Starting phenix.real_space_refine on Thu Aug 6 00:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cma_45745/08_2026/9cma_45745.map" } resolution = 3.97 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= 0.010 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: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 74 5.16 5 C 7755 2.51 5 N 2189 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4936 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 22, 'TRANS': 591} Chain breaks: 2 Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "E" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 949 Classifications: {'DNA': 46} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 817 Classifications: {'DNA': 40} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 39} Time building chain proxies: 2.36, per 1000 atoms: 0.19 Number of scatterers: 12726 At special positions: 0 Unit cell: (98.53, 111.89, 148.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 86 15.00 O 2622 8.00 N 2189 7.00 C 7755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 162 " 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 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 550.7 milliseconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 39.7% alpha, 16.5% beta 23 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 372 through 388 removed outlier: 3.549A pdb=" N LEU A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 411 through 423 removed outlier: 4.054A pdb=" N LYS A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 513 removed outlier: 4.240A pdb=" N GLY A 513 " --> pdb=" O CYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.749A pdb=" N ARG A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 620 removed outlier: 3.540A pdb=" N LEU A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.935A pdb=" N ALA A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.590A pdb=" N GLU A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 removed outlier: 3.667A pdb=" N GLN A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 718 removed outlier: 4.123A pdb=" N HIS A 718 " --> pdb=" O ASN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 735 removed outlier: 3.666A pdb=" N LYS A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 756 removed outlier: 4.313A pdb=" N LEU A 746 " --> pdb=" O HIS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.853A pdb=" N LYS A 763 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N HIS A 764 " --> pdb=" O LYS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 4.203A pdb=" N LEU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.641A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 879 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 894 through 909 removed outlier: 3.570A pdb=" N TRP A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 924 through 935 Processing helix chain 'A' and resid 937 through 950 removed outlier: 4.589A pdb=" N VAL A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.556A pdb=" N TRP A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.800A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.635A pdb=" N ILE B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.162A pdb=" N ARG B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.660A pdb=" N LEU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 255 through 261 removed outlier: 4.259A pdb=" N GLU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 261' Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.080A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 19 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 removed outlier: 3.501A pdb=" N ILE C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.551A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.834A pdb=" N LEU D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 15 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 19 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.610A pdb=" N LYS D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 153 removed outlier: 3.511A pdb=" N ARG D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 456 through 458 Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.522A pdb=" N ILE B 87 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 104 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 89 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL B 102 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 91 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.877A pdb=" N ALA B 26 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 199 removed outlier: 3.618A pdb=" N VAL B 136 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.532A pdb=" N ARG C 61 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 102 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 112 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.906A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.777A pdb=" N SER C 39 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 48 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 236 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 228 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 181 removed outlier: 3.597A pdb=" N SER C 161 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER C 170 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.704A pdb=" N GLU D 3 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 71 removed outlier: 3.656A pdb=" N VAL D 70 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 26 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU D 25 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET D 40 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 48 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 49 " --> pdb=" O LYS D 248 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS D 248 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 51 " --> pdb=" O HIS D 246 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 246 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 236 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D 136 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'D' and resid 177 through 181 removed outlier: 3.676A pdb=" N GLY D 166 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER D 161 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 170 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3574 1.33 - 1.46: 2677 1.46 - 1.58: 6590 1.58 - 1.70: 170 1.70 - 1.82: 114 Bond restraints: 13125 Sorted by residual: bond pdb=" C3' DT E 6 " pdb=" C2' DT E 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC F 14 " pdb=" C2' DC F 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DC E 24 " pdb=" C2' DC E 24 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.37e+00 bond pdb=" C3' DC F 13 " pdb=" C2' DC F 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.25e+00 bond pdb=" C3' DA E 19 " pdb=" C2' DA E 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 ... (remaining 13120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17183 1.60 - 3.21: 826 3.21 - 4.81: 77 4.81 - 6.42: 24 6.42 - 8.02: 4 Bond angle restraints: 18114 Sorted by residual: angle pdb=" C ASP B 94 " pdb=" CA ASP B 94 " pdb=" CB ASP B 94 " ideal model delta sigma weight residual 116.54 109.38 7.16 1.15e+00 7.56e-01 3.87e+01 angle pdb=" O4' DC E 21 " pdb=" C4' DC E 21 " pdb=" C3' DC E 21 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.46e+01 angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 113.42 108.31 5.11 1.17e+00 7.31e-01 1.91e+01 angle pdb=" N3 DT E 14 " pdb=" C4 DT E 14 " pdb=" O4 DT E 14 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT E 31 " pdb=" C4 DT E 31 " pdb=" O4 DT E 31 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 18109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6519 17.91 - 35.83: 782 35.83 - 53.74: 350 53.74 - 71.65: 100 71.65 - 89.57: 13 Dihedral angle restraints: 7764 sinusoidal: 3693 harmonic: 4071 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 162 " pdb=" CB CYS D 162 " ideal model delta sinusoidal sigma weight residual 93.00 34.98 58.02 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CA GLN A 775 " pdb=" C GLN A 775 " pdb=" N ASP A 776 " pdb=" CA ASP A 776 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA GLU A 459 " pdb=" C GLU A 459 " pdb=" N SER A 460 " pdb=" CA SER A 460 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 7761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1561 0.049 - 0.098: 426 0.098 - 0.147: 83 0.147 - 0.196: 3 0.196 - 0.245: 1 Chirality restraints: 2074 Sorted by residual: chirality pdb=" CG LEU D 221 " pdb=" CB LEU D 221 " pdb=" CD1 LEU D 221 " pdb=" CD2 LEU D 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU A 958 " pdb=" CB LEU A 958 " pdb=" CD1 LEU A 958 " pdb=" CD2 LEU A 958 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" P DC E 1 " pdb=" OP1 DC E 1 " pdb=" OP2 DC E 1 " pdb=" O5' DC E 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2071 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 937 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 938 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 938 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 938 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 495 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" CD GLN A 495 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN A 495 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN A 495 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 723 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 724 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 724 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 724 " -0.025 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 418 2.68 - 3.24: 13160 3.24 - 3.79: 21548 3.79 - 4.35: 28119 4.35 - 4.90: 41674 Nonbonded interactions: 104919 Sorted by model distance: nonbonded pdb=" OD2 ASP B 41 " pdb=" OG SER B 43 " model vdw 2.126 3.040 nonbonded pdb=" OE1 GLN A 492 " pdb=" NZ LYS A 493 " model vdw 2.147 3.120 nonbonded pdb=" OG SER D 43 " pdb=" OH TYR D 211 " model vdw 2.157 3.040 nonbonded pdb=" O GLY A 826 " pdb=" ND2 ASN A 965 " model vdw 2.181 3.120 nonbonded pdb=" O ARG C 149 " pdb=" OG SER C 152 " model vdw 2.192 3.040 ... (remaining 104914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13128 Z= 0.306 Angle : 0.761 8.024 18120 Z= 0.524 Chirality : 0.045 0.245 2074 Planarity : 0.005 0.062 2020 Dihedral : 19.095 89.568 5109 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1385 helix: -0.40 (0.26), residues: 387 sheet: -0.90 (0.31), residues: 295 loop : -1.28 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 53 TYR 0.014 0.002 TYR D 60 PHE 0.019 0.002 PHE A 407 TRP 0.028 0.002 TRP A 990 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.31 (13125) covalent geometry : angle 0.76116 / 0.52 (18114) SS BOND : bond 0.00273 / 0.14 ( 3) SS BOND : angle 1.04745 / 0.81 ( 6) hydrogen bonds : bond 0.30393 / 19.57 ( 509) hydrogen bonds : angle 9.89567 / 6.91 ( 1357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.455 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 MET cc_start: 0.9101 (ttt) cc_final: 0.8770 (ttm) REVERT: B 75 MET cc_start: 0.8401 (mmp) cc_final: 0.8146 (mmm) REVERT: B 229 MET cc_start: 0.7368 (tpt) cc_final: 0.6484 (tpp) REVERT: B 239 TYR cc_start: 0.9256 (m-80) cc_final: 0.8764 (m-80) REVERT: C 23 ILE cc_start: 0.4249 (mm) cc_final: 0.3813 (mm) REVERT: C 68 MET cc_start: 0.8187 (tpt) cc_final: 0.7739 (tpp) REVERT: C 144 PHE cc_start: 0.9423 (t80) cc_final: 0.9008 (t80) REVERT: C 169 PHE cc_start: 0.9455 (m-80) cc_final: 0.9086 (m-80) REVERT: C 235 LEU cc_start: 0.9117 (tp) cc_final: 0.8845 (tp) REVERT: D 40 MET cc_start: 0.4892 (tpt) cc_final: 0.4429 (tpt) REVERT: D 68 MET cc_start: 0.9123 (tmm) cc_final: 0.8680 (tmm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1299 time to fit residues: 27.8984 Evaluate side-chains 116 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN A 716 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 929 GLN A 970 HIS C 246 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.080256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.060784 restraints weight = 109644.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.062091 restraints weight = 85964.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.063022 restraints weight = 71914.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.063752 restraints weight = 62887.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.064266 restraints weight = 56933.945| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13128 Z= 0.168 Angle : 0.741 7.826 18120 Z= 0.400 Chirality : 0.047 0.197 2074 Planarity : 0.005 0.055 2020 Dihedral : 22.041 88.541 2439 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.50 % Favored : 93.29 % Rotamer: Outliers : 0.82 % Allowed : 8.28 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.22), residues: 1385 helix: -0.37 (0.23), residues: 442 sheet: -0.81 (0.30), residues: 307 loop : -1.36 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 721 TYR 0.029 0.003 TYR A 605 PHE 0.022 0.003 PHE B 214 TRP 0.011 0.002 TRP A 906 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (13125) covalent geometry : angle 0.74072 / 0.40 (18114) SS BOND : bond 0.00411 / 0.20 ( 3) SS BOND : angle 1.19771 / 1.06 ( 6) hydrogen bonds : bond 0.07847 / 4.97 ( 509) hydrogen bonds : angle 6.95870 / 4.89 ( 1357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.430 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 MET cc_start: 0.2999 (tpt) cc_final: 0.2687 (tmm) REVERT: A 988 MET cc_start: 0.9002 (ttt) cc_final: 0.8584 (ttm) REVERT: B 75 MET cc_start: 0.8333 (mmp) cc_final: 0.8004 (mmp) REVERT: B 199 MET cc_start: 0.8245 (tpp) cc_final: 0.7950 (mmm) REVERT: B 229 MET cc_start: 0.7611 (tpt) cc_final: 0.7020 (tpp) REVERT: B 239 TYR cc_start: 0.9295 (m-80) cc_final: 0.8852 (m-80) REVERT: C 23 ILE cc_start: 0.4547 (mm) cc_final: 0.4080 (mm) REVERT: C 68 MET cc_start: 0.8269 (tpt) cc_final: 0.7955 (tpt) REVERT: C 116 MET cc_start: 0.7324 (tpt) cc_final: 0.6789 (tpt) REVERT: C 144 PHE cc_start: 0.9363 (t80) cc_final: 0.9003 (t80) REVERT: C 169 PHE cc_start: 0.9428 (m-80) cc_final: 0.9139 (m-80) REVERT: D 40 MET cc_start: 0.4172 (tpt) cc_final: 0.3861 (tpt) REVERT: D 119 MET cc_start: 0.7176 (ppp) cc_final: 0.6965 (ppp) outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.1296 time to fit residues: 23.4595 Evaluate side-chains 119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS A 987 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.076400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.057541 restraints weight = 114714.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.058795 restraints weight = 89572.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.059621 restraints weight = 74604.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.060344 restraints weight = 65325.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.060550 restraints weight = 58989.200| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13128 Z= 0.235 Angle : 0.761 13.233 18120 Z= 0.410 Chirality : 0.047 0.358 2074 Planarity : 0.005 0.062 2020 Dihedral : 22.204 88.339 2439 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.42 % Rotamer: Outliers : 1.56 % Allowed : 12.70 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.22), residues: 1385 helix: -0.45 (0.23), residues: 433 sheet: -0.84 (0.33), residues: 256 loop : -1.47 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 752 TYR 0.020 0.003 TYR A 666 PHE 0.022 0.003 PHE A 951 TRP 0.028 0.003 TRP A 624 HIS 0.008 0.002 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (13125) covalent geometry : angle 0.76104 / 0.41 (18114) SS BOND : bond 0.00434 / 0.22 ( 3) SS BOND : angle 1.09068 / 0.88 ( 6) hydrogen bonds : bond 0.08173 / 5.02 ( 509) hydrogen bonds : angle 6.77623 / 4.73 ( 1357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.557 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: symmetry clash REVERT: A 676 ILE cc_start: 0.8307 (mm) cc_final: 0.7977 (mt) REVERT: A 961 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9228 (mt) REVERT: A 988 MET cc_start: 0.8920 (ttt) cc_final: 0.8629 (ttm) REVERT: B 28 TRP cc_start: 0.6811 (m-10) cc_final: 0.6587 (m-10) REVERT: B 75 MET cc_start: 0.8665 (mmp) cc_final: 0.8397 (mmp) REVERT: B 229 MET cc_start: 0.7742 (tpt) cc_final: 0.7291 (tpp) REVERT: B 239 TYR cc_start: 0.9378 (m-80) cc_final: 0.8954 (m-80) REVERT: C 23 ILE cc_start: 0.4562 (mm) cc_final: 0.3673 (mm) REVERT: C 68 MET cc_start: 0.8440 (tpt) cc_final: 0.8107 (tpp) REVERT: C 72 LEU cc_start: 0.8753 (mm) cc_final: 0.8468 (mm) REVERT: C 144 PHE cc_start: 0.9437 (t80) cc_final: 0.9111 (t80) REVERT: C 169 PHE cc_start: 0.9445 (m-80) cc_final: 0.9227 (m-80) REVERT: C 229 MET cc_start: 0.6274 (mmm) cc_final: 0.5958 (mmm) REVERT: D 14 LYS cc_start: 0.9674 (tmtt) cc_final: 0.9466 (tptt) REVERT: D 116 MET cc_start: 0.7409 (tpt) cc_final: 0.7041 (tmm) REVERT: D 139 MET cc_start: 0.9790 (OUTLIER) cc_final: 0.9528 (pmm) REVERT: D 221 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7608 (mm) REVERT: D 244 MET cc_start: 0.9059 (tpt) cc_final: 0.8848 (tpt) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 0.1261 time to fit residues: 21.9100 Evaluate side-chains 120 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 50.0000 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.075722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.056304 restraints weight = 112543.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.057567 restraints weight = 88182.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.058444 restraints weight = 73928.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.059085 restraints weight = 64931.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.059532 restraints weight = 58902.085| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13128 Z= 0.182 Angle : 0.718 12.440 18120 Z= 0.378 Chirality : 0.045 0.187 2074 Planarity : 0.005 0.095 2020 Dihedral : 22.274 87.988 2439 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 1.97 % Allowed : 14.75 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.22), residues: 1385 helix: -0.37 (0.23), residues: 441 sheet: -0.94 (0.29), residues: 302 loop : -1.37 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 860 TYR 0.031 0.002 TYR A 605 PHE 0.016 0.002 PHE A 875 TRP 0.014 0.002 TRP A 624 HIS 0.007 0.002 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (13125) covalent geometry : angle 0.71740 / 0.38 (18114) SS BOND : bond 0.00612 / 0.32 ( 3) SS BOND : angle 1.32009 / 0.87 ( 6) hydrogen bonds : bond 0.06135 / 3.83 ( 509) hydrogen bonds : angle 6.39287 / 4.48 ( 1357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.369 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: symmetry clash REVERT: A 946 HIS cc_start: 0.9349 (OUTLIER) cc_final: 0.9081 (p-80) REVERT: A 961 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9345 (mt) REVERT: A 988 MET cc_start: 0.8855 (ttt) cc_final: 0.8617 (ttm) REVERT: B 1 MET cc_start: 0.9213 (tpp) cc_final: 0.8950 (tpp) REVERT: B 28 TRP cc_start: 0.6770 (OUTLIER) cc_final: 0.6383 (m-10) REVERT: B 75 MET cc_start: 0.8644 (mmp) cc_final: 0.8407 (mmp) REVERT: B 199 MET cc_start: 0.8076 (mmm) cc_final: 0.7577 (tpp) REVERT: B 239 TYR cc_start: 0.9327 (m-80) cc_final: 0.8945 (m-80) REVERT: C 68 MET cc_start: 0.8433 (tpt) cc_final: 0.8053 (tpp) REVERT: C 72 LEU cc_start: 0.8818 (mm) cc_final: 0.8558 (mm) REVERT: C 116 MET cc_start: 0.7509 (tpt) cc_final: 0.6861 (tpt) REVERT: C 144 PHE cc_start: 0.9416 (t80) cc_final: 0.9077 (t80) REVERT: D 14 LYS cc_start: 0.9698 (tmtt) cc_final: 0.9488 (tptt) REVERT: D 40 MET cc_start: 0.5126 (tpp) cc_final: 0.4807 (tpp) REVERT: D 116 MET cc_start: 0.7334 (tpt) cc_final: 0.6979 (tmm) REVERT: D 119 MET cc_start: 0.7337 (ppp) cc_final: 0.7134 (ppp) REVERT: D 221 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7945 (mm) REVERT: D 244 MET cc_start: 0.8890 (tpt) cc_final: 0.8353 (tpt) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.1168 time to fit residues: 20.6976 Evaluate side-chains 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 50.0000 chunk 66 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 overall best weight: 2.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.076564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.057280 restraints weight = 113768.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058637 restraints weight = 87747.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.059598 restraints weight = 72730.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.060188 restraints weight = 63222.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.060758 restraints weight = 57419.195| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13128 Z= 0.140 Angle : 0.688 11.497 18120 Z= 0.356 Chirality : 0.044 0.224 2074 Planarity : 0.004 0.051 2020 Dihedral : 22.208 88.664 2439 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.50 % Favored : 93.29 % Rotamer: Outliers : 2.46 % Allowed : 15.57 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1385 helix: -0.18 (0.24), residues: 443 sheet: -0.89 (0.30), residues: 302 loop : -1.35 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 91 TYR 0.014 0.002 TYR D 114 PHE 0.024 0.002 PHE D 144 TRP 0.011 0.001 TRP A 624 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (13125) covalent geometry : angle 0.68766 / 0.36 (18114) SS BOND : bond 0.00414 / 0.21 ( 3) SS BOND : angle 1.00128 / 0.74 ( 6) hydrogen bonds : bond 0.05602 / 3.57 ( 509) hydrogen bonds : angle 6.19014 / 4.34 ( 1357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8758 (tt0) REVERT: A 946 HIS cc_start: 0.9322 (OUTLIER) cc_final: 0.9040 (p90) REVERT: A 961 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9277 (mt) REVERT: A 988 MET cc_start: 0.8817 (ttt) cc_final: 0.8474 (ttt) REVERT: B 28 TRP cc_start: 0.6694 (OUTLIER) cc_final: 0.6078 (m-10) REVERT: B 75 MET cc_start: 0.8631 (mmp) cc_final: 0.8384 (mmp) REVERT: B 199 MET cc_start: 0.7955 (mmm) cc_final: 0.7487 (tpp) REVERT: B 207 PHE cc_start: 0.8973 (m-80) cc_final: 0.8434 (m-80) REVERT: B 211 TYR cc_start: 0.9618 (m-80) cc_final: 0.9390 (m-80) REVERT: B 229 MET cc_start: 0.8103 (mmm) cc_final: 0.7249 (ptt) REVERT: B 239 TYR cc_start: 0.9299 (m-80) cc_final: 0.8943 (m-80) REVERT: C 28 TRP cc_start: 0.9139 (t-100) cc_final: 0.8341 (t-100) REVERT: C 68 MET cc_start: 0.8343 (tpt) cc_final: 0.8064 (tpp) REVERT: C 72 LEU cc_start: 0.8780 (mm) cc_final: 0.8516 (mm) REVERT: C 116 MET cc_start: 0.7510 (tpt) cc_final: 0.6803 (tpt) REVERT: C 144 PHE cc_start: 0.9384 (t80) cc_final: 0.9039 (t80) REVERT: C 195 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8430 (t) REVERT: C 229 MET cc_start: 0.6225 (mmm) cc_final: 0.5831 (mmm) REVERT: D 14 LYS cc_start: 0.9709 (tmtt) cc_final: 0.9494 (tptt) REVERT: D 116 MET cc_start: 0.7310 (tpt) cc_final: 0.6984 (tmm) REVERT: D 119 MET cc_start: 0.7377 (ppp) cc_final: 0.7131 (ppp) REVERT: D 144 PHE cc_start: 0.9686 (t80) cc_final: 0.9440 (t80) REVERT: D 221 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 229 MET cc_start: 0.7345 (tpt) cc_final: 0.6593 (mpp) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 0.0969 time to fit residues: 18.9247 Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 0.0170 chunk 122 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.078473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.058296 restraints weight = 112262.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.059628 restraints weight = 87926.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.060583 restraints weight = 73549.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.061270 restraints weight = 64581.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.061782 restraints weight = 58627.027| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13128 Z= 0.129 Angle : 0.700 13.024 18120 Z= 0.359 Chirality : 0.045 0.258 2074 Planarity : 0.005 0.085 2020 Dihedral : 22.091 89.568 2439 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.57 % Favored : 93.21 % Rotamer: Outliers : 2.54 % Allowed : 16.80 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1385 helix: -0.15 (0.24), residues: 447 sheet: -0.82 (0.30), residues: 298 loop : -1.36 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 591 TYR 0.013 0.002 TYR A 842 PHE 0.053 0.002 PHE A 407 TRP 0.010 0.001 TRP C 28 HIS 0.008 0.001 HIS A 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (13125) covalent geometry : angle 0.69967 / 0.36 (18114) SS BOND : bond 0.00331 / 0.17 ( 3) SS BOND : angle 0.88444 / 0.62 ( 6) hydrogen bonds : bond 0.05217 / 3.37 ( 509) hydrogen bonds : angle 5.93966 / 4.17 ( 1357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.456 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: A 484 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: A 664 TRP cc_start: 0.7967 (t60) cc_final: 0.7405 (t60) REVERT: A 717 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: A 946 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.9028 (p90) REVERT: A 961 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9288 (mt) REVERT: A 988 MET cc_start: 0.8910 (ttt) cc_final: 0.8617 (ttt) REVERT: B 28 TRP cc_start: 0.6668 (OUTLIER) cc_final: 0.6207 (m-90) REVERT: B 199 MET cc_start: 0.7925 (mmm) cc_final: 0.7563 (tpp) REVERT: B 211 TYR cc_start: 0.9625 (m-80) cc_final: 0.9415 (m-80) REVERT: B 229 MET cc_start: 0.8141 (mmm) cc_final: 0.7289 (ptt) REVERT: B 239 TYR cc_start: 0.9228 (m-80) cc_final: 0.8902 (m-80) REVERT: B 244 MET cc_start: 0.7908 (tpt) cc_final: 0.7339 (tmm) REVERT: C 28 TRP cc_start: 0.9141 (t-100) cc_final: 0.8338 (t-100) REVERT: C 40 MET cc_start: 0.8062 (tpp) cc_final: 0.7725 (tpp) REVERT: C 68 MET cc_start: 0.8339 (tpt) cc_final: 0.8071 (tpp) REVERT: C 72 LEU cc_start: 0.8784 (mm) cc_final: 0.8531 (mm) REVERT: C 116 MET cc_start: 0.7438 (tpt) cc_final: 0.6735 (tpt) REVERT: C 144 PHE cc_start: 0.9386 (t80) cc_final: 0.9025 (t80) REVERT: C 195 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (t) REVERT: D 2 PHE cc_start: 0.8023 (t80) cc_final: 0.7326 (t80) REVERT: D 14 LYS cc_start: 0.9710 (tmtt) cc_final: 0.9488 (tptt) REVERT: D 40 MET cc_start: 0.5287 (tpp) cc_final: 0.4952 (tpp) REVERT: D 68 MET cc_start: 0.9185 (tmm) cc_final: 0.8943 (tmm) REVERT: D 116 MET cc_start: 0.7402 (tpt) cc_final: 0.7068 (tmm) REVERT: D 119 MET cc_start: 0.7292 (ppp) cc_final: 0.6976 (ppp) REVERT: D 144 PHE cc_start: 0.9691 (t80) cc_final: 0.9274 (t80) REVERT: D 221 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7619 (mm) REVERT: D 229 MET cc_start: 0.7352 (tpt) cc_final: 0.6616 (mpp) REVERT: D 244 MET cc_start: 0.8813 (tpt) cc_final: 0.8034 (tpt) outliers start: 31 outliers final: 11 residues processed: 139 average time/residue: 0.1104 time to fit residues: 22.1039 Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 0.0770 chunk 104 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 93 optimal weight: 0.0170 chunk 121 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 142 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.075817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.055936 restraints weight = 115001.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.057221 restraints weight = 90098.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.058112 restraints weight = 75565.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.058784 restraints weight = 66322.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.059235 restraints weight = 60322.392| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13128 Z= 0.170 Angle : 0.705 12.415 18120 Z= 0.368 Chirality : 0.044 0.246 2074 Planarity : 0.004 0.050 2020 Dihedral : 22.079 88.114 2439 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 2.38 % Allowed : 17.70 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1385 helix: -0.13 (0.24), residues: 445 sheet: -0.89 (0.30), residues: 294 loop : -1.37 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 53 TYR 0.015 0.002 TYR C 249 PHE 0.014 0.002 PHE A 859 TRP 0.009 0.002 TRP C 28 HIS 0.009 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (13125) covalent geometry : angle 0.70465 / 0.37 (18114) SS BOND : bond 0.00424 / 0.22 ( 3) SS BOND : angle 0.97196 / 0.70 ( 6) hydrogen bonds : bond 0.05755 / 3.61 ( 509) hydrogen bonds : angle 5.97288 / 4.13 ( 1357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8748 (m-80) REVERT: A 717 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8800 (tt0) REVERT: A 946 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.9102 (p-80) REVERT: A 961 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9303 (mt) REVERT: B 28 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: B 199 MET cc_start: 0.7905 (mmm) cc_final: 0.7644 (tpp) REVERT: B 211 TYR cc_start: 0.9629 (m-80) cc_final: 0.9412 (m-80) REVERT: B 229 MET cc_start: 0.8340 (mmm) cc_final: 0.7405 (ptm) REVERT: B 239 TYR cc_start: 0.9260 (m-80) cc_final: 0.8929 (m-80) REVERT: C 28 TRP cc_start: 0.9133 (t-100) cc_final: 0.8409 (t-100) REVERT: C 68 MET cc_start: 0.8474 (tpt) cc_final: 0.8210 (tpp) REVERT: C 72 LEU cc_start: 0.8881 (mm) cc_final: 0.8575 (mm) REVERT: C 116 MET cc_start: 0.7498 (tpt) cc_final: 0.6794 (tpt) REVERT: C 144 PHE cc_start: 0.9417 (t80) cc_final: 0.9079 (t80) REVERT: C 195 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8413 (t) REVERT: C 229 MET cc_start: 0.5784 (mmm) cc_final: 0.5214 (mmm) REVERT: D 2 PHE cc_start: 0.8092 (t80) cc_final: 0.7367 (t80) REVERT: D 14 LYS cc_start: 0.9737 (tmtt) cc_final: 0.9520 (tptp) REVERT: D 116 MET cc_start: 0.7388 (tpt) cc_final: 0.6926 (tmm) REVERT: D 119 MET cc_start: 0.7341 (ppp) cc_final: 0.7083 (ppp) REVERT: D 144 PHE cc_start: 0.9719 (t80) cc_final: 0.9469 (t80) REVERT: D 221 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8073 (mm) outliers start: 29 outliers final: 13 residues processed: 131 average time/residue: 0.0914 time to fit residues: 17.6155 Evaluate side-chains 123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 11 optimal weight: 0.0770 chunk 122 optimal weight: 7.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.076950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.057050 restraints weight = 112295.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.058290 restraints weight = 88878.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.059165 restraints weight = 75245.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.059839 restraints weight = 66406.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.060327 restraints weight = 60522.414| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13128 Z= 0.135 Angle : 0.710 12.937 18120 Z= 0.365 Chirality : 0.044 0.262 2074 Planarity : 0.005 0.076 2020 Dihedral : 22.010 88.161 2439 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.00 % Favored : 92.78 % Rotamer: Outliers : 2.13 % Allowed : 18.93 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.22), residues: 1385 helix: -0.05 (0.24), residues: 445 sheet: -0.79 (0.30), residues: 298 loop : -1.34 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 53 TYR 0.013 0.002 TYR D 114 PHE 0.020 0.002 PHE A 407 TRP 0.011 0.001 TRP A 624 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13125) covalent geometry : angle 0.71002 / 0.37 (18114) SS BOND : bond 0.00340 / 0.18 ( 3) SS BOND : angle 0.84439 / 0.60 ( 6) hydrogen bonds : bond 0.05009 / 3.21 ( 509) hydrogen bonds : angle 5.76653 / 4.01 ( 1357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9380 (mpp) cc_final: 0.9140 (pmm) REVERT: A 484 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: A 717 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: A 946 HIS cc_start: 0.9289 (OUTLIER) cc_final: 0.9027 (p90) REVERT: A 961 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9288 (mt) REVERT: B 28 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: B 75 MET cc_start: 0.8835 (mmp) cc_final: 0.8592 (mmp) REVERT: B 199 MET cc_start: 0.7886 (mmm) cc_final: 0.7663 (tpp) REVERT: B 211 TYR cc_start: 0.9633 (m-80) cc_final: 0.9413 (m-80) REVERT: B 229 MET cc_start: 0.8284 (mmm) cc_final: 0.7538 (ttt) REVERT: B 239 TYR cc_start: 0.9216 (m-80) cc_final: 0.8909 (m-80) REVERT: C 28 TRP cc_start: 0.9154 (t-100) cc_final: 0.8379 (t-100) REVERT: C 40 MET cc_start: 0.8019 (tpp) cc_final: 0.7580 (tpp) REVERT: C 68 MET cc_start: 0.8425 (tpt) cc_final: 0.8155 (tpp) REVERT: C 72 LEU cc_start: 0.8823 (mm) cc_final: 0.8547 (mm) REVERT: C 75 MET cc_start: 0.9224 (mmm) cc_final: 0.8977 (mmm) REVERT: C 116 MET cc_start: 0.7490 (tpt) cc_final: 0.6656 (tpt) REVERT: C 144 PHE cc_start: 0.9395 (t80) cc_final: 0.9036 (t80) REVERT: C 195 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8417 (t) REVERT: D 2 PHE cc_start: 0.8071 (t80) cc_final: 0.7307 (t80) REVERT: D 14 LYS cc_start: 0.9735 (tmtt) cc_final: 0.9518 (tptp) REVERT: D 40 MET cc_start: 0.5221 (tpp) cc_final: 0.4981 (tpp) REVERT: D 68 MET cc_start: 0.9118 (tmm) cc_final: 0.8832 (tmm) REVERT: D 119 MET cc_start: 0.7408 (ppp) cc_final: 0.7115 (ppp) REVERT: D 144 PHE cc_start: 0.9722 (t80) cc_final: 0.9343 (t80) REVERT: D 221 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8073 (mm) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 0.1002 time to fit residues: 17.9741 Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 0.0070 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.076764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.056843 restraints weight = 112758.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058107 restraints weight = 89412.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.058997 restraints weight = 75542.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.059666 restraints weight = 66618.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.060137 restraints weight = 60663.200| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13128 Z= 0.133 Angle : 0.707 12.839 18120 Z= 0.361 Chirality : 0.044 0.262 2074 Planarity : 0.004 0.052 2020 Dihedral : 21.940 88.239 2439 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 2.21 % Allowed : 18.85 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.22), residues: 1385 helix: 0.01 (0.25), residues: 445 sheet: -0.76 (0.30), residues: 298 loop : -1.32 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 53 TYR 0.015 0.002 TYR B 250 PHE 0.022 0.002 PHE A 407 TRP 0.013 0.001 TRP A 624 HIS 0.005 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (13125) covalent geometry : angle 0.70678 / 0.36 (18114) SS BOND : bond 0.00360 / 0.19 ( 3) SS BOND : angle 0.88777 / 0.65 ( 6) hydrogen bonds : bond 0.04932 / 3.16 ( 509) hydrogen bonds : angle 5.68374 / 3.95 ( 1357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.481 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: A 484 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8796 (m-80) REVERT: A 946 HIS cc_start: 0.9294 (OUTLIER) cc_final: 0.9031 (p90) REVERT: A 961 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9287 (mt) REVERT: A 988 MET cc_start: 0.8915 (ttt) cc_final: 0.8473 (tmm) REVERT: B 28 TRP cc_start: 0.6723 (OUTLIER) cc_final: 0.6319 (m-10) REVERT: B 75 MET cc_start: 0.8890 (mmp) cc_final: 0.8644 (mmp) REVERT: B 211 TYR cc_start: 0.9633 (m-80) cc_final: 0.9420 (m-80) REVERT: B 229 MET cc_start: 0.8341 (mmm) cc_final: 0.7693 (ttt) REVERT: B 239 TYR cc_start: 0.9188 (m-80) cc_final: 0.8890 (m-80) REVERT: C 28 TRP cc_start: 0.9158 (t-100) cc_final: 0.8374 (t-100) REVERT: C 40 MET cc_start: 0.8044 (tpp) cc_final: 0.7664 (tpp) REVERT: C 68 MET cc_start: 0.8402 (tpt) cc_final: 0.8140 (tpp) REVERT: C 72 LEU cc_start: 0.8909 (mm) cc_final: 0.8641 (mm) REVERT: C 75 MET cc_start: 0.9195 (mmm) cc_final: 0.8947 (mmm) REVERT: C 116 MET cc_start: 0.7481 (tpt) cc_final: 0.6644 (tpt) REVERT: C 195 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8409 (t) REVERT: D 2 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7189 (t80) REVERT: D 14 LYS cc_start: 0.9746 (tmtt) cc_final: 0.9530 (tptp) REVERT: D 40 MET cc_start: 0.5198 (tpp) cc_final: 0.4952 (tpp) REVERT: D 68 MET cc_start: 0.9132 (tmm) cc_final: 0.8846 (tmm) REVERT: D 119 MET cc_start: 0.7398 (ppp) cc_final: 0.7095 (ppp) REVERT: D 144 PHE cc_start: 0.9711 (t80) cc_final: 0.9474 (t80) REVERT: D 221 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8190 (mm) outliers start: 27 outliers final: 16 residues processed: 122 average time/residue: 0.1092 time to fit residues: 19.5235 Evaluate side-chains 125 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 11 optimal weight: 0.0040 chunk 142 optimal weight: 40.0000 chunk 62 optimal weight: 0.4980 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 overall best weight: 4.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.074749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.055093 restraints weight = 115594.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.056316 restraints weight = 91874.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.057162 restraints weight = 77758.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.057781 restraints weight = 68856.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.058165 restraints weight = 62939.619| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13128 Z= 0.166 Angle : 0.732 13.354 18120 Z= 0.377 Chirality : 0.044 0.219 2074 Planarity : 0.004 0.051 2020 Dihedral : 21.959 87.294 2439 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 1.80 % Allowed : 19.34 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1385 helix: -0.04 (0.24), residues: 448 sheet: -0.96 (0.28), residues: 319 loop : -1.37 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 53 TYR 0.023 0.002 TYR D 250 PHE 0.016 0.002 PHE C 144 TRP 0.015 0.002 TRP A 624 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (13125) covalent geometry : angle 0.73244 / 0.38 (18114) SS BOND : bond 0.00265 / 0.14 ( 3) SS BOND : angle 0.62389 / 0.51 ( 6) hydrogen bonds : bond 0.05509 / 3.44 ( 509) hydrogen bonds : angle 5.78919 / 4.02 ( 1357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.9350 (mpp) cc_final: 0.9136 (pmm) REVERT: A 946 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.9087 (p-80) REVERT: A 961 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9295 (mt) REVERT: A 988 MET cc_start: 0.8958 (ttt) cc_final: 0.8586 (tmm) REVERT: B 28 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.6286 (m-10) REVERT: B 75 MET cc_start: 0.8960 (mmp) cc_final: 0.8725 (mmp) REVERT: B 211 TYR cc_start: 0.9627 (m-80) cc_final: 0.9400 (m-80) REVERT: B 229 MET cc_start: 0.8377 (mmm) cc_final: 0.7667 (ttt) REVERT: B 239 TYR cc_start: 0.9236 (m-80) cc_final: 0.8925 (m-80) REVERT: C 28 TRP cc_start: 0.9191 (t-100) cc_final: 0.8468 (t-100) REVERT: C 40 MET cc_start: 0.8028 (tpp) cc_final: 0.7694 (tpp) REVERT: C 75 MET cc_start: 0.9202 (mmm) cc_final: 0.8960 (mmm) REVERT: C 116 MET cc_start: 0.7620 (tpt) cc_final: 0.6756 (tpt) REVERT: D 2 PHE cc_start: 0.8054 (t80) cc_final: 0.7252 (t80) REVERT: D 14 LYS cc_start: 0.9751 (tmtt) cc_final: 0.9543 (tptp) REVERT: D 40 MET cc_start: 0.5266 (tpp) cc_final: 0.4986 (tpp) REVERT: D 68 MET cc_start: 0.9140 (tmm) cc_final: 0.8869 (tmm) REVERT: D 116 MET cc_start: 0.7316 (tpt) cc_final: 0.6885 (tmm) REVERT: D 119 MET cc_start: 0.7468 (ppp) cc_final: 0.7166 (ppp) REVERT: D 144 PHE cc_start: 0.9735 (t80) cc_final: 0.9396 (t80) REVERT: D 221 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8223 (mm) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 0.1105 time to fit residues: 19.0719 Evaluate side-chains 122 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 946 HIS Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.075476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.055800 restraints weight = 114272.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.056998 restraints weight = 90331.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.057847 restraints weight = 76207.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058492 restraints weight = 67371.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.058947 restraints weight = 61523.831| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13128 Z= 0.139 Angle : 0.718 13.434 18120 Z= 0.366 Chirality : 0.044 0.230 2074 Planarity : 0.004 0.052 2020 Dihedral : 21.924 87.857 2439 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 2.05 % Allowed : 19.43 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.22), residues: 1385 helix: 0.02 (0.24), residues: 448 sheet: -0.91 (0.28), residues: 321 loop : -1.36 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 53 TYR 0.024 0.002 TYR D 250 PHE 0.027 0.002 PHE C 144 TRP 0.015 0.002 TRP A 624 HIS 0.006 0.001 HIS A 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (13125) covalent geometry : angle 0.71827 / 0.37 (18114) SS BOND : bond 0.00437 / 0.23 ( 3) SS BOND : angle 0.88756 / 0.61 ( 6) hydrogen bonds : bond 0.04926 / 3.15 ( 509) hydrogen bonds : angle 5.67517 / 3.95 ( 1357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.77 seconds wall clock time: 51 minutes 40.76 seconds (3100.76 seconds total)