Starting phenix.real_space_refine on Thu Mar 5 15:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyy_32898/03_2026/7wyy_32898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyy_32898/03_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_32898/03_2026/7wyy_32898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyy_32898/03_2026/7wyy_32898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wyy_32898/03_2026/7wyy_32898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyy_32898/03_2026/7wyy_32898.map" } 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-5986/lib/python3.9/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 dihedrals: 18 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 dihedrals: 18 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 dihedrals: 15 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 dihedrals: 6 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: 10.34, per 1000 atoms: 0.46 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: 2.03 Conformation dependent library (CDL) restraints added in 843.6 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: 0.85 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: 4.70 Time building geometry restraints manager: 2.56 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: 14167 35.90 - 71.80: 771 71.80 - 107.70: 84 107.70 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15064 sinusoidal: 7408 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 15061 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: 0.04 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 26.630 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 20.042 179.507 10134 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 covalent geometry : bond 0.01158 (23082) covalent geometry : angle 1.46977 (31148) SS BOND : bond 0.00426 ( 6) SS BOND : angle 2.20050 ( 12) hydrogen bonds : bond 0.17498 ( 994) hydrogen bonds : angle 7.49451 ( 2886) link_ALPHA1-3 : bond 0.00839 ( 6) link_ALPHA1-3 : angle 3.15551 ( 18) link_ALPHA1-6 : bond 0.00762 ( 4) link_ALPHA1-6 : angle 1.25286 ( 12) link_BETA1-2 : bond 0.00896 ( 2) link_BETA1-2 : angle 5.50601 ( 6) link_BETA1-4 : bond 0.01023 ( 14) link_BETA1-4 : angle 6.27841 ( 42) link_BETA1-6 : bond 0.00313 ( 4) link_BETA1-6 : angle 1.39389 ( 12) link_NAG-ASN : bond 0.01897 ( 8) link_NAG-ASN : angle 4.18387 ( 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 : 0.823 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: 0.1919 time to fit residues: 202.4098 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 : 0.818 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 209 HIS 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109920 restraints weight = 43620.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110075 restraints weight = 41562.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112092 restraints weight = 31609.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.111986 restraints weight = 25081.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112492 restraints weight = 24064.056| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23126 Z= 0.156 Angle : 0.725 11.377 31274 Z= 0.354 Chirality : 0.046 0.414 3524 Planarity : 0.006 0.076 3810 Dihedral : 17.081 175.837 5294 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.33 % Allowed : 15.25 % 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: -1.63 (0.15), residues: 2636 helix: -0.02 (0.15), residues: 1206 sheet: -1.77 (0.28), residues: 256 loop : -2.05 (0.16), residues: 1174 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 0.016 0.002 PHE D 25 TRP 0.020 0.002 TRP C 392 HIS 0.010 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00339 (23082) covalent geometry : angle 0.69758 (31148) SS BOND : bond 0.00179 ( 6) SS BOND : angle 1.08775 ( 12) hydrogen bonds : bond 0.06220 ( 994) hydrogen bonds : angle 5.20839 ( 2886) link_ALPHA1-3 : bond 0.01129 ( 6) link_ALPHA1-3 : angle 3.84954 ( 18) link_ALPHA1-6 : bond 0.00710 ( 4) link_ALPHA1-6 : angle 2.04464 ( 12) link_BETA1-2 : bond 0.00698 ( 2) link_BETA1-2 : angle 4.88790 ( 6) link_BETA1-4 : bond 0.01048 ( 14) link_BETA1-4 : angle 3.86209 ( 42) link_BETA1-6 : bond 0.00689 ( 4) link_BETA1-6 : angle 1.49598 ( 12) link_NAG-ASN : bond 0.00794 ( 8) link_NAG-ASN : angle 2.36193 ( 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 354 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 256 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.7101 (mt) cc_final: 0.6686 (mm) REVERT: A 308 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 324 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 351 MET cc_start: 0.8047 (mmm) cc_final: 0.7670 (mtp) REVERT: A 470 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8020 (mpp) REVERT: B 20 SER cc_start: 0.5780 (OUTLIER) cc_final: 0.5008 (p) REVERT: B 142 ASP cc_start: 0.5915 (t0) cc_final: 0.5298 (t0) REVERT: C 71 ILE cc_start: 0.7143 (mt) cc_final: 0.6685 (mm) REVERT: C 351 MET cc_start: 0.8092 (mmm) cc_final: 0.7842 (mtp) REVERT: C 470 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6811 (mpp) REVERT: C 721 ASP cc_start: 0.8695 (m-30) cc_final: 0.8080 (m-30) REVERT: D 20 SER cc_start: 0.6172 (OUTLIER) cc_final: 0.5399 (p) REVERT: D 142 ASP cc_start: 0.5591 (t0) cc_final: 0.5368 (t0) REVERT: E 4 GLU cc_start: 0.4642 (pm20) cc_final: 0.4339 (pp20) outliers start: 98 outliers final: 58 residues processed: 334 average time/residue: 0.1430 time to fit residues: 77.7060 Evaluate side-chains 247 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 324 LEU 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 470 MET 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 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 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 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 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 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 196 THR 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: 3.9990 chunk 127 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 242 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN A 557 HIS A 826 GLN B 243 GLN C 486 ASN ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN D 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100644 restraints weight = 43590.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099944 restraints weight = 48414.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101091 restraints weight = 40579.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101737 restraints weight = 31843.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101948 restraints weight = 28912.704| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23126 Z= 0.170 Angle : 0.688 10.617 31274 Z= 0.330 Chirality : 0.046 0.443 3524 Planarity : 0.005 0.056 3810 Dihedral : 15.306 164.039 5223 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.51 % Allowed : 15.87 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2636 helix: 0.76 (0.15), residues: 1198 sheet: -1.28 (0.29), residues: 248 loop : -1.33 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 430 TYR 0.020 0.002 TYR A 488 PHE 0.023 0.002 PHE A 411 TRP 0.013 0.002 TRP A 890 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00395 (23082) covalent geometry : angle 0.66392 (31148) SS BOND : bond 0.00082 ( 6) SS BOND : angle 1.97293 ( 12) hydrogen bonds : bond 0.05684 ( 994) hydrogen bonds : angle 4.57284 ( 2886) link_ALPHA1-3 : bond 0.01347 ( 6) link_ALPHA1-3 : angle 3.55855 ( 18) link_ALPHA1-6 : bond 0.00766 ( 4) link_ALPHA1-6 : angle 1.57666 ( 12) link_BETA1-2 : bond 0.00639 ( 2) link_BETA1-2 : angle 4.13055 ( 6) link_BETA1-4 : bond 0.00930 ( 14) link_BETA1-4 : angle 3.58149 ( 42) link_BETA1-6 : bond 0.00367 ( 4) link_BETA1-6 : angle 1.58216 ( 12) link_NAG-ASN : bond 0.00928 ( 8) link_NAG-ASN : angle 2.03749 ( 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 329 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 227 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7147 (tp) cc_final: 0.6682 (tp) REVERT: A 71 ILE cc_start: 0.6995 (mt) cc_final: 0.6457 (mm) REVERT: A 100 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7853 (m-10) REVERT: A 158 MET cc_start: 0.7977 (tpp) cc_final: 0.7286 (tpt) REVERT: A 351 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: A 466 SER cc_start: 0.7660 (t) cc_final: 0.7453 (p) REVERT: A 719 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8736 (t) REVERT: A 721 ASP cc_start: 0.8657 (m-30) cc_final: 0.8182 (m-30) REVERT: B 20 SER cc_start: 0.6155 (OUTLIER) cc_final: 0.5286 (p) REVERT: B 94 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8471 (p) REVERT: B 111 ASP cc_start: 0.7736 (t70) cc_final: 0.6847 (t0) REVERT: C 48 LEU cc_start: 0.7113 (tp) cc_final: 0.6675 (tp) REVERT: C 64 THR cc_start: 0.5785 (OUTLIER) cc_final: 0.5412 (p) REVERT: C 71 ILE cc_start: 0.7194 (mt) cc_final: 0.6968 (mm) REVERT: C 158 MET cc_start: 0.7945 (tpp) cc_final: 0.7316 (tpt) REVERT: C 351 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7737 (mtp) REVERT: C 391 MET cc_start: 0.7486 (mtm) cc_final: 0.7281 (mtm) REVERT: C 411 PHE cc_start: 0.6534 (p90) cc_final: 0.6304 (p90) REVERT: C 466 SER cc_start: 0.7577 (t) cc_final: 0.6919 (p) REVERT: C 470 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7141 (mpp) REVERT: C 507 MET cc_start: 0.8710 (tpp) cc_final: 0.8465 (tpp) REVERT: C 719 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 721 ASP cc_start: 0.8708 (m-30) cc_final: 0.8222 (m-30) REVERT: D 20 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.6166 (p) REVERT: D 142 ASP cc_start: 0.6186 (t0) cc_final: 0.5591 (t0) outliers start: 102 outliers final: 57 residues processed: 309 average time/residue: 0.1369 time to fit residues: 69.6405 Evaluate side-chains 259 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 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 968 LEU 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 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 641 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 D residue 229 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: 0.9990 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 194 optimal weight: 40.0000 chunk 156 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN A 486 ASN A 489 GLN A 826 GLN B 270 GLN C 685 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099476 restraints weight = 43466.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099096 restraints weight = 48268.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101217 restraints weight = 40266.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100883 restraints weight = 29498.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101259 restraints weight = 27784.401| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23126 Z= 0.165 Angle : 0.636 10.697 31274 Z= 0.303 Chirality : 0.046 0.467 3524 Planarity : 0.004 0.049 3810 Dihedral : 14.434 152.126 5206 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.93 % Allowed : 17.42 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2636 helix: 1.04 (0.15), residues: 1198 sheet: -1.01 (0.30), residues: 258 loop : -1.13 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.015 0.001 TYR A 488 PHE 0.021 0.002 PHE C 793 TRP 0.011 0.002 TRP C 988 HIS 0.005 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00389 (23082) covalent geometry : angle 0.61172 (31148) SS BOND : bond 0.00064 ( 6) SS BOND : angle 1.48451 ( 12) hydrogen bonds : bond 0.05317 ( 994) hydrogen bonds : angle 4.36819 ( 2886) link_ALPHA1-3 : bond 0.01209 ( 6) link_ALPHA1-3 : angle 3.80802 ( 18) link_ALPHA1-6 : bond 0.00657 ( 4) link_ALPHA1-6 : angle 1.59850 ( 12) link_BETA1-2 : bond 0.00628 ( 2) link_BETA1-2 : angle 4.04550 ( 6) link_BETA1-4 : bond 0.00690 ( 14) link_BETA1-4 : angle 3.30666 ( 42) link_BETA1-6 : bond 0.00153 ( 4) link_BETA1-6 : angle 1.57945 ( 12) link_NAG-ASN : bond 0.00400 ( 8) link_NAG-ASN : angle 1.77294 ( 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 282 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 193 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: A 158 MET cc_start: 0.7950 (tpp) cc_final: 0.7734 (tpp) REVERT: A 351 MET cc_start: 0.8053 (mmm) cc_final: 0.7708 (mtp) REVERT: A 675 THR cc_start: 0.8591 (p) cc_final: 0.8170 (t) REVERT: A 719 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8524 (t) REVERT: A 847 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: B 20 SER cc_start: 0.6695 (OUTLIER) cc_final: 0.5814 (p) REVERT: B 111 ASP cc_start: 0.7834 (t70) cc_final: 0.6929 (t70) REVERT: B 142 ASP cc_start: 0.5972 (t0) cc_final: 0.5537 (t0) REVERT: C 64 THR cc_start: 0.6220 (OUTLIER) cc_final: 0.5866 (p) REVERT: C 71 ILE cc_start: 0.6985 (mt) cc_final: 0.6765 (mm) REVERT: C 100 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: C 351 MET cc_start: 0.8124 (mmm) cc_final: 0.7800 (mtp) REVERT: C 466 SER cc_start: 0.7636 (t) cc_final: 0.7156 (p) REVERT: C 470 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7178 (mpp) REVERT: C 719 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8681 (t) REVERT: C 721 ASP cc_start: 0.8652 (m-30) cc_final: 0.8038 (m-30) REVERT: D 142 ASP cc_start: 0.6297 (t0) cc_final: 0.5709 (t0) REVERT: D 287 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7939 (m-80) outliers start: 89 outliers final: 52 residues processed: 270 average time/residue: 0.1293 time to fit residues: 58.7813 Evaluate side-chains 230 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 PHE 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 440 VAL Chi-restraints excluded: chain A residue 480 ILE 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 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 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 178 VAL 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 100 PHE 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 641 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 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 17 LEU 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 D residue 287 TYR Chi-restraints excluded: chain E residue 33 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: 4.9990 chunk 172 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 170 optimal weight: 8.9990 chunk 114 optimal weight: 0.0040 chunk 159 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 3.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 HIS A 826 GLN C 683 HIS D 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.121732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091366 restraints weight = 42785.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089610 restraints weight = 42883.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090973 restraints weight = 40185.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091182 restraints weight = 34341.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091392 restraints weight = 32069.757| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23126 Z= 0.208 Angle : 0.685 9.565 31274 Z= 0.328 Chirality : 0.047 0.488 3524 Planarity : 0.004 0.047 3810 Dihedral : 14.062 158.843 5201 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.82 % Allowed : 17.51 % Favored : 77.67 % 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: -0.22 (0.16), residues: 2636 helix: 1.08 (0.15), residues: 1176 sheet: -1.12 (0.31), residues: 246 loop : -1.16 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 473 TYR 0.016 0.002 TYR D 256 PHE 0.028 0.002 PHE C 578 TRP 0.020 0.002 TRP A 988 HIS 0.013 0.002 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00504 (23082) covalent geometry : angle 0.66441 (31148) SS BOND : bond 0.00160 ( 6) SS BOND : angle 1.32146 ( 12) hydrogen bonds : bond 0.05870 ( 994) hydrogen bonds : angle 4.43165 ( 2886) link_ALPHA1-3 : bond 0.01289 ( 6) link_ALPHA1-3 : angle 3.89494 ( 18) link_ALPHA1-6 : bond 0.00708 ( 4) link_ALPHA1-6 : angle 1.40229 ( 12) link_BETA1-2 : bond 0.00679 ( 2) link_BETA1-2 : angle 4.14698 ( 6) link_BETA1-4 : bond 0.00614 ( 14) link_BETA1-4 : angle 3.11397 ( 42) link_BETA1-6 : bond 0.00161 ( 4) link_BETA1-6 : angle 1.68789 ( 12) link_NAG-ASN : bond 0.00504 ( 8) link_NAG-ASN : angle 1.76422 ( 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 296 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 187 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7518 (mm) cc_final: 0.7046 (tp) REVERT: A 100 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: A 158 MET cc_start: 0.8005 (tpp) cc_final: 0.7725 (tpp) REVERT: A 287 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6602 (mm-30) REVERT: A 351 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: A 675 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8233 (t) REVERT: A 719 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8651 (t) REVERT: A 847 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: B 142 ASP cc_start: 0.6245 (t0) cc_final: 0.5690 (t0) REVERT: B 287 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: C 48 LEU cc_start: 0.7747 (mm) cc_final: 0.7388 (tp) REVERT: C 64 THR cc_start: 0.6272 (OUTLIER) cc_final: 0.5948 (p) REVERT: C 71 ILE cc_start: 0.7019 (mt) cc_final: 0.6451 (mm) REVERT: C 100 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7641 (m-10) REVERT: C 158 MET cc_start: 0.7863 (tpp) cc_final: 0.7444 (tpt) REVERT: C 351 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: C 466 SER cc_start: 0.7770 (t) cc_final: 0.7382 (p) REVERT: C 470 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7372 (mpp) REVERT: C 675 THR cc_start: 0.8604 (p) cc_final: 0.8141 (t) REVERT: C 719 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8755 (t) REVERT: C 847 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: D 55 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8558 (tp) REVERT: D 111 ASP cc_start: 0.7778 (t70) cc_final: 0.7029 (t0) REVERT: D 142 ASP cc_start: 0.6395 (t0) cc_final: 0.5782 (t0) REVERT: D 287 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7885 (m-80) outliers start: 109 outliers final: 69 residues processed: 275 average time/residue: 0.1285 time to fit residues: 59.1224 Evaluate side-chains 246 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 296 THR 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 659 ASP Chi-restraints excluded: chain A residue 675 THR 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 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 847 GLU 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 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 100 PHE 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 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 560 LEU Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 641 ILE 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 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 C residue 1000 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 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 287 TYR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 683 HIS C 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092198 restraints weight = 42691.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091625 restraints weight = 43386.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093143 restraints weight = 37453.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093660 restraints weight = 29358.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093946 restraints weight = 27977.102| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23126 Z= 0.153 Angle : 0.616 9.420 31274 Z= 0.294 Chirality : 0.045 0.491 3524 Planarity : 0.004 0.044 3810 Dihedral : 13.670 156.479 5199 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.29 % Allowed : 18.74 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.16), residues: 2636 helix: 1.29 (0.16), residues: 1178 sheet: -0.89 (0.30), residues: 256 loop : -1.09 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.029 0.001 TYR C 488 PHE 0.026 0.002 PHE C 967 TRP 0.019 0.001 TRP C 988 HIS 0.015 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00359 (23082) covalent geometry : angle 0.59437 (31148) SS BOND : bond 0.00137 ( 6) SS BOND : angle 1.10433 ( 12) hydrogen bonds : bond 0.05192 ( 994) hydrogen bonds : angle 4.23150 ( 2886) link_ALPHA1-3 : bond 0.01195 ( 6) link_ALPHA1-3 : angle 3.81542 ( 18) link_ALPHA1-6 : bond 0.00727 ( 4) link_ALPHA1-6 : angle 1.47057 ( 12) link_BETA1-2 : bond 0.00660 ( 2) link_BETA1-2 : angle 4.17672 ( 6) link_BETA1-4 : bond 0.00568 ( 14) link_BETA1-4 : angle 2.88569 ( 42) link_BETA1-6 : bond 0.00155 ( 4) link_BETA1-6 : angle 1.64068 ( 12) link_NAG-ASN : bond 0.00293 ( 8) link_NAG-ASN : angle 1.66406 ( 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 284 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 187 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: A 158 MET cc_start: 0.7991 (tpp) cc_final: 0.7633 (tpp) REVERT: A 287 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6694 (mm-30) REVERT: A 351 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7590 (mtp) REVERT: A 675 THR cc_start: 0.8649 (p) cc_final: 0.8202 (t) REVERT: A 719 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8538 (t) REVERT: B 142 ASP cc_start: 0.6214 (t0) cc_final: 0.5581 (t0) REVERT: B 287 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: C 100 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: C 158 MET cc_start: 0.7986 (tpp) cc_final: 0.7415 (tpt) REVERT: C 351 MET cc_start: 0.8146 (mmm) cc_final: 0.7747 (mtp) REVERT: C 466 SER cc_start: 0.7882 (t) cc_final: 0.7481 (p) REVERT: C 470 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7377 (mpp) REVERT: C 675 THR cc_start: 0.8539 (p) cc_final: 0.8039 (t) REVERT: C 719 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8609 (t) REVERT: C 847 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: D 142 ASP cc_start: 0.6321 (t0) cc_final: 0.5652 (t0) REVERT: D 287 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7855 (m-80) outliers start: 97 outliers final: 62 residues processed: 266 average time/residue: 0.1477 time to fit residues: 64.7575 Evaluate side-chains 242 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 171 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 741 VAL 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 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 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 51 LEU Chi-restraints excluded: chain C residue 81 THR 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 184 PHE 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 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 641 ILE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 767 LEU 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 C residue 998 ILE 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 101 SER 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: 2.9990 chunk 182 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090621 restraints weight = 43035.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090121 restraints weight = 47068.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091598 restraints weight = 41434.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.091742 restraints weight = 29841.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091888 restraints weight = 30646.423| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23126 Z= 0.205 Angle : 0.669 9.542 31274 Z= 0.322 Chirality : 0.046 0.480 3524 Planarity : 0.004 0.043 3810 Dihedral : 13.492 157.425 5195 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.73 % Allowed : 18.70 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2636 helix: 1.12 (0.15), residues: 1174 sheet: -0.85 (0.31), residues: 260 loop : -1.16 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.015 0.002 TYR B 256 PHE 0.026 0.002 PHE C 967 TRP 0.012 0.002 TRP C 988 HIS 0.009 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00493 (23082) covalent geometry : angle 0.64920 (31148) SS BOND : bond 0.00156 ( 6) SS BOND : angle 1.10368 ( 12) hydrogen bonds : bond 0.05666 ( 994) hydrogen bonds : angle 4.35297 ( 2886) link_ALPHA1-3 : bond 0.01130 ( 6) link_ALPHA1-3 : angle 3.85459 ( 18) link_ALPHA1-6 : bond 0.00721 ( 4) link_ALPHA1-6 : angle 1.41947 ( 12) link_BETA1-2 : bond 0.00683 ( 2) link_BETA1-2 : angle 4.08181 ( 6) link_BETA1-4 : bond 0.00548 ( 14) link_BETA1-4 : angle 2.80271 ( 42) link_BETA1-6 : bond 0.00151 ( 4) link_BETA1-6 : angle 1.73777 ( 12) link_NAG-ASN : bond 0.00234 ( 8) link_NAG-ASN : angle 1.79641 ( 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 289 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 182 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: A 158 MET cc_start: 0.8079 (tpp) cc_final: 0.7747 (tpp) REVERT: A 287 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 351 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7570 (mtp) REVERT: A 675 THR cc_start: 0.8628 (p) cc_final: 0.8193 (t) REVERT: A 719 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 142 ASP cc_start: 0.6339 (t0) cc_final: 0.5677 (t0) REVERT: B 287 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: C 100 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7496 (m-10) REVERT: C 158 MET cc_start: 0.8059 (tpp) cc_final: 0.7481 (tpt) REVERT: C 351 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: C 466 SER cc_start: 0.7863 (t) cc_final: 0.7550 (p) REVERT: C 470 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: C 566 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7327 (p0) REVERT: C 675 THR cc_start: 0.8614 (p) cc_final: 0.8161 (t) REVERT: C 719 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8727 (t) REVERT: C 847 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: D 142 ASP cc_start: 0.6409 (t0) cc_final: 0.5748 (t0) REVERT: D 287 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7705 (m-80) outliers start: 107 outliers final: 79 residues processed: 270 average time/residue: 0.1496 time to fit residues: 66.1738 Evaluate side-chains 258 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 168 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 296 THR 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 490 LEU Chi-restraints excluded: chain A residue 659 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 782 SER 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 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 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 81 THR 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 205 ILE 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 566 ASN Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 641 ILE 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 767 LEU 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 C residue 998 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 17 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 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 287 TYR Chi-restraints excluded: chain D residue 305 SER 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: 7.9990 chunk 8 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092822 restraints weight = 42765.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090664 restraints weight = 41344.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091860 restraints weight = 41537.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092447 restraints weight = 34921.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092605 restraints weight = 30478.189| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23126 Z= 0.137 Angle : 0.601 9.313 31274 Z= 0.287 Chirality : 0.044 0.474 3524 Planarity : 0.004 0.056 3810 Dihedral : 13.010 151.963 5195 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.89 % Allowed : 19.50 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2636 helix: 1.35 (0.16), residues: 1178 sheet: -0.82 (0.31), residues: 260 loop : -1.09 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 154 TYR 0.013 0.001 TYR A 869 PHE 0.022 0.001 PHE C 967 TRP 0.013 0.001 TRP C 988 HIS 0.010 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00318 (23082) covalent geometry : angle 0.58121 (31148) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.94543 ( 12) hydrogen bonds : bond 0.04896 ( 994) hydrogen bonds : angle 4.16195 ( 2886) link_ALPHA1-3 : bond 0.01052 ( 6) link_ALPHA1-3 : angle 3.72275 ( 18) link_ALPHA1-6 : bond 0.00752 ( 4) link_ALPHA1-6 : angle 1.54353 ( 12) link_BETA1-2 : bond 0.00690 ( 2) link_BETA1-2 : angle 4.16032 ( 6) link_BETA1-4 : bond 0.00526 ( 14) link_BETA1-4 : angle 2.54209 ( 42) link_BETA1-6 : bond 0.00077 ( 4) link_BETA1-6 : angle 1.65712 ( 12) link_NAG-ASN : bond 0.00532 ( 8) link_NAG-ASN : angle 1.88011 ( 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 274 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 186 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8067 (tpp) cc_final: 0.7742 (tpp) REVERT: A 287 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 351 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7511 (mtp) REVERT: A 675 THR cc_start: 0.8669 (p) cc_final: 0.8191 (t) REVERT: A 719 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 142 ASP cc_start: 0.6390 (t0) cc_final: 0.5732 (t0) REVERT: B 234 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8350 (tm) REVERT: B 287 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: C 70 GLU cc_start: 0.7614 (tp30) cc_final: 0.6899 (mt-10) REVERT: C 100 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: C 158 MET cc_start: 0.8028 (tpp) cc_final: 0.7507 (tpt) REVERT: C 351 MET cc_start: 0.8095 (mmm) cc_final: 0.7624 (mtp) REVERT: C 466 SER cc_start: 0.7984 (t) cc_final: 0.7616 (p) REVERT: C 470 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7461 (mpp) REVERT: C 675 THR cc_start: 0.8568 (p) cc_final: 0.8068 (t) REVERT: C 719 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8632 (t) REVERT: D 111 ASP cc_start: 0.7810 (t70) cc_final: 0.7012 (t70) REVERT: D 142 ASP cc_start: 0.6382 (t0) cc_final: 0.5753 (t0) REVERT: D 234 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8285 (tm) REVERT: D 287 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7712 (m-80) outliers start: 88 outliers final: 69 residues processed: 260 average time/residue: 0.1424 time to fit residues: 61.5124 Evaluate side-chains 245 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 167 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 96 LEU 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 197 ASP 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 351 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 490 LEU 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 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 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 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 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 312 ILE Chi-restraints excluded: chain C residue 334 GLU 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 641 ILE 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 762 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 782 SER 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 998 ILE 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 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 Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 253 optimal weight: 0.3980 chunk 212 optimal weight: 0.0770 chunk 42 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 249 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 overall best weight: 1.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS B 118 GLN D 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094381 restraints weight = 43139.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093497 restraints weight = 54550.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094613 restraints weight = 47676.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095108 restraints weight = 35925.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095343 restraints weight = 32981.845| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23126 Z= 0.137 Angle : 0.604 9.478 31274 Z= 0.288 Chirality : 0.044 0.466 3524 Planarity : 0.004 0.046 3810 Dihedral : 12.666 145.465 5193 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.71 % Allowed : 20.03 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2636 helix: 1.38 (0.16), residues: 1188 sheet: -0.94 (0.30), residues: 268 loop : -0.97 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.027 0.001 TYR C 488 PHE 0.025 0.002 PHE B 25 TRP 0.049 0.002 TRP A 392 HIS 0.010 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00321 (23082) covalent geometry : angle 0.58325 (31148) SS BOND : bond 0.00525 ( 6) SS BOND : angle 2.02943 ( 12) hydrogen bonds : bond 0.04756 ( 994) hydrogen bonds : angle 4.11735 ( 2886) link_ALPHA1-3 : bond 0.01023 ( 6) link_ALPHA1-3 : angle 3.73703 ( 18) link_ALPHA1-6 : bond 0.00754 ( 4) link_ALPHA1-6 : angle 1.53265 ( 12) link_BETA1-2 : bond 0.00698 ( 2) link_BETA1-2 : angle 4.16015 ( 6) link_BETA1-4 : bond 0.00520 ( 14) link_BETA1-4 : angle 2.51403 ( 42) link_BETA1-6 : bond 0.00071 ( 4) link_BETA1-6 : angle 1.63972 ( 12) link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 1.82320 ( 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 254 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 170 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: A 158 MET cc_start: 0.8060 (tpp) cc_final: 0.7779 (tpp) REVERT: A 287 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 351 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7488 (mtp) REVERT: A 675 THR cc_start: 0.8604 (p) cc_final: 0.8144 (t) REVERT: A 719 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8614 (t) REVERT: B 16 PHE cc_start: 0.7390 (t80) cc_final: 0.7167 (t80) REVERT: B 142 ASP cc_start: 0.6503 (t0) cc_final: 0.5790 (t0) REVERT: B 287 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: C 70 GLU cc_start: 0.7252 (tp30) cc_final: 0.6907 (mt-10) REVERT: C 100 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: C 158 MET cc_start: 0.7947 (tpp) cc_final: 0.7483 (tpt) REVERT: C 351 MET cc_start: 0.8078 (mmm) cc_final: 0.7503 (mtp) REVERT: C 675 THR cc_start: 0.8478 (p) cc_final: 0.7969 (t) REVERT: C 719 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8668 (t) REVERT: D 111 ASP cc_start: 0.7749 (t70) cc_final: 0.7024 (t70) REVERT: D 142 ASP cc_start: 0.6492 (t0) cc_final: 0.5785 (t0) REVERT: D 234 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8214 (tm) REVERT: D 287 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7734 (m-80) outliers start: 84 outliers final: 69 residues processed: 241 average time/residue: 0.1462 time to fit residues: 58.7068 Evaluate side-chains 239 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 51 LEU 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 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 296 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 552 VAL 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 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 998 ILE Chi-restraints excluded: chain A residue 1000 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 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 G residue 36 ILE 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 312 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 641 ILE 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 767 LEU 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 998 ILE 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 101 SER 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 Chi-restraints excluded: chain E residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 217 optimal weight: 0.5980 chunk 229 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096757 restraints weight = 42277.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094658 restraints weight = 39673.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095460 restraints weight = 38103.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096056 restraints weight = 30577.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096214 restraints weight = 27703.177| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23126 Z= 0.108 Angle : 0.584 9.528 31274 Z= 0.278 Chirality : 0.043 0.458 3524 Planarity : 0.004 0.059 3810 Dihedral : 12.087 131.586 5189 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.17 % Allowed : 21.71 % Favored : 76.13 % 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: 0.37 (0.17), residues: 2636 helix: 1.61 (0.16), residues: 1188 sheet: -0.93 (0.31), residues: 268 loop : -0.89 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.025 0.001 TYR C 488 PHE 0.034 0.001 PHE A 231 TRP 0.046 0.002 TRP A 392 HIS 0.010 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00235 (23082) covalent geometry : angle 0.56483 (31148) SS BOND : bond 0.00189 ( 6) SS BOND : angle 1.35284 ( 12) hydrogen bonds : bond 0.04108 ( 994) hydrogen bonds : angle 3.98380 ( 2886) link_ALPHA1-3 : bond 0.00972 ( 6) link_ALPHA1-3 : angle 3.67555 ( 18) link_ALPHA1-6 : bond 0.00750 ( 4) link_ALPHA1-6 : angle 1.61814 ( 12) link_BETA1-2 : bond 0.00668 ( 2) link_BETA1-2 : angle 4.19469 ( 6) link_BETA1-4 : bond 0.00531 ( 14) link_BETA1-4 : angle 2.42486 ( 42) link_BETA1-6 : bond 0.00039 ( 4) link_BETA1-6 : angle 1.54828 ( 12) link_NAG-ASN : bond 0.00513 ( 8) link_NAG-ASN : angle 1.61763 ( 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 239 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8114 (tpp) cc_final: 0.7857 (tpp) REVERT: A 351 MET cc_start: 0.8015 (mmm) cc_final: 0.7540 (mtp) REVERT: A 589 MET cc_start: 0.7065 (tpp) cc_final: 0.6795 (mtt) REVERT: A 675 THR cc_start: 0.8582 (p) cc_final: 0.8102 (t) REVERT: B 111 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.6904 (t70) REVERT: B 142 ASP cc_start: 0.6542 (t0) cc_final: 0.5754 (t0) REVERT: B 202 LEU cc_start: 0.8029 (mp) cc_final: 0.7810 (mt) REVERT: B 234 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8312 (tm) REVERT: B 287 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: C 70 GLU cc_start: 0.7333 (tp30) cc_final: 0.6869 (mt-10) REVERT: C 158 MET cc_start: 0.8028 (tpp) cc_final: 0.7524 (tpt) REVERT: C 675 THR cc_start: 0.8448 (p) cc_final: 0.7916 (t) REVERT: D 111 ASP cc_start: 0.7744 (t70) cc_final: 0.6873 (t70) REVERT: D 142 ASP cc_start: 0.6576 (t0) cc_final: 0.5811 (t0) REVERT: D 202 LEU cc_start: 0.8103 (mp) cc_final: 0.7889 (mt) REVERT: D 234 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8218 (tm) REVERT: D 287 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 49 outliers final: 40 residues processed: 233 average time/residue: 0.1413 time to fit residues: 54.9277 Evaluate side-chains 214 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 96 LEU 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 432 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 741 VAL 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 943 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 178 VAL 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 C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 552 VAL 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 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 998 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 37 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091514 restraints weight = 43252.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090245 restraints weight = 44969.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091661 restraints weight = 41953.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091859 restraints weight = 31262.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092037 restraints weight = 28885.262| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23126 Z= 0.172 Angle : 0.639 9.959 31274 Z= 0.306 Chirality : 0.045 0.445 3524 Planarity : 0.004 0.049 3810 Dihedral : 12.028 133.063 5186 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.56 % Allowed : 21.71 % Favored : 75.73 % 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: 1.30 (0.16), residues: 1206 sheet: -1.05 (0.29), residues: 288 loop : -0.89 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 154 TYR 0.015 0.001 TYR A 869 PHE 0.030 0.002 PHE B 25 TRP 0.037 0.002 TRP A 392 HIS 0.008 0.001 HIS C 683 Details of bonding type rmsd covalent geometry : bond 0.00413 (23082) covalent geometry : angle 0.62073 (31148) SS BOND : bond 0.00199 ( 6) SS BOND : angle 1.51925 ( 12) hydrogen bonds : bond 0.04984 ( 994) hydrogen bonds : angle 4.17600 ( 2886) link_ALPHA1-3 : bond 0.01044 ( 6) link_ALPHA1-3 : angle 3.78279 ( 18) link_ALPHA1-6 : bond 0.00673 ( 4) link_ALPHA1-6 : angle 1.48968 ( 12) link_BETA1-2 : bond 0.00794 ( 2) link_BETA1-2 : angle 4.02905 ( 6) link_BETA1-4 : bond 0.00516 ( 14) link_BETA1-4 : angle 2.48957 ( 42) link_BETA1-6 : bond 0.00106 ( 4) link_BETA1-6 : angle 1.65547 ( 12) link_NAG-ASN : bond 0.00400 ( 8) link_NAG-ASN : angle 1.87528 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.82 seconds wall clock time: 59 minutes 54.06 seconds (3594.06 seconds total)