Starting phenix.real_space_refine on Thu Sep 18 00:37:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cma_45745/09_2025/9cma_45745.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 74 5.16 5 C 7755 2.51 5 N 2189 2.21 5 O 2622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.94, per 1000 atoms: 0.31 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: 1.08 Conformation dependent library (CDL) restraints added in 525.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.62 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: 2.66 Time building geometry restraints manager: 1.44 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=" CA GLU A 737 " pdb=" C GLU A 737 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.38e-02 5.25e+03 3.92e+00 bond pdb=" C GLN A 506 " pdb=" O GLN A 506 " ideal model delta sigma weight residual 1.236 1.225 0.012 7.30e-03 1.88e+04 2.60e+00 bond pdb=" CA ASN D 95 " pdb=" CB ASN D 95 " ideal model delta sigma weight residual 1.524 1.542 -0.017 1.22e-02 6.72e+03 1.98e+00 bond pdb=" CA PRO D 220 " pdb=" C PRO D 220 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.42e-02 4.96e+03 1.34e+00 bond pdb=" N ILE C 241 " pdb=" CA ILE C 241 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.21e+00 ... (remaining 13120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17370 1.60 - 3.21: 641 3.21 - 4.81: 75 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=" 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=" C THR A 588 " pdb=" CA THR A 588 " pdb=" CB THR A 588 " ideal model delta sigma weight residual 117.23 111.67 5.56 1.36e+00 5.41e-01 1.67e+01 angle pdb=" N SER A 508 " pdb=" CA SER A 508 " pdb=" C SER A 508 " ideal model delta sigma weight residual 114.56 109.38 5.18 1.27e+00 6.20e-01 1.67e+01 angle pdb=" N ASP B 94 " pdb=" CA ASP B 94 " pdb=" C ASP B 94 " ideal model delta sigma weight residual 108.31 114.11 -5.80 1.52e+00 4.33e-01 1.46e+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: 1649 0.049 - 0.098: 358 0.098 - 0.147: 65 0.147 - 0.196: 1 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=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.32e-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: 1.900 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.003 0.028 13128 Z= 0.166 Angle : 0.715 8.024 18120 Z= 0.425 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00322 (13125) covalent geometry : angle 0.71484 (18114) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.04745 ( 6) hydrogen bonds : bond 0.30393 ( 509) hydrogen bonds : angle 9.89567 ( 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 : 0.469 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: 0.1410 time to fit residues: 29.9241 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 : 0.489 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 650 HIS A 696 GLN A 716 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 929 GLN A 970 HIS ** 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 = 0.4161 r_free = 0.4161 target = 0.078665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.059295 restraints weight = 110475.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.060603 restraints weight = 86588.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.061436 restraints weight = 72335.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.062191 restraints weight = 63588.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.062686 restraints weight = 57523.857| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13128 Z= 0.183 Angle : 0.703 7.642 18120 Z= 0.380 Chirality : 0.044 0.157 2074 Planarity : 0.005 0.050 2020 Dihedral : 21.886 89.771 2439 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 0.90 % Allowed : 8.93 % Favored : 90.16 % 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 aren not related in a simple way. whole: -1.40 (0.22), residues: 1385 helix: -0.14 (0.23), residues: 440 sheet: -0.97 (0.30), residues: 297 loop : -1.39 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 721 TYR 0.020 0.003 TYR A 747 PHE 0.028 0.002 PHE D 144 TRP 0.011 0.002 TRP C 28 HIS 0.008 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00382 (13125) covalent geometry : angle 0.70324 (18114) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.06789 ( 6) hydrogen bonds : bond 0.06763 ( 509) hydrogen bonds : angle 6.73241 ( 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 138 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.474 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: A 988 MET cc_start: 0.8933 (ttt) cc_final: 0.8598 (ttm) REVERT: B 75 MET cc_start: 0.8375 (mmp) cc_final: 0.8066 (mmp) REVERT: B 229 MET cc_start: 0.7670 (tpt) cc_final: 0.7188 (tpp) REVERT: B 239 TYR cc_start: 0.9345 (m-80) cc_final: 0.8927 (m-80) REVERT: C 23 ILE cc_start: 0.4771 (mm) cc_final: 0.3925 (mm) REVERT: C 68 MET cc_start: 0.8308 (tpt) cc_final: 0.7938 (tpp) REVERT: C 72 LEU cc_start: 0.8729 (mm) cc_final: 0.8454 (mm) REVERT: C 116 MET cc_start: 0.7175 (tpt) cc_final: 0.6508 (tpt) REVERT: C 144 PHE cc_start: 0.9411 (t80) cc_final: 0.9047 (t80) REVERT: C 169 PHE cc_start: 0.9447 (m-80) cc_final: 0.9206 (m-80) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 0.1371 time to fit residues: 25.2902 Evaluate side-chains 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 605 TYR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 ASN A 644 HIS ** 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 B 213 ASN C 44 HIS ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.073703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054254 restraints weight = 112596.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.055464 restraints weight = 88150.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.056334 restraints weight = 73889.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.056905 restraints weight = 64716.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.057417 restraints weight = 58894.017| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13128 Z= 0.232 Angle : 0.748 11.075 18120 Z= 0.397 Chirality : 0.045 0.247 2074 Planarity : 0.005 0.043 2020 Dihedral : 22.026 84.959 2439 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.42 % Rotamer: Outliers : 1.72 % Allowed : 13.11 % Favored : 85.16 % 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 aren not related in a simple way. whole: -1.51 (0.22), residues: 1385 helix: -0.33 (0.23), residues: 437 sheet: -0.86 (0.31), residues: 274 loop : -1.46 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 721 TYR 0.025 0.003 TYR D 250 PHE 0.035 0.003 PHE B 214 TRP 0.014 0.002 TRP A 624 HIS 0.010 0.002 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00496 (13125) covalent geometry : angle 0.74830 (18114) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.05634 ( 6) hydrogen bonds : bond 0.07201 ( 509) hydrogen bonds : angle 6.44085 ( 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 135 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.522 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 988 MET cc_start: 0.8844 (ttt) cc_final: 0.8498 (ttt) REVERT: B 75 MET cc_start: 0.8623 (mmp) cc_final: 0.8364 (mmp) REVERT: B 229 MET cc_start: 0.7853 (tpt) cc_final: 0.7490 (tpp) REVERT: B 239 TYR cc_start: 0.9275 (m-80) cc_final: 0.8877 (m-80) REVERT: C 68 MET cc_start: 0.8436 (tpt) cc_final: 0.8073 (tpp) REVERT: C 144 PHE cc_start: 0.9409 (t80) cc_final: 0.9083 (t80) REVERT: D 139 MET cc_start: 0.9795 (OUTLIER) cc_final: 0.9594 (pmm) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.1326 time to fit residues: 23.4765 Evaluate side-chains 112 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain A residue 468 VAL 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 B residue 19 LEU 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: 7.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 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 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.076822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.056627 restraints weight = 113038.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.057917 restraints weight = 89474.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.058846 restraints weight = 75292.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.059518 restraints weight = 66118.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.059962 restraints weight = 60048.018| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13128 Z= 0.144 Angle : 0.668 11.395 18120 Z= 0.348 Chirality : 0.042 0.202 2074 Planarity : 0.004 0.069 2020 Dihedral : 21.912 86.843 2439 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.21 % Favored : 93.57 % Rotamer: Outliers : 1.56 % Allowed : 15.49 % Favored : 82.95 % 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 aren not related in a simple way. whole: -1.36 (0.22), residues: 1385 helix: -0.18 (0.23), residues: 449 sheet: -0.90 (0.28), residues: 320 loop : -1.35 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 547 TYR 0.016 0.002 TYR D 114 PHE 0.039 0.002 PHE B 214 TRP 0.015 0.002 TRP B 28 HIS 0.007 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00307 (13125) covalent geometry : angle 0.66798 (18114) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.76065 ( 6) hydrogen bonds : bond 0.04942 ( 509) hydrogen bonds : angle 5.92166 ( 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 139 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.465 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 448 GLU cc_start: 0.9240 (tp30) cc_final: 0.8942 (mm-30) REVERT: A 582 MET cc_start: 0.7480 (ptt) cc_final: 0.7185 (ptp) REVERT: A 628 LYS cc_start: 0.9560 (pttm) cc_final: 0.9347 (ptpp) REVERT: A 988 MET cc_start: 0.8995 (ttt) cc_final: 0.8739 (ttt) REVERT: B 28 TRP cc_start: 0.7024 (m-10) cc_final: 0.6652 (m-90) REVERT: B 75 MET cc_start: 0.8739 (mmp) cc_final: 0.8471 (mmp) REVERT: B 239 TYR cc_start: 0.9210 (m-80) cc_final: 0.8879 (m-80) REVERT: C 28 TRP cc_start: 0.9138 (t-100) cc_final: 0.8374 (t-100) REVERT: C 68 MET cc_start: 0.8409 (tpt) cc_final: 0.8149 (tpp) REVERT: C 72 LEU cc_start: 0.8888 (mm) cc_final: 0.8613 (mm) REVERT: C 116 MET cc_start: 0.7482 (tpt) cc_final: 0.6790 (tpt) REVERT: C 144 PHE cc_start: 0.9418 (t80) cc_final: 0.9073 (t80) REVERT: C 229 MET cc_start: 0.6671 (mmm) cc_final: 0.6418 (mmm) REVERT: D 2 PHE cc_start: 0.8073 (t80) cc_final: 0.7205 (t80) REVERT: D 40 MET cc_start: 0.5197 (tpp) cc_final: 0.4921 (tpp) REVERT: D 61 ARG cc_start: 0.9349 (ttp80) cc_final: 0.9114 (ttp80) REVERT: D 119 MET cc_start: 0.7191 (ppp) cc_final: 0.6216 (pmm) REVERT: D 139 MET cc_start: 0.9820 (ppp) cc_final: 0.9497 (pmm) REVERT: D 144 PHE cc_start: 0.9628 (t80) cc_final: 0.9134 (t80) REVERT: D 229 MET cc_start: 0.7551 (tpt) cc_final: 0.7121 (mpp) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 0.1348 time to fit residues: 24.6777 Evaluate side-chains 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 945 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 92 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 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 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.075200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.055424 restraints weight = 115407.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.056600 restraints weight = 91647.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.057438 restraints weight = 77831.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058047 restraints weight = 68971.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.058510 restraints weight = 63040.354| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13128 Z= 0.167 Angle : 0.678 10.020 18120 Z= 0.355 Chirality : 0.043 0.196 2074 Planarity : 0.004 0.050 2020 Dihedral : 21.804 86.808 2439 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 2.79 % Allowed : 16.97 % Favored : 80.25 % 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 aren not related in a simple way. whole: -1.39 (0.22), residues: 1385 helix: -0.18 (0.24), residues: 442 sheet: -0.94 (0.29), residues: 316 loop : -1.36 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 53 TYR 0.030 0.002 TYR A 408 PHE 0.058 0.002 PHE A 407 TRP 0.010 0.002 TRP A 624 HIS 0.006 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00362 (13125) covalent geometry : angle 0.67755 (18114) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.94648 ( 6) hydrogen bonds : bond 0.05362 ( 509) hydrogen bonds : angle 5.82146 ( 1357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: A 582 MET cc_start: 0.7612 (ptt) cc_final: 0.7381 (ptt) REVERT: B 28 TRP cc_start: 0.7025 (OUTLIER) cc_final: 0.6332 (m-90) REVERT: B 75 MET cc_start: 0.8736 (mmp) cc_final: 0.8516 (mmp) REVERT: B 199 MET cc_start: 0.8021 (mmm) cc_final: 0.7533 (tpp) REVERT: B 211 TYR cc_start: 0.9660 (m-80) cc_final: 0.9458 (m-80) REVERT: B 239 TYR cc_start: 0.9218 (m-80) cc_final: 0.8891 (m-80) REVERT: C 28 TRP cc_start: 0.9152 (t-100) cc_final: 0.8403 (t-100) REVERT: C 68 MET cc_start: 0.8488 (tpt) cc_final: 0.8205 (tpp) REVERT: C 72 LEU cc_start: 0.8897 (mm) cc_final: 0.8613 (mm) REVERT: C 116 MET cc_start: 0.7503 (tpt) cc_final: 0.6760 (tpt) REVERT: C 144 PHE cc_start: 0.9412 (t80) cc_final: 0.9014 (t80) REVERT: D 2 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7054 (t80) REVERT: D 40 MET cc_start: 0.5169 (tpp) cc_final: 0.4907 (tpp) REVERT: D 61 ARG cc_start: 0.9344 (ttp80) cc_final: 0.9104 (ttp80) REVERT: D 119 MET cc_start: 0.7343 (ppp) cc_final: 0.6601 (pmm) REVERT: D 139 MET cc_start: 0.9808 (ppp) cc_final: 0.9534 (pmm) REVERT: D 144 PHE cc_start: 0.9687 (t80) cc_final: 0.9205 (t80) outliers start: 34 outliers final: 18 residues processed: 133 average time/residue: 0.1252 time to fit residues: 23.7127 Evaluate side-chains 124 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 484 PHE 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 772 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP 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 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** 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** C 246 HIS D 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.070665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.051527 restraints weight = 118490.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.052664 restraints weight = 93480.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.053451 restraints weight = 78992.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.053968 restraints weight = 69936.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.054410 restraints weight = 64154.769| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13128 Z= 0.255 Angle : 0.766 11.218 18120 Z= 0.407 Chirality : 0.045 0.190 2074 Planarity : 0.006 0.125 2020 Dihedral : 21.999 85.423 2439 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.01 % Favored : 91.77 % Rotamer: Outliers : 3.28 % Allowed : 17.95 % Favored : 78.77 % 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 aren not related in a simple way. whole: -1.69 (0.22), residues: 1385 helix: -0.52 (0.23), residues: 439 sheet: -0.99 (0.27), residues: 339 loop : -1.54 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.038 0.003 TYR A 408 PHE 0.058 0.003 PHE A 407 TRP 0.015 0.003 TRP B 28 HIS 0.012 0.002 HIS A 716 Details of bonding type rmsd covalent geometry : bond 0.00541 (13125) covalent geometry : angle 0.76540 (18114) SS BOND : bond 0.00460 ( 3) SS BOND : angle 1.15119 ( 6) hydrogen bonds : bond 0.07102 ( 509) hydrogen bonds : angle 6.20815 ( 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 143 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.480 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 449 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: A 484 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8936 (m-80) REVERT: A 582 MET cc_start: 0.7746 (ptt) cc_final: 0.7476 (ptt) REVERT: A 988 MET cc_start: 0.8945 (ttm) cc_final: 0.8604 (tmm) REVERT: B 199 MET cc_start: 0.7820 (mmm) cc_final: 0.7435 (tpp) REVERT: B 211 TYR cc_start: 0.9656 (m-80) cc_final: 0.9406 (m-80) REVERT: B 229 MET cc_start: 0.8467 (mmm) cc_final: 0.7712 (ttt) REVERT: B 239 TYR cc_start: 0.9268 (m-80) cc_final: 0.8959 (m-80) REVERT: C 28 TRP cc_start: 0.9210 (t-100) cc_final: 0.8645 (t-100) REVERT: C 116 MET cc_start: 0.7720 (tpt) cc_final: 0.6949 (tpt) REVERT: C 121 LEU cc_start: 0.3637 (OUTLIER) cc_final: 0.2874 (mm) REVERT: C 144 PHE cc_start: 0.9437 (t80) cc_final: 0.9116 (t80) REVERT: D 2 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7265 (t80) REVERT: D 40 MET cc_start: 0.5244 (tpp) cc_final: 0.4951 (tpp) REVERT: D 61 ARG cc_start: 0.9269 (ttp80) cc_final: 0.8932 (ttp80) REVERT: D 119 MET cc_start: 0.7638 (ppp) cc_final: 0.6989 (pmm) REVERT: D 139 MET cc_start: 0.9822 (ppp) cc_final: 0.9536 (pmm) REVERT: D 144 PHE cc_start: 0.9751 (t80) cc_final: 0.9294 (t80) outliers start: 40 outliers final: 24 residues processed: 132 average time/residue: 0.1332 time to fit residues: 24.7741 Evaluate side-chains 128 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 GLU 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 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 637 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 953 HIS Chi-restraints excluded: chain A residue 976 VAL 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 B residue 133 TYR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 121 LEU 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 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** 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 = 0.4025 r_free = 0.4025 target = 0.073367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.053792 restraints weight = 112679.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.055020 restraints weight = 88312.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.055886 restraints weight = 74171.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.056458 restraints weight = 65173.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.056942 restraints weight = 59505.423| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13128 Z= 0.149 Angle : 0.699 12.201 18120 Z= 0.360 Chirality : 0.044 0.296 2074 Planarity : 0.004 0.052 2020 Dihedral : 21.898 85.946 2439 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.64 % Favored : 93.14 % Rotamer: Outliers : 2.13 % Allowed : 20.41 % Favored : 77.46 % 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 aren not related in a simple way. whole: -1.49 (0.22), residues: 1385 helix: -0.24 (0.24), residues: 451 sheet: -0.99 (0.28), residues: 337 loop : -1.45 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 860 TYR 0.038 0.002 TYR A 408 PHE 0.047 0.002 PHE A 407 TRP 0.012 0.001 TRP B 28 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00325 (13125) covalent geometry : angle 0.69915 (18114) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.97429 ( 6) hydrogen bonds : bond 0.04932 ( 509) hydrogen bonds : angle 5.70705 ( 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 134 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: A 526 ARG cc_start: 0.8839 (mtt180) cc_final: 0.8457 (mtt180) REVERT: A 582 MET cc_start: 0.7754 (ptt) cc_final: 0.7535 (ptt) REVERT: A 834 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2053 (tt0) REVERT: A 853 ASP cc_start: 0.8283 (p0) cc_final: 0.7355 (m-30) REVERT: B 28 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6384 (m-90) REVERT: B 199 MET cc_start: 0.7658 (mmm) cc_final: 0.7323 (tpp) REVERT: B 229 MET cc_start: 0.8436 (mmm) cc_final: 0.7725 (ttt) REVERT: B 239 TYR cc_start: 0.9216 (m-80) cc_final: 0.8958 (m-80) REVERT: C 28 TRP cc_start: 0.9317 (t-100) cc_final: 0.8541 (t-100) REVERT: C 75 MET cc_start: 0.9352 (mmm) cc_final: 0.9056 (mmm) REVERT: C 116 MET cc_start: 0.7513 (tpt) cc_final: 0.6650 (tpt) REVERT: C 144 PHE cc_start: 0.9488 (t80) cc_final: 0.9084 (t80) REVERT: C 229 MET cc_start: 0.6976 (mmm) cc_final: 0.6318 (mmp) REVERT: D 2 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7066 (t80) REVERT: D 61 ARG cc_start: 0.9278 (ttp80) cc_final: 0.8902 (ttp80) REVERT: D 119 MET cc_start: 0.7623 (ppp) cc_final: 0.7068 (pmm) REVERT: D 139 MET cc_start: 0.9830 (ppp) cc_final: 0.9552 (pmm) REVERT: D 144 PHE cc_start: 0.9724 (t80) cc_final: 0.9275 (t80) outliers start: 26 outliers final: 18 residues processed: 125 average time/residue: 0.1288 time to fit residues: 22.9953 Evaluate side-chains 123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 760 LYS Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 953 HIS 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 2 PHE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.071267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.052101 restraints weight = 115923.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.053253 restraints weight = 90143.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.054073 restraints weight = 75709.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.054605 restraints weight = 66597.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.055050 restraints weight = 60985.800| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13128 Z= 0.192 Angle : 0.725 13.046 18120 Z= 0.378 Chirality : 0.044 0.218 2074 Planarity : 0.005 0.056 2020 Dihedral : 21.888 84.700 2439 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 2.70 % Allowed : 20.57 % Favored : 76.72 % 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 aren not related in a simple way. whole: -1.60 (0.22), residues: 1385 helix: -0.27 (0.24), residues: 453 sheet: -1.14 (0.28), residues: 327 loop : -1.53 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 53 TYR 0.036 0.002 TYR A 408 PHE 0.043 0.002 PHE B 214 TRP 0.013 0.002 TRP B 28 HIS 0.008 0.002 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00413 (13125) covalent geometry : angle 0.72466 (18114) SS BOND : bond 0.00397 ( 3) SS BOND : angle 1.01259 ( 6) hydrogen bonds : bond 0.05843 ( 509) hydrogen bonds : angle 5.90363 ( 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 137 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: A 484 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8984 (m-80) REVERT: A 834 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.2194 (tt0) REVERT: A 988 MET cc_start: 0.8940 (ttt) cc_final: 0.8716 (tmm) REVERT: B 229 MET cc_start: 0.8514 (mmm) cc_final: 0.7805 (ttt) REVERT: B 239 TYR cc_start: 0.9230 (m-80) cc_final: 0.8957 (m-80) REVERT: C 28 TRP cc_start: 0.9280 (t-100) cc_final: 0.8553 (t-100) REVERT: C 75 MET cc_start: 0.9377 (mmm) cc_final: 0.8944 (mmp) REVERT: C 116 MET cc_start: 0.7626 (tpt) cc_final: 0.6696 (tpt) REVERT: C 144 PHE cc_start: 0.9482 (t80) cc_final: 0.9100 (t80) REVERT: C 229 MET cc_start: 0.7190 (mmm) cc_final: 0.6364 (mmm) REVERT: C 235 LEU cc_start: 0.9507 (tp) cc_final: 0.8909 (pp) REVERT: D 2 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7235 (t80) REVERT: D 40 MET cc_start: 0.5251 (tpp) cc_final: 0.4946 (tpp) REVERT: D 61 ARG cc_start: 0.9259 (ttp80) cc_final: 0.9030 (ttp80) REVERT: D 68 MET cc_start: 0.9234 (tmm) cc_final: 0.8926 (tmm) REVERT: D 119 MET cc_start: 0.7626 (ppp) cc_final: 0.7057 (pmm) REVERT: D 139 MET cc_start: 0.9835 (ppp) cc_final: 0.9558 (pmm) REVERT: D 144 PHE cc_start: 0.9754 (t80) cc_final: 0.9309 (t80) outliers start: 33 outliers final: 24 residues processed: 126 average time/residue: 0.1208 time to fit residues: 22.0594 Evaluate side-chains 127 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 449 GLU Chi-restraints excluded: chain A residue 450 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 760 LYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 247 LEU 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 2 PHE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 128 optimal weight: 0.0970 chunk 12 optimal weight: 6.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS A 623 ASN ** A 717 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.073448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.054141 restraints weight = 111908.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.055359 restraints weight = 86611.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.056210 restraints weight = 72381.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.056849 restraints weight = 63598.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.057236 restraints weight = 57685.225| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13128 Z= 0.137 Angle : 0.716 13.036 18120 Z= 0.364 Chirality : 0.044 0.249 2074 Planarity : 0.004 0.056 2020 Dihedral : 21.807 85.246 2439 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.63 % Favored : 94.15 % Rotamer: Outliers : 2.21 % Allowed : 21.39 % Favored : 76.39 % 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 aren not related in a simple way. whole: -1.39 (0.22), residues: 1385 helix: -0.08 (0.24), residues: 452 sheet: -0.97 (0.28), residues: 338 loop : -1.46 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 53 TYR 0.049 0.002 TYR A 408 PHE 0.045 0.002 PHE B 214 TRP 0.010 0.001 TRP B 28 HIS 0.013 0.001 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00298 (13125) covalent geometry : angle 0.71503 (18114) SS BOND : bond 0.00161 ( 3) SS BOND : angle 1.71122 ( 6) hydrogen bonds : bond 0.04709 ( 509) hydrogen bonds : angle 5.60139 ( 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 133 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8940 (m-80) REVERT: A 526 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8478 (mtt180) REVERT: A 834 GLU cc_start: 0.3491 (OUTLIER) cc_final: 0.2166 (tt0) REVERT: A 853 ASP cc_start: 0.8446 (p0) cc_final: 0.7500 (m-30) REVERT: B 28 TRP cc_start: 0.6760 (OUTLIER) cc_final: 0.6369 (m-90) REVERT: B 229 MET cc_start: 0.8542 (mmm) cc_final: 0.7870 (ttt) REVERT: C 28 TRP cc_start: 0.9253 (t-100) cc_final: 0.8506 (t-100) REVERT: C 75 MET cc_start: 0.9365 (mmm) cc_final: 0.8954 (mmp) REVERT: C 116 MET cc_start: 0.7514 (tpt) cc_final: 0.6572 (tpt) REVERT: C 121 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2602 (mm) REVERT: C 144 PHE cc_start: 0.9480 (t80) cc_final: 0.9124 (t80) REVERT: C 229 MET cc_start: 0.7433 (mmm) cc_final: 0.6575 (mmp) REVERT: C 235 LEU cc_start: 0.9467 (tp) cc_final: 0.8858 (pp) REVERT: D 2 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7026 (t80) REVERT: D 40 MET cc_start: 0.5376 (tpp) cc_final: 0.5073 (tpp) REVERT: D 61 ARG cc_start: 0.9260 (ttp80) cc_final: 0.9009 (ttp80) REVERT: D 68 MET cc_start: 0.9370 (tmm) cc_final: 0.9114 (tmm) REVERT: D 119 MET cc_start: 0.7537 (ppp) cc_final: 0.7002 (pmm) REVERT: D 139 MET cc_start: 0.9831 (ppp) cc_final: 0.9545 (pmm) REVERT: D 144 PHE cc_start: 0.9717 (t80) cc_final: 0.9276 (t80) REVERT: D 229 MET cc_start: 0.7741 (tpt) cc_final: 0.6934 (tpp) outliers start: 27 outliers final: 19 residues processed: 124 average time/residue: 0.1132 time to fit residues: 20.5867 Evaluate side-chains 124 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 760 LYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain C residue 121 LEU 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 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 10.0000 chunk 7 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 overall best weight: 6.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.068729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.050123 restraints weight = 118386.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.051213 restraints weight = 92561.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.051979 restraints weight = 78104.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.052540 restraints weight = 69050.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.052806 restraints weight = 63194.417| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13128 Z= 0.240 Angle : 0.784 13.599 18120 Z= 0.407 Chirality : 0.046 0.236 2074 Planarity : 0.005 0.065 2020 Dihedral : 21.970 83.665 2439 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.58 % Favored : 92.20 % Rotamer: Outliers : 2.70 % Allowed : 21.07 % Favored : 76.23 % 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 aren not related in a simple way. whole: -1.71 (0.22), residues: 1385 helix: -0.38 (0.24), residues: 450 sheet: -1.08 (0.28), residues: 335 loop : -1.65 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 547 TYR 0.040 0.003 TYR A 408 PHE 0.049 0.003 PHE B 214 TRP 0.014 0.002 TRP B 28 HIS 0.017 0.002 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00515 (13125) covalent geometry : angle 0.78389 (18114) SS BOND : bond 0.00501 ( 3) SS BOND : angle 1.05528 ( 6) hydrogen bonds : bond 0.06993 ( 509) hydrogen bonds : angle 6.00602 ( 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 129 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 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: A 449 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: A 834 GLU cc_start: 0.4269 (OUTLIER) cc_final: 0.2736 (tt0) REVERT: A 988 MET cc_start: 0.8857 (ttt) cc_final: 0.8331 (pmm) REVERT: B 199 MET cc_start: 0.7819 (mmm) cc_final: 0.7201 (tpt) REVERT: B 229 MET cc_start: 0.8514 (mmm) cc_final: 0.7863 (ttt) REVERT: C 28 TRP cc_start: 0.9251 (t-100) cc_final: 0.8572 (t-100) REVERT: C 121 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.2945 (mm) REVERT: C 144 PHE cc_start: 0.9498 (t80) cc_final: 0.9146 (t80) REVERT: C 229 MET cc_start: 0.7574 (mmm) cc_final: 0.7038 (mmm) REVERT: C 235 LEU cc_start: 0.9510 (tp) cc_final: 0.8957 (pp) REVERT: D 2 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7350 (t80) REVERT: D 40 MET cc_start: 0.5306 (tpp) cc_final: 0.4998 (tpp) REVERT: D 115 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: D 119 MET cc_start: 0.7813 (ppp) cc_final: 0.7333 (pmm) REVERT: D 139 MET cc_start: 0.9835 (ppp) cc_final: 0.9564 (pmm) REVERT: D 144 PHE cc_start: 0.9760 (t80) cc_final: 0.9326 (t80) outliers start: 33 outliers final: 26 residues processed: 118 average time/residue: 0.1183 time to fit residues: 20.4335 Evaluate side-chains 123 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 449 GLU Chi-restraints excluded: chain A residue 450 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 680 LEU Chi-restraints excluded: chain A residue 760 LYS Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 953 HIS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain C residue 121 LEU 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 2 PHE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 57 optimal weight: 0.0170 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS ** A 717 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.073039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.053670 restraints weight = 111835.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.054984 restraints weight = 85533.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.055896 restraints weight = 70780.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.056492 restraints weight = 61775.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.056982 restraints weight = 56018.800| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13128 Z= 0.135 Angle : 0.735 14.074 18120 Z= 0.370 Chirality : 0.044 0.246 2074 Planarity : 0.004 0.050 2020 Dihedral : 21.817 84.606 2439 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.56 % Favored : 94.22 % Rotamer: Outliers : 1.97 % Allowed : 21.97 % Favored : 76.07 % 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 aren not related in a simple way. whole: -1.42 (0.23), residues: 1385 helix: -0.08 (0.24), residues: 461 sheet: -0.98 (0.28), residues: 342 loop : -1.52 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 53 TYR 0.018 0.002 TYR A 408 PHE 0.044 0.002 PHE B 214 TRP 0.013 0.002 TRP A 847 HIS 0.008 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00292 (13125) covalent geometry : angle 0.73455 (18114) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.06404 ( 6) hydrogen bonds : bond 0.04794 ( 509) hydrogen bonds : angle 5.52955 ( 1357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.07 seconds wall clock time: 62 minutes 50.91 seconds (3770.91 seconds total)