP cc_start: 0.7974 (t70) cc_final: 0.7035 (t70) REVERT: B 142 ASP cc_start: 0.6025 (t0) cc_final: 0.5621 (t0) REVERT: B 287 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: C 64 THR cc_start: 0.5950 (OUTLIER) cc_final: 0.5548 (p) REVERT: C 71 ILE cc_start: 0.7002 (mt) cc_final: 0.6754 (mm) REVERT: C 158 MET cc_start: 0.8039 (tpp) cc_final: 0.7781 (tpp) REVERT: C 287 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6884 (mm-30) REVERT: C 351 MET cc_start: 0.8231 (mmm) cc_final: 0.7904 (mtp) REVERT: C 466 SER cc_start: 0.7763 (t) cc_final: 0.7272 (p) REVERT: C 470 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7273 (mpp) REVERT: C 719 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8670 (t) REVERT: C 847 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: D 142 ASP cc_start: 0.6326 (t0) cc_final: 0.5640 (t0) REVERT: D 287 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7948 (m-80) outliers start: 102 outliers final: 63 residues processed: 275 average time/residue: 0.1400 time to fit residues: 64.5366 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 169 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN C 683 HIS C 946 GLN D 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.116822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085726 restraints weight = 42982.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084597 restraints weight = 46784.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084674 restraints weight = 44939.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085244 restraints weight = 39616.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085472 restraints weight = 36129.319| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 23126 Z= 0.272 Angle : 0.749 9.867 31274 Z= 0.363 Chirality : 0.047 0.389 3524 Planarity : 0.005 0.047 3810 Dihedral : 13.178 164.297 3668 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.04 % Allowed : 18.26 % Favored : 76.70 % 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: -0.47 (0.16), residues: 2636 helix: 0.82 (0.15), residues: 1174 sheet: -0.98 (0.31), residues: 238 loop : -1.29 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 473 TYR 0.030 0.002 TYR A 488 PHE 0.027 0.003 PHE C 793 TRP 0.018 0.002 TRP A 988 HIS 0.012 0.002 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.27 (23082) covalent geometry : angle 0.73471 / 0.36 (31148) SS BOND : bond 0.00177 / 0.11 ( 6) SS BOND : angle 1.46814 / 0.86 ( 12) hydrogen bonds : bond 0.06490 / 4.31 ( 994) hydrogen bonds : angle 4.62131 / 3.20 ( 2886) link_ALPHA1-3 : bond 0.00999 / 0.58 ( 6) link_ALPHA1-3 : angle 2.52692 / 1.47 ( 18) link_ALPHA1-6 : bond 0.00410 / 0.20 ( 4) link_ALPHA1-6 : angle 1.60040 / 1.05 ( 12) link_BETA1-2 : bond 0.00762 / 0.38 ( 2) link_BETA1-2 : angle 3.52585 / 1.71 ( 6) link_BETA1-4 : bond 0.00590 / 0.37 ( 14) link_BETA1-4 : angle 2.79707 / 1.55 ( 42) link_BETA1-6 : bond 0.00258 / 0.13 ( 4) link_BETA1-6 : angle 1.56007 / 1.04 ( 12) link_NAG-ASN : bond 0.00405 / 0.21 ( 8) link_NAG-ASN : angle 2.17921 / 1.36 ( 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 291 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 177 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7196 (tp) cc_final: 0.6484 (tp) REVERT: A 52 HIS cc_start: 0.5355 (m-70) cc_final: 0.5022 (m-70) REVERT: A 100 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7621 (m-10) REVERT: A 158 MET cc_start: 0.7986 (tpp) cc_final: 0.7537 (tpt) REVERT: A 351 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: A 507 MET cc_start: 0.8509 (tpp) cc_final: 0.8280 (tpp) REVERT: A 675 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8401 (t) REVERT: A 847 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: B 142 ASP cc_start: 0.6407 (t0) cc_final: 0.5873 (t0) REVERT: B 287 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: C 64 THR cc_start: 0.6118 (OUTLIER) cc_final: 0.5739 (p) REVERT: C 158 MET cc_start: 0.8062 (tpp) cc_final: 0.7765 (tpp) REVERT: C 287 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6864 (mm-30) REVERT: C 351 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: C 466 SER cc_start: 0.7877 (t) cc_final: 0.7463 (p) REVERT: C 470 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7436 (mpp) REVERT: C 675 THR cc_start: 0.8696 (p) cc_final: 0.8267 (t) REVERT: C 847 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: C 924 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8702 (tp) REVERT: D 142 ASP cc_start: 0.6541 (t0) cc_final: 0.5973 (t0) REVERT: D 287 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7864 (m-80) outliers start: 114 outliers final: 80 residues processed: 271 average time/residue: 0.1426 time to fit residues: 64.0580 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 155 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 784 ILE Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088179 restraints weight = 42825.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086754 restraints weight = 47800.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087995 restraints weight = 40839.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088252 restraints weight = 31620.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088439 restraints weight = 30699.437| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23126 Z= 0.187 Angle : 0.643 9.863 31274 Z= 0.310 Chirality : 0.044 0.379 3524 Planarity : 0.004 0.051 3810 Dihedral : 12.696 164.524 3667 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.64 % Allowed : 19.32 % Favored : 76.04 % 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: -0.25 (0.16), residues: 2636 helix: 1.05 (0.15), residues: 1178 sheet: -0.88 (0.31), residues: 248 loop : -1.24 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 204 TYR 0.027 0.001 TYR A 488 PHE 0.029 0.002 PHE A 967 TRP 0.013 0.001 TRP A 988 HIS 0.009 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (23082) covalent geometry : angle 0.62825 / 0.31 (31148) SS BOND : bond 0.00169 / 0.10 ( 6) SS BOND : angle 1.23167 / 0.76 ( 12) hydrogen bonds : bond 0.05672 / 3.77 ( 994) hydrogen bonds : angle 4.36732 / 3.03 ( 2886) link_ALPHA1-3 : bond 0.00921 / 0.50 ( 6) link_ALPHA1-3 : angle 2.42093 / 1.41 ( 18) link_ALPHA1-6 : bond 0.00413 / 0.20 ( 4) link_ALPHA1-6 : angle 1.44122 / 0.96 ( 12) link_BETA1-2 : bond 0.00752 / 0.38 ( 2) link_BETA1-2 : angle 3.66330 / 1.77 ( 6) link_BETA1-4 : bond 0.00518 / 0.32 ( 14) link_BETA1-4 : angle 2.66850 / 1.46 ( 42) link_BETA1-6 : bond 0.00210 / 0.11 ( 4) link_BETA1-6 : angle 1.46721 / 0.95 ( 12) link_NAG-ASN : bond 0.00260 / 0.13 ( 8) link_NAG-ASN : angle 1.89967 / 1.14 ( 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 288 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 183 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: A 158 MET cc_start: 0.8049 (tpp) cc_final: 0.7549 (tpt) REVERT: A 351 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7599 (mtp) REVERT: A 675 THR cc_start: 0.8668 (p) cc_final: 0.8208 (t) REVERT: A 719 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8637 (t) REVERT: B 142 ASP cc_start: 0.6456 (t0) cc_final: 0.5835 (t0) REVERT: B 287 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: C 64 THR cc_start: 0.6302 (OUTLIER) cc_final: 0.5964 (p) REVERT: C 158 MET cc_start: 0.7941 (tpp) cc_final: 0.7544 (tpp) REVERT: C 287 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6708 (mm-30) REVERT: C 351 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7682 (mtp) REVERT: C 466 SER cc_start: 0.7868 (t) cc_final: 0.7471 (p) REVERT: C 470 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7510 (mpp) REVERT: C 566 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7322 (p0) REVERT: C 675 THR cc_start: 0.8625 (p) cc_final: 0.8157 (t) REVERT: C 719 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8655 (t) REVERT: D 142 ASP cc_start: 0.6522 (t0) cc_final: 0.5869 (t0) REVERT: D 287 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7854 (m-80) outliers start: 105 outliers final: 70 residues processed: 270 average time/residue: 0.1442 time to fit residues: 63.8682 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 166 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 866 PHE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 184 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.117724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087007 restraints weight = 42830.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086064 restraints weight = 45539.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087093 restraints weight = 40942.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087395 restraints weight = 33010.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087591 restraints weight = 31183.665| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23126 Z= 0.186 Angle : 0.647 9.387 31274 Z= 0.312 Chirality : 0.044 0.375 3524 Planarity : 0.004 0.048 3810 Dihedral : 12.268 163.766 3661 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.47 % Allowed : 19.58 % Favored : 75.95 % 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: -0.21 (0.16), residues: 2636 helix: 1.08 (0.15), residues: 1178 sheet: -0.89 (0.32), residues: 238 loop : -1.20 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.025 0.001 TYR A 488 PHE 0.027 0.002 PHE C 967 TRP 0.020 0.002 TRP C 988 HIS 0.006 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (23082) covalent geometry : angle 0.63314 / 0.31 (31148) SS BOND : bond 0.00170 / 0.10 ( 6) SS BOND : angle 1.15979 / 0.71 ( 12) hydrogen bonds : bond 0.05533 / 3.68 ( 994) hydrogen bonds : angle 4.33136 / 3.01 ( 2886) link_ALPHA1-3 : bond 0.00937 / 0.52 ( 6) link_ALPHA1-3 : angle 2.43315 / 1.40 ( 18) link_ALPHA1-6 : bond 0.00415 / 0.20 ( 4) link_ALPHA1-6 : angle 1.41120 / 0.94 ( 12) link_BETA1-2 : bond 0.00722 / 0.36 ( 2) link_BETA1-2 : angle 3.60248 / 1.73 ( 6) link_BETA1-4 : bond 0.00501 / 0.31 ( 14) link_BETA1-4 : angle 2.56802 / 1.40 ( 42) link_BETA1-6 : bond 0.00221 / 0.11 ( 4) link_BETA1-6 : angle 1.45322 / 0.94 ( 12) link_NAG-ASN : bond 0.00255 / 0.12 ( 8) link_NAG-ASN : angle 1.81548 / 1.09 ( 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 281 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7694 (mm) cc_final: 0.7307 (tp) REVERT: A 100 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7542 (m-10) REVERT: A 158 MET cc_start: 0.8090 (tpp) cc_final: 0.7590 (tpt) REVERT: A 351 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7598 (mtp) REVERT: A 675 THR cc_start: 0.8721 (p) cc_final: 0.8292 (t) REVERT: B 18 TRP cc_start: 0.7549 (t-100) cc_final: 0.7334 (t60) REVERT: B 142 ASP cc_start: 0.6452 (t0) cc_final: 0.5772 (t0) REVERT: B 203 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8451 (mm-40) REVERT: B 287 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: C 158 MET cc_start: 0.7982 (tpp) cc_final: 0.7520 (tpp) REVERT: C 287 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6686 (mm-30) REVERT: C 351 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: C 466 SER cc_start: 0.7882 (t) cc_final: 0.7542 (p) REVERT: C 470 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: C 675 THR cc_start: 0.8640 (p) cc_final: 0.8191 (t) REVERT: D 142 ASP cc_start: 0.6533 (t0) cc_final: 0.5880 (t0) REVERT: D 287 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7669 (m-80) outliers start: 101 outliers final: 74 residues processed: 261 average time/residue: 0.1421 time to fit residues: 60.5152 Evaluate side-chains 253 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 172 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 209 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089309 restraints weight = 42089.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088318 restraints weight = 42287.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089324 restraints weight = 38442.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089675 restraints weight = 30334.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089760 restraints weight = 29815.397| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23126 Z= 0.131 Angle : 0.601 9.025 31274 Z= 0.290 Chirality : 0.042 0.374 3524 Planarity : 0.004 0.058 3810 Dihedral : 11.798 159.628 3660 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.23 % Allowed : 20.87 % Favored : 75.91 % 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: -0.01 (0.16), residues: 2636 helix: 1.30 (0.16), residues: 1178 sheet: -0.91 (0.30), residues: 268 loop : -1.13 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 473 TYR 0.024 0.001 TYR A 488 PHE 0.029 0.002 PHE C 967 TRP 0.045 0.002 TRP A 392 HIS 0.024 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (23082) covalent geometry : angle 0.58670 / 0.29 (31148) SS BOND : bond 0.00161 / 0.10 ( 6) SS BOND : angle 0.95311 / 0.58 ( 12) hydrogen bonds : bond 0.04977 / 3.31 ( 994) hydrogen bonds : angle 4.16911 / 2.90 ( 2886) link_ALPHA1-3 : bond 0.00910 / 0.50 ( 6) link_ALPHA1-3 : angle 2.40252 / 1.40 ( 18) link_ALPHA1-6 : bond 0.00491 / 0.24 ( 4) link_ALPHA1-6 : angle 1.34664 / 0.90 ( 12) link_BETA1-2 : bond 0.00710 / 0.35 ( 2) link_BETA1-2 : angle 3.63882 / 1.75 ( 6) link_BETA1-4 : bond 0.00493 / 0.31 ( 14) link_BETA1-4 : angle 2.43683 / 1.31 ( 42) link_BETA1-6 : bond 0.00148 / 0.07 ( 4) link_BETA1-6 : angle 1.40335 / 0.89 ( 12) link_NAG-ASN : bond 0.00365 / 0.17 ( 8) link_NAG-ASN : angle 1.85142 / 1.15 ( 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 262 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 189 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7878 (mmtp) REVERT: A 158 MET cc_start: 0.8160 (tpp) cc_final: 0.7650 (tpt) REVERT: A 351 MET cc_start: 0.8016 (mmm) cc_final: 0.7585 (mtp) REVERT: A 577 ASN cc_start: 0.5949 (m-40) cc_final: 0.5182 (t0) REVERT: A 675 THR cc_start: 0.8672 (p) cc_final: 0.8243 (t) REVERT: A 719 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8658 (t) REVERT: B 111 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7032 (t70) REVERT: B 142 ASP cc_start: 0.6494 (t0) cc_final: 0.5821 (t0) REVERT: B 203 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8455 (mm-40) REVERT: B 234 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8367 (tm) REVERT: B 287 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: G 4 GLU cc_start: 0.4359 (pm20) cc_final: 0.4124 (tm-30) REVERT: C 158 MET cc_start: 0.7895 (tpp) cc_final: 0.7376 (tpp) REVERT: C 287 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6657 (mm-30) REVERT: C 351 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7504 (mtp) REVERT: C 470 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7424 (mpp) REVERT: C 675 THR cc_start: 0.8572 (p) cc_final: 0.8050 (t) REVERT: C 684 TYR cc_start: 0.8102 (m-10) cc_final: 0.7720 (m-10) REVERT: C 719 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8654 (t) REVERT: D 142 ASP cc_start: 0.6493 (t0) cc_final: 0.5878 (t0) REVERT: D 234 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8269 (tm) REVERT: D 287 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7698 (m-80) outliers start: 73 outliers final: 55 residues processed: 249 average time/residue: 0.1425 time to fit residues: 58.3535 Evaluate side-chains 239 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 866 PHE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 253 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN C 683 HIS ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087033 restraints weight = 42867.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084852 restraints weight = 39308.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086044 restraints weight = 41923.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086374 restraints weight = 32567.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086476 restraints weight = 29591.992| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23126 Z= 0.193 Angle : 0.656 9.042 31274 Z= 0.318 Chirality : 0.044 0.372 3524 Planarity : 0.004 0.049 3810 Dihedral : 11.702 158.499 3660 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.67 % Allowed : 21.04 % Favored : 75.29 % 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: -0.13 (0.16), residues: 2636 helix: 1.15 (0.15), residues: 1184 sheet: -0.97 (0.30), residues: 258 loop : -1.14 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.026 0.002 TYR C 488 PHE 0.030 0.002 PHE C 967 TRP 0.044 0.002 TRP C 392 HIS 0.009 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (23082) covalent geometry : angle 0.64316 / 0.32 (31148) SS BOND : bond 0.00317 / 0.17 ( 6) SS BOND : angle 1.56643 / 0.90 ( 12) hydrogen bonds : bond 0.05514 / 3.66 ( 994) hydrogen bonds : angle 4.29753 / 2.98 ( 2886) link_ALPHA1-3 : bond 0.00958 / 0.53 ( 6) link_ALPHA1-3 : angle 2.42859 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00438 / 0.21 ( 4) link_ALPHA1-6 : angle 1.37216 / 0.92 ( 12) link_BETA1-2 : bond 0.00723 / 0.36 ( 2) link_BETA1-2 : angle 3.59861 / 1.72 ( 6) link_BETA1-4 : bond 0.00452 / 0.28 ( 14) link_BETA1-4 : angle 2.35213 / 1.28 ( 42) link_BETA1-6 : bond 0.00217 / 0.11 ( 4) link_BETA1-6 : angle 1.40521 / 0.90 ( 12) link_NAG-ASN : bond 0.00270 / 0.12 ( 8) link_NAG-ASN : angle 2.02958 / 1.28 ( 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 265 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 182 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7864 (mmtp) REVERT: A 351 MET cc_start: 0.7991 (mmm) cc_final: 0.7477 (mtp) REVERT: A 428 CYS cc_start: 0.6390 (t) cc_final: 0.6162 (t) REVERT: A 577 ASN cc_start: 0.6346 (m-40) cc_final: 0.5436 (t0) REVERT: A 675 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 16 PHE cc_start: 0.7448 (t80) cc_final: 0.7151 (t80) REVERT: B 111 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7036 (t70) REVERT: B 142 ASP cc_start: 0.6530 (t0) cc_final: 0.5806 (t0) REVERT: B 203 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8417 (mm-40) REVERT: B 234 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8401 (tm) REVERT: B 287 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: C 36 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7862 (mmtp) REVERT: C 100 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7407 (m-10) REVERT: C 158 MET cc_start: 0.7940 (tpp) cc_final: 0.7446 (tpp) REVERT: C 287 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6721 (mm-30) REVERT: C 351 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7416 (mtp) REVERT: C 470 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7399 (mpp) REVERT: C 507 MET cc_start: 0.8540 (tpp) cc_final: 0.7983 (tpp) REVERT: C 675 THR cc_start: 0.8624 (p) cc_final: 0.8135 (t) REVERT: D 142 ASP cc_start: 0.6522 (t0) cc_final: 0.5863 (t0) REVERT: D 234 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8307 (tm) REVERT: D 287 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7695 (m-80) outliers start: 83 outliers final: 65 residues processed: 247 average time/residue: 0.1347 time to fit residues: 54.7027 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 782 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 42 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 HIS A 683 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN C 683 HIS ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.119393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088824 restraints weight = 42524.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088129 restraints weight = 48871.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088699 restraints weight = 42404.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089127 restraints weight = 36750.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089318 restraints weight = 33434.501| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23126 Z= 0.128 Angle : 0.611 10.784 31274 Z= 0.294 Chirality : 0.042 0.371 3524 Planarity : 0.004 0.049 3810 Dihedral : 11.289 152.428 3660 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.01 % Allowed : 21.93 % Favored : 75.07 % 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: 1.33 (0.16), residues: 1188 sheet: -0.87 (0.30), residues: 258 loop : -1.10 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.031 0.001 TYR A 488 PHE 0.027 0.001 PHE C 967 TRP 0.039 0.002 TRP A 392 HIS 0.018 0.001 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23082) covalent geometry : angle 0.59743 / 0.29 (31148) SS BOND : bond 0.00691 / 0.35 ( 6) SS BOND : angle 1.73089 / 1.00 ( 12) hydrogen bonds : bond 0.04816 / 3.19 ( 994) hydrogen bonds : angle 4.12265 / 2.86 ( 2886) link_ALPHA1-3 : bond 0.00919 / 0.51 ( 6) link_ALPHA1-3 : angle 2.37827 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00494 / 0.24 ( 4) link_ALPHA1-6 : angle 1.32853 / 0.88 ( 12) link_BETA1-2 : bond 0.00775 / 0.39 ( 2) link_BETA1-2 : angle 3.60640 / 1.74 ( 6) link_BETA1-4 : bond 0.00453 / 0.28 ( 14) link_BETA1-4 : angle 2.30053 / 1.25 ( 42) link_BETA1-6 : bond 0.00057 / 0.03 ( 4) link_BETA1-6 : angle 1.38012 / 0.89 ( 12) link_NAG-ASN : bond 0.00440 / 0.20 ( 8) link_NAG-ASN : angle 1.87771 / 1.22 ( 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 253 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7892 (mmtp) REVERT: A 158 MET cc_start: 0.8101 (tpp) cc_final: 0.7748 (tmm) REVERT: A 351 MET cc_start: 0.7997 (mmm) cc_final: 0.7560 (mtp) REVERT: A 577 ASN cc_start: 0.5978 (m-40) cc_final: 0.5260 (t0) REVERT: A 675 THR cc_start: 0.8622 (p) cc_final: 0.8205 (t) REVERT: A 719 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 16 PHE cc_start: 0.7410 (t80) cc_final: 0.7112 (t80) REVERT: B 111 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7001 (t70) REVERT: B 142 ASP cc_start: 0.6560 (t0) cc_final: 0.5857 (t0) REVERT: B 203 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8450 (mm-40) REVERT: B 234 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8364 (tm) REVERT: B 287 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: G 4 GLU cc_start: 0.3658 (tm-30) cc_final: 0.3457 (tm-30) REVERT: C 70 GLU cc_start: 0.7487 (tp30) cc_final: 0.6876 (mt-10) REVERT: C 158 MET cc_start: 0.7826 (tpp) cc_final: 0.7301 (tpp) REVERT: C 287 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6630 (mm-30) REVERT: C 351 MET cc_start: 0.8053 (mmm) cc_final: 0.7435 (mtp) REVERT: C 507 MET cc_start: 0.8477 (tpp) cc_final: 0.8023 (tpp) REVERT: C 675 THR cc_start: 0.8505 (p) cc_final: 0.7991 (t) REVERT: C 719 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8622 (t) REVERT: D 16 PHE cc_start: 0.7418 (t80) cc_final: 0.7086 (t80) REVERT: D 142 ASP cc_start: 0.6596 (t0) cc_final: 0.5944 (t0) REVERT: D 234 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8252 (tm) REVERT: D 287 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7599 (m-80) outliers start: 68 outliers final: 58 residues processed: 240 average time/residue: 0.1278 time to fit residues: 50.7865 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 949 MET Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain E residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 0.0030 chunk 128 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 683 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089608 restraints weight = 42504.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088706 restraints weight = 40065.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090190 restraints weight = 36273.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090201 restraints weight = 28598.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.090334 restraints weight = 26882.929| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23126 Z= 0.122 Angle : 0.600 10.474 31274 Z= 0.290 Chirality : 0.042 0.373 3524 Planarity : 0.004 0.048 3810 Dihedral : 10.955 145.435 3657 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.96 % Allowed : 22.15 % Favored : 74.89 % 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: 0.16 (0.16), residues: 2636 helix: 1.43 (0.16), residues: 1188 sheet: -0.79 (0.31), residues: 258 loop : -1.05 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.036 0.001 TYR C 684 PHE 0.031 0.001 PHE B 25 TRP 0.036 0.001 TRP A 392 HIS 0.032 0.002 HIS C 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (23082) covalent geometry : angle 0.58614 / 0.29 (31148) SS BOND : bond 0.00185 / 0.11 ( 6) SS BOND : angle 1.45959 / 0.84 ( 12) hydrogen bonds : bond 0.04582 / 3.04 ( 994) hydrogen bonds : angle 4.06426 / 2.82 ( 2886) link_ALPHA1-3 : bond 0.00910 / 0.51 ( 6) link_ALPHA1-3 : angle 2.39139 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00494 / 0.25 ( 4) link_ALPHA1-6 : angle 1.32759 / 0.88 ( 12) link_BETA1-2 : bond 0.00671 / 0.34 ( 2) link_BETA1-2 : angle 3.60515 / 1.73 ( 6) link_BETA1-4 : bond 0.00461 / 0.29 ( 14) link_BETA1-4 : angle 2.26860 / 1.23 ( 42) link_BETA1-6 : bond 0.00076 / 0.04 ( 4) link_BETA1-6 : angle 1.34443 / 0.86 ( 12) link_NAG-ASN : bond 0.00451 / 0.21 ( 8) link_NAG-ASN : angle 1.77331 / 1.16 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.93 seconds wall clock time: 58 minutes 12.79 seconds (3492.79 seconds total)