Starting phenix.real_space_refine on Fri Jul 3 06:35:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cma_45745/07_2026/9cma_45745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cma_45745/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cma_45745/07_2026/9cma_45745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cma_45745/07_2026/9cma_45745.map" model { file = "/net/cci-nas-00/data/ceres_data/9cma_45745/07_2026/9cma_45745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cma_45745/07_2026/9cma_45745_neut.cif" } 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-dev-6108/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: 2.09, per 1000 atoms: 0.16 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: 1.04 Conformation dependent library (CDL) restraints added in 474.8 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: 1.06 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: 2.19 Time building geometry restraints manager: 1.39 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: 17186 1.60 - 3.21: 823 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: 1.090 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.490 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- 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 : 0.760 8.024 18120 Z= 0.522 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 0.75960 / 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 : 0.286 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: 0.1116 time to fit residues: 23.9709 Evaluate side-chains 117 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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: 0.0050 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 3.7800 ------------------------------------------------------------------------------- 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 696 GLN A 716 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN A 764 HIS ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 929 GLN A 970 HIS ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.079219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.059822 restraints weight = 110416.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.061118 restraints weight = 86771.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.062032 restraints weight = 72640.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.062651 restraints weight = 63783.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.063202 restraints weight = 57893.491| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13128 Z= 0.186 Angle : 0.742 7.966 18120 Z= 0.406 Chirality : 0.047 0.178 2074 Planarity : 0.005 0.051 2020 Dihedral : 22.094 89.039 2439 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.00 % Favored : 92.78 % Rotamer: Outliers : 0.82 % Allowed : 8.77 % Favored : 90.41 % 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: -1.50 (0.22), residues: 1385 helix: -0.42 (0.23), residues: 439 sheet: -0.87 (0.30), residues: 307 loop : -1.38 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 721 TYR 0.027 0.003 TYR A 605 PHE 0.021 0.003 PHE A 673 TRP 0.012 0.002 TRP A 624 HIS 0.007 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (13125) covalent geometry : angle 0.74157 / 0.41 (18114) SS BOND : bond 0.00425 / 0.21 ( 3) SS BOND : angle 1.15028 / 1.02 ( 6) hydrogen bonds : bond 0.08180 / 5.13 ( 509) hydrogen bonds : angle 7.09074 / 4.98 ( 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 132 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.345 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: A 988 MET cc_start: 0.9010 (ttt) cc_final: 0.8608 (ttm) REVERT: B 1 MET cc_start: 0.9234 (tpt) cc_final: 0.8717 (tpp) REVERT: B 75 MET cc_start: 0.8357 (mmp) cc_final: 0.8122 (mmp) REVERT: B 229 MET cc_start: 0.7525 (tpt) cc_final: 0.6903 (tpp) REVERT: B 239 TYR cc_start: 0.9307 (m-80) cc_final: 0.8847 (m-80) REVERT: C 23 ILE cc_start: 0.4651 (mm) cc_final: 0.4117 (mm) REVERT: C 61 ARG cc_start: 0.8753 (ptt90) cc_final: 0.8470 (ttp80) REVERT: C 68 MET cc_start: 0.8313 (tpt) cc_final: 0.7930 (tpp) REVERT: C 116 MET cc_start: 0.7366 (tpt) cc_final: 0.6703 (tpt) REVERT: C 144 PHE cc_start: 0.9383 (t80) cc_final: 0.9028 (t80) REVERT: C 169 PHE cc_start: 0.9435 (m-80) cc_final: 0.9142 (m-80) REVERT: D 40 MET cc_start: 0.4274 (tpt) cc_final: 0.3935 (tpt) REVERT: D 119 MET cc_start: 0.7165 (ppp) cc_final: 0.6937 (ppp) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.1084 time to fit residues: 19.1289 Evaluate side-chains 120 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 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** A 946 HIS A 987 GLN B 213 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.077423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.058430 restraints weight = 111825.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.059693 restraints weight = 87181.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.060607 restraints weight = 72608.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.061304 restraints weight = 63212.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.061793 restraints weight = 57017.904| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13128 Z= 0.196 Angle : 0.714 10.935 18120 Z= 0.384 Chirality : 0.045 0.234 2074 Planarity : 0.005 0.045 2020 Dihedral : 22.237 88.880 2439 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.42 % Rotamer: Outliers : 1.56 % Allowed : 11.72 % Favored : 86.72 % 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: -1.56 (0.22), residues: 1385 helix: -0.45 (0.23), residues: 438 sheet: -0.76 (0.32), residues: 268 loop : -1.49 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 721 TYR 0.019 0.002 TYR A 842 PHE 0.039 0.003 PHE B 214 TRP 0.024 0.003 TRP B 28 HIS 0.007 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (13125) covalent geometry : angle 0.71387 / 0.38 (18114) SS BOND : bond 0.00359 / 0.18 ( 3) SS BOND : angle 0.91419 / 0.78 ( 6) hydrogen bonds : bond 0.07256 / 4.51 ( 509) hydrogen bonds : angle 6.66327 / 4.65 ( 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 133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.471 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 419 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 676 ILE cc_start: 0.8229 (mm) cc_final: 0.7852 (mt) REVERT: A 961 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9212 (mt) REVERT: A 988 MET cc_start: 0.8929 (ttt) cc_final: 0.8620 (ttm) REVERT: B 28 TRP cc_start: 0.6802 (m-10) cc_final: 0.6479 (m-10) REVERT: B 75 MET cc_start: 0.8645 (mmp) cc_final: 0.8384 (mmp) REVERT: B 199 MET cc_start: 0.8285 (tpp) cc_final: 0.7984 (mmm) REVERT: B 229 MET cc_start: 0.7689 (tpt) cc_final: 0.7231 (tpp) REVERT: B 239 TYR cc_start: 0.9343 (m-80) cc_final: 0.8926 (m-80) REVERT: C 23 ILE cc_start: 0.4510 (mm) cc_final: 0.3624 (mm) REVERT: C 61 ARG cc_start: 0.8862 (ptt90) cc_final: 0.8528 (ttp80) REVERT: C 68 MET cc_start: 0.8392 (tpt) cc_final: 0.8070 (tpp) REVERT: C 72 LEU cc_start: 0.8735 (mm) cc_final: 0.8455 (mm) REVERT: C 144 PHE cc_start: 0.9413 (t80) cc_final: 0.9075 (t80) REVERT: C 169 PHE cc_start: 0.9421 (m-80) cc_final: 0.9198 (m-80) REVERT: D 116 MET cc_start: 0.7369 (tpt) cc_final: 0.7020 (tmm) REVERT: D 119 MET cc_start: 0.7159 (ppp) cc_final: 0.6827 (ppp) REVERT: D 139 MET cc_start: 0.9789 (OUTLIER) cc_final: 0.9514 (pmm) REVERT: D 144 PHE cc_start: 0.9669 (t80) cc_final: 0.9469 (t80) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 0.1291 time to fit residues: 22.1309 Evaluate side-chains 120 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 637 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 D residue 139 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 126 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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** C 246 HIS ** 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 = 0.4153 r_free = 0.4153 target = 0.078070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058547 restraints weight = 109012.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.059777 restraints weight = 84742.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.060756 restraints weight = 70743.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.061410 restraints weight = 61889.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.061885 restraints weight = 56036.076| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13128 Z= 0.143 Angle : 0.674 10.657 18120 Z= 0.356 Chirality : 0.044 0.164 2074 Planarity : 0.004 0.065 2020 Dihedral : 22.187 89.439 2439 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 1.72 % Allowed : 14.18 % Favored : 84.10 % 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: -1.40 (0.22), residues: 1385 helix: -0.27 (0.23), residues: 446 sheet: -0.86 (0.30), residues: 302 loop : -1.36 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 710 TYR 0.034 0.002 TYR A 605 PHE 0.043 0.002 PHE B 214 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 0.00285 / 0.14 (13125) covalent geometry : angle 0.67406 / 0.36 (18114) SS BOND : bond 0.00320 / 0.16 ( 3) SS BOND : angle 0.80494 / 0.61 ( 6) hydrogen bonds : bond 0.05803 / 3.68 ( 509) hydrogen bonds : angle 6.25582 / 4.37 ( 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 136 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.458 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: 0.9261 (OUTLIER) cc_final: 0.9013 (p90) REVERT: A 961 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9291 (mt) REVERT: A 988 MET cc_start: 0.8804 (ttt) cc_final: 0.8338 (ttt) REVERT: B 28 TRP cc_start: 0.6706 (OUTLIER) cc_final: 0.6097 (m-90) REVERT: B 75 MET cc_start: 0.8568 (mmp) cc_final: 0.8320 (mmp) REVERT: B 199 MET cc_start: 0.8096 (tpp) cc_final: 0.7866 (mmp) REVERT: B 229 MET cc_start: 0.7814 (tpt) cc_final: 0.7518 (tpp) REVERT: B 239 TYR cc_start: 0.9246 (m-80) cc_final: 0.8841 (m-80) REVERT: C 61 ARG cc_start: 0.8861 (ptt90) cc_final: 0.8501 (ttp80) REVERT: C 68 MET cc_start: 0.8311 (tpt) cc_final: 0.7964 (tpp) REVERT: C 72 LEU cc_start: 0.8686 (mm) cc_final: 0.8446 (mm) REVERT: C 116 MET cc_start: 0.7365 (tpt) cc_final: 0.6672 (tpt) REVERT: C 144 PHE cc_start: 0.9357 (t80) cc_final: 0.9006 (t80) REVERT: D 119 MET cc_start: 0.7152 (ppp) cc_final: 0.6866 (ppp) REVERT: D 139 MET cc_start: 0.9800 (OUTLIER) cc_final: 0.9533 (pmm) REVERT: D 144 PHE cc_start: 0.9647 (t80) cc_final: 0.9431 (t80) outliers start: 21 outliers final: 9 residues processed: 127 average time/residue: 0.1187 time to fit residues: 21.7718 Evaluate side-chains 123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 888 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.074938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.055364 restraints weight = 113619.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.056648 restraints weight = 88194.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.057525 restraints weight = 73632.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.058079 restraints weight = 64681.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.058557 restraints weight = 59018.832| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13128 Z= 0.205 Angle : 0.728 12.198 18120 Z= 0.384 Chirality : 0.045 0.241 2074 Planarity : 0.004 0.047 2020 Dihedral : 22.255 87.816 2439 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.44 % Favored : 92.35 % Rotamer: Outliers : 2.30 % Allowed : 15.49 % Favored : 82.21 % 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: -1.50 (0.22), residues: 1385 helix: -0.35 (0.23), residues: 437 sheet: -0.92 (0.29), residues: 302 loop : -1.42 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 860 TYR 0.016 0.002 TYR D 114 PHE 0.044 0.003 PHE A 407 TRP 0.013 0.002 TRP A 624 HIS 0.007 0.002 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (13125) covalent geometry : angle 0.72754 / 0.38 (18114) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 0.91483 / 0.66 ( 6) hydrogen bonds : bond 0.06689 / 4.12 ( 509) hydrogen bonds : angle 6.28409 / 4.36 ( 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 138 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.463 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: A 946 HIS cc_start: 0.9330 (OUTLIER) cc_final: 0.9125 (p-80) REVERT: A 961 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9287 (mt) REVERT: A 988 MET cc_start: 0.8816 (ttt) cc_final: 0.8582 (ttm) REVERT: B 28 TRP cc_start: 0.6762 (OUTLIER) cc_final: 0.6312 (m-90) REVERT: B 207 PHE cc_start: 0.9051 (m-80) cc_final: 0.8755 (m-80) REVERT: B 239 TYR cc_start: 0.9306 (m-80) cc_final: 0.8914 (m-80) REVERT: C 68 MET cc_start: 0.8460 (tpt) cc_final: 0.8106 (tpp) REVERT: C 72 LEU cc_start: 0.8814 (mm) cc_final: 0.8563 (mm) REVERT: C 116 MET cc_start: 0.7484 (tpt) cc_final: 0.6759 (tpt) REVERT: C 144 PHE cc_start: 0.9373 (t80) cc_final: 0.9042 (t80) REVERT: C 195 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (t) REVERT: C 229 MET cc_start: 0.5774 (mmm) cc_final: 0.5566 (mmm) REVERT: D 40 MET cc_start: 0.4922 (tpp) cc_final: 0.4616 (tpp) REVERT: D 116 MET cc_start: 0.7073 (tpt) cc_final: 0.6582 (tmm) REVERT: D 119 MET cc_start: 0.7320 (ppp) cc_final: 0.6933 (ppp) REVERT: D 139 MET cc_start: 0.9804 (OUTLIER) cc_final: 0.9527 (pmm) REVERT: D 144 PHE cc_start: 0.9679 (t80) cc_final: 0.9445 (t80) outliers start: 28 outliers final: 12 residues processed: 129 average time/residue: 0.1130 time to fit residues: 21.1969 Evaluate side-chains 119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 637 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 89 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 20 optimal weight: 0.0070 chunk 48 optimal weight: 20.0000 overall best weight: 4.6006 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.075950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.056123 restraints weight = 114074.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.057346 restraints weight = 90092.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.058230 restraints weight = 75983.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.058867 restraints weight = 66989.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.059282 restraints weight = 61111.155| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13128 Z= 0.169 Angle : 0.718 12.436 18120 Z= 0.376 Chirality : 0.045 0.200 2074 Planarity : 0.004 0.048 2020 Dihedral : 22.255 87.520 2439 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 3.28 % Allowed : 16.39 % Favored : 80.33 % 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: -1.45 (0.22), residues: 1385 helix: -0.27 (0.23), residues: 442 sheet: -0.94 (0.29), residues: 308 loop : -1.38 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 53 TYR 0.050 0.002 TYR A 408 PHE 0.059 0.002 PHE A 407 TRP 0.011 0.002 TRP A 624 HIS 0.010 0.002 HIS A 970 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (13125) covalent geometry : angle 0.71822 / 0.38 (18114) SS BOND : bond 0.00373 / 0.19 ( 3) SS BOND : angle 0.80607 / 0.58 ( 6) hydrogen bonds : bond 0.05700 / 3.57 ( 509) hydrogen bonds : angle 6.16134 / 4.30 ( 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 151 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8826 (tt0) REVERT: A 946 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.9085 (p-80) REVERT: A 961 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9318 (mt) REVERT: B 28 TRP cc_start: 0.6672 (OUTLIER) cc_final: 0.6251 (m-90) REVERT: B 199 MET cc_start: 0.7515 (mmp) cc_final: 0.7222 (tpp) REVERT: B 211 TYR cc_start: 0.9622 (m-80) cc_final: 0.9393 (m-80) REVERT: B 229 MET cc_start: 0.8125 (mmm) cc_final: 0.7271 (ptm) REVERT: B 239 TYR cc_start: 0.9247 (m-80) cc_final: 0.8886 (m-80) REVERT: C 28 TRP cc_start: 0.9159 (t-100) cc_final: 0.8410 (t-100) REVERT: C 40 MET cc_start: 0.8124 (tpp) cc_final: 0.7738 (tpp) REVERT: C 68 MET cc_start: 0.8433 (tpt) cc_final: 0.8128 (tpp) REVERT: C 116 MET cc_start: 0.7495 (tpt) cc_final: 0.6731 (tpt) REVERT: C 144 PHE cc_start: 0.9378 (t80) cc_final: 0.9005 (t80) REVERT: C 195 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8417 (t) REVERT: C 229 MET cc_start: 0.6401 (mmm) cc_final: 0.6166 (mmm) REVERT: D 116 MET cc_start: 0.7179 (tpt) cc_final: 0.6685 (tmm) REVERT: D 119 MET cc_start: 0.7281 (ppp) cc_final: 0.6878 (ppp) REVERT: D 139 MET cc_start: 0.9816 (OUTLIER) cc_final: 0.9567 (pmm) REVERT: D 144 PHE cc_start: 0.9676 (t80) cc_final: 0.9425 (t80) outliers start: 40 outliers final: 16 residues processed: 138 average time/residue: 0.1220 time to fit residues: 24.7126 Evaluate side-chains 125 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 637 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 C residue 139 MET Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 30.0000 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 131 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.074967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.055331 restraints weight = 116221.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.056497 restraints weight = 92116.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.057336 restraints weight = 78268.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.057965 restraints weight = 69262.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.058378 restraints weight = 63461.636| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13128 Z= 0.180 Angle : 0.733 13.255 18120 Z= 0.381 Chirality : 0.045 0.221 2074 Planarity : 0.004 0.054 2020 Dihedral : 22.254 87.027 2439 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 2.54 % Allowed : 18.44 % Favored : 79.02 % 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: -1.54 (0.22), residues: 1385 helix: -0.34 (0.23), residues: 445 sheet: -0.99 (0.29), residues: 310 loop : -1.46 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 860 TYR 0.018 0.002 TYR A 408 PHE 0.056 0.002 PHE A 407 TRP 0.011 0.002 TRP A 624 HIS 0.007 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (13125) covalent geometry : angle 0.73251 / 0.38 (18114) SS BOND : bond 0.00416 / 0.21 ( 3) SS BOND : angle 0.94174 / 0.65 ( 6) hydrogen bonds : bond 0.05871 / 3.68 ( 509) hydrogen bonds : angle 6.10096 / 4.25 ( 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 138 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.433 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: A 484 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: A 717 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8846 (tt0) REVERT: A 961 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9304 (mt) REVERT: B 211 TYR cc_start: 0.9638 (m-80) cc_final: 0.9404 (m-80) REVERT: B 229 MET cc_start: 0.8314 (mmm) cc_final: 0.7540 (ttt) REVERT: B 239 TYR cc_start: 0.9252 (m-80) cc_final: 0.8899 (m-80) REVERT: C 28 TRP cc_start: 0.9143 (t-100) cc_final: 0.8414 (t-100) REVERT: C 68 MET cc_start: 0.8539 (tpt) cc_final: 0.8253 (tpp) REVERT: C 116 MET cc_start: 0.7656 (tpt) cc_final: 0.6937 (tpt) REVERT: C 144 PHE cc_start: 0.9386 (t80) cc_final: 0.9021 (t80) REVERT: C 195 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8492 (t) REVERT: D 40 MET cc_start: 0.5183 (tpp) cc_final: 0.4920 (tpp) REVERT: D 119 MET cc_start: 0.7393 (ppp) cc_final: 0.6919 (ppp) REVERT: D 139 MET cc_start: 0.9817 (OUTLIER) cc_final: 0.9592 (pmm) REVERT: D 144 PHE cc_start: 0.9695 (t80) cc_final: 0.9439 (t80) outliers start: 31 outliers final: 23 residues processed: 126 average time/residue: 0.1076 time to fit residues: 19.9510 Evaluate side-chains 130 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 468 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 637 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 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 C residue 249 TYR 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 139 MET Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 122 optimal weight: 0.0670 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 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** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.076889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.056905 restraints weight = 111172.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.058130 restraints weight = 88127.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.059039 restraints weight = 74537.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.059611 restraints weight = 65793.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.060126 restraints weight = 60213.224| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13128 Z= 0.136 Angle : 0.724 13.159 18120 Z= 0.369 Chirality : 0.045 0.260 2074 Planarity : 0.004 0.052 2020 Dihedral : 22.145 87.974 2439 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 2.54 % Allowed : 18.85 % Favored : 78.61 % 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: -1.37 (0.22), residues: 1385 helix: -0.17 (0.24), residues: 446 sheet: -0.81 (0.29), residues: 314 loop : -1.43 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 547 TYR 0.018 0.002 TYR A 408 PHE 0.047 0.002 PHE A 407 TRP 0.012 0.001 TRP A 624 HIS 0.006 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (13125) covalent geometry : angle 0.72423 / 0.37 (18114) SS BOND : bond 0.00256 / 0.13 ( 3) SS BOND : angle 0.52110 / 0.40 ( 6) hydrogen bonds : bond 0.05011 / 3.22 ( 509) hydrogen bonds : angle 5.83633 / 4.07 ( 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 142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: A 946 HIS cc_start: 0.9277 (OUTLIER) cc_final: 0.9019 (p90) REVERT: A 961 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9290 (mt) REVERT: A 988 MET cc_start: 0.8923 (ttt) cc_final: 0.8548 (tmm) REVERT: B 28 TRP cc_start: 0.6627 (OUTLIER) cc_final: 0.6242 (m-90) REVERT: B 211 TYR cc_start: 0.9635 (m-80) cc_final: 0.9425 (m-80) REVERT: B 229 MET cc_start: 0.8324 (mmm) cc_final: 0.7568 (ttt) REVERT: B 239 TYR cc_start: 0.9193 (m-80) cc_final: 0.8890 (m-80) REVERT: C 28 TRP cc_start: 0.9171 (t-100) cc_final: 0.8402 (t-100) REVERT: C 40 MET cc_start: 0.8011 (tpp) cc_final: 0.7617 (tpp) REVERT: C 68 MET cc_start: 0.8424 (tpt) cc_final: 0.8136 (tpp) REVERT: C 72 LEU cc_start: 0.8880 (mm) cc_final: 0.8619 (mm) REVERT: C 75 MET cc_start: 0.9225 (mmm) cc_final: 0.8974 (mmm) REVERT: C 116 MET cc_start: 0.7464 (tpt) cc_final: 0.6659 (tpt) REVERT: C 144 PHE cc_start: 0.9385 (t80) cc_final: 0.9002 (t80) REVERT: C 195 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8529 (t) REVERT: C 229 MET cc_start: 0.5957 (mmm) cc_final: 0.5267 (mmp) REVERT: D 2 PHE cc_start: 0.8156 (t80) cc_final: 0.7394 (t80) REVERT: D 40 MET cc_start: 0.5210 (tpp) cc_final: 0.4976 (tpp) REVERT: D 119 MET cc_start: 0.7476 (ppp) cc_final: 0.7001 (ppp) REVERT: D 139 MET cc_start: 0.9820 (OUTLIER) cc_final: 0.9599 (pmm) REVERT: D 144 PHE cc_start: 0.9690 (t80) cc_final: 0.9413 (t80) outliers start: 31 outliers final: 18 residues processed: 132 average time/residue: 0.0932 time to fit residues: 18.2976 Evaluate side-chains 128 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 C residue 249 TYR 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 139 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 0.0040 chunk 83 optimal weight: 40.0000 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.076431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.056542 restraints weight = 113120.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.057755 restraints weight = 89293.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.058642 restraints weight = 75411.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.059275 restraints weight = 66564.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.059736 restraints weight = 60841.435| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13128 Z= 0.137 Angle : 0.716 13.277 18120 Z= 0.367 Chirality : 0.045 0.295 2074 Planarity : 0.004 0.051 2020 Dihedral : 22.057 88.220 2439 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 2.05 % Allowed : 19.59 % Favored : 78.36 % 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: -1.28 (0.22), residues: 1385 helix: -0.05 (0.24), residues: 448 sheet: -0.79 (0.29), residues: 308 loop : -1.40 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 53 TYR 0.020 0.002 TYR A 408 PHE 0.046 0.002 PHE B 214 TRP 0.012 0.001 TRP A 624 HIS 0.005 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (13125) covalent geometry : angle 0.71587 / 0.37 (18114) SS BOND : bond 0.00357 / 0.19 ( 3) SS BOND : angle 0.70355 / 0.50 ( 6) hydrogen bonds : bond 0.05009 / 3.21 ( 509) hydrogen bonds : angle 5.71973 / 3.98 ( 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 131 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.441 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: 0.9385 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: A 946 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.9041 (p90) REVERT: A 961 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9295 (mt) REVERT: B 28 TRP cc_start: 0.6569 (OUTLIER) cc_final: 0.6181 (m-90) REVERT: B 211 TYR cc_start: 0.9651 (m-80) cc_final: 0.9437 (m-80) REVERT: B 229 MET cc_start: 0.8363 (mmm) cc_final: 0.7699 (ttt) REVERT: B 239 TYR cc_start: 0.9210 (m-80) cc_final: 0.8935 (m-80) REVERT: C 28 TRP cc_start: 0.9191 (t-100) cc_final: 0.8425 (t-100) REVERT: C 40 MET cc_start: 0.8046 (tpp) cc_final: 0.7707 (tpp) REVERT: C 68 MET cc_start: 0.8439 (tpt) cc_final: 0.8147 (tpp) REVERT: C 72 LEU cc_start: 0.8894 (mm) cc_final: 0.8636 (mm) REVERT: C 75 MET cc_start: 0.9184 (mmm) cc_final: 0.8926 (mmm) REVERT: C 116 MET cc_start: 0.7458 (tpt) cc_final: 0.6646 (tpt) REVERT: C 144 PHE cc_start: 0.9371 (t80) cc_final: 0.8996 (t80) REVERT: C 229 MET cc_start: 0.6287 (mmm) cc_final: 0.5738 (mmm) REVERT: D 2 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7215 (t80) REVERT: D 40 MET cc_start: 0.5232 (tpp) cc_final: 0.4989 (tpp) REVERT: D 119 MET cc_start: 0.7478 (ppp) cc_final: 0.7061 (ppp) REVERT: D 139 MET cc_start: 0.9828 (OUTLIER) cc_final: 0.9614 (pmm) REVERT: D 144 PHE cc_start: 0.9696 (t80) cc_final: 0.9415 (t80) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.0913 time to fit residues: 16.3182 Evaluate side-chains 128 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 HIS 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 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP 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 C residue 249 TYR 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 139 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 0.0970 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 142 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.076372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.056470 restraints weight = 113533.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.057674 restraints weight = 89966.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.058544 restraints weight = 76176.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.059183 restraints weight = 67399.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.059573 restraints weight = 61496.489| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13128 Z= 0.143 Angle : 0.746 14.153 18120 Z= 0.379 Chirality : 0.045 0.309 2074 Planarity : 0.004 0.052 2020 Dihedral : 22.013 88.127 2439 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.57 % Favored : 93.21 % Rotamer: Outliers : 2.30 % Allowed : 19.92 % Favored : 77.79 % 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: -1.40 (0.22), residues: 1385 helix: -0.14 (0.24), residues: 449 sheet: -0.93 (0.28), residues: 326 loop : -1.43 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.023 0.002 TYR A 374 PHE 0.069 0.002 PHE A 407 TRP 0.023 0.002 TRP A 664 HIS 0.013 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (13125) covalent geometry : angle 0.74579 / 0.38 (18114) SS BOND : bond 0.00225 / 0.12 ( 3) SS BOND : angle 0.54732 / 0.44 ( 6) hydrogen bonds : bond 0.04960 / 3.17 ( 509) hydrogen bonds : angle 5.70467 / 3.95 ( 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 133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.420 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: 0.9386 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: A 946 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.9032 (p90) REVERT: A 961 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9301 (mt) REVERT: B 28 TRP cc_start: 0.6558 (OUTLIER) cc_final: 0.6166 (m-90) REVERT: B 211 TYR cc_start: 0.9649 (m-80) cc_final: 0.9440 (m-80) REVERT: B 229 MET cc_start: 0.8434 (mmm) cc_final: 0.7856 (ttt) REVERT: B 239 TYR cc_start: 0.9202 (m-80) cc_final: 0.8948 (m-80) REVERT: C 28 TRP cc_start: 0.9195 (t-100) cc_final: 0.8417 (t-100) REVERT: C 40 MET cc_start: 0.8019 (tpp) cc_final: 0.7716 (tpp) REVERT: C 68 MET cc_start: 0.8415 (tpt) cc_final: 0.8131 (tpp) REVERT: C 72 LEU cc_start: 0.8900 (mm) cc_final: 0.8644 (mm) REVERT: C 75 MET cc_start: 0.9169 (mmm) cc_final: 0.8910 (mmm) REVERT: C 116 MET cc_start: 0.7477 (tpt) cc_final: 0.6666 (tpt) REVERT: C 144 PHE cc_start: 0.9375 (t80) cc_final: 0.9007 (t80) REVERT: C 229 MET cc_start: 0.6558 (mmm) cc_final: 0.5881 (mmp) REVERT: D 2 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7171 (t80) REVERT: D 40 MET cc_start: 0.5279 (tpp) cc_final: 0.5027 (tpp) REVERT: D 68 MET cc_start: 0.9216 (tmm) cc_final: 0.8734 (tmm) REVERT: D 119 MET cc_start: 0.7383 (ppp) cc_final: 0.6837 (ppp) REVERT: D 139 MET cc_start: 0.9829 (OUTLIER) cc_final: 0.9615 (pmm) REVERT: D 144 PHE cc_start: 0.9697 (t80) cc_final: 0.9400 (t80) outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.0900 time to fit residues: 16.1014 Evaluate side-chains 127 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 249 TYR 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 139 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.073290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.053108 restraints weight = 110678.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.054284 restraints weight = 87817.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.055100 restraints weight = 74458.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.055675 restraints weight = 66147.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.056070 restraints weight = 60889.616| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13128 Z= 0.178 Angle : 0.767 13.569 18120 Z= 0.393 Chirality : 0.045 0.235 2074 Planarity : 0.004 0.049 2020 Dihedral : 22.043 87.313 2439 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 2.05 % Allowed : 20.16 % Favored : 77.79 % 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: -1.53 (0.22), residues: 1385 helix: -0.29 (0.24), residues: 450 sheet: -1.07 (0.28), residues: 318 loop : -1.43 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 860 TYR 0.036 0.003 TYR A 408 PHE 0.068 0.003 PHE A 407 TRP 0.021 0.002 TRP A 664 HIS 0.010 0.002 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (13125) covalent geometry : angle 0.76661 / 0.39 (18114) SS BOND : bond 0.00510 / 0.27 ( 3) SS BOND : angle 1.04363 / 0.69 ( 6) hydrogen bonds : bond 0.05906 / 3.68 ( 509) hydrogen bonds : angle 5.85805 / 4.05 ( 1357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.43 seconds wall clock time: 52 minutes 21.80 seconds (3141.80 seconds total)