Starting phenix.real_space_refine on Wed Jun 11 08:35:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cma_45745/06_2025/9cma_45745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cma_45745/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cma_45745/06_2025/9cma_45745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cma_45745/06_2025/9cma_45745.map" model { file = "/net/cci-nas-00/data/ceres_data/9cma_45745/06_2025/9cma_45745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cma_45745/06_2025/9cma_45745_neut.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.62, per 1000 atoms: 0.60 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.35 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: 5.15 Time building geometry restraints manager: 3.87 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- 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 : 22.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.002 TRP A 990 HIS 0.006 0.001 HIS A 485 PHE 0.019 0.002 PHE A 407 TYR 0.014 0.002 TYR D 60 ARG 0.008 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.30393 ( 509) hydrogen bonds : angle 9.89567 ( 1357) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.04745 ( 6) covalent geometry : bond 0.00322 (13125) covalent geometry : angle 0.71484 (18114) *********************** 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 : 1.379 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: 0.2980 time to fit residues: 62.9640 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN A 716 HIS ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 HIS A 929 GLN A 970 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.078622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.059292 restraints weight = 108401.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.060581 restraints weight = 85104.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.061486 restraints weight = 71156.031| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13128 Z= 0.191 Angle : 0.705 7.500 18120 Z= 0.381 Chirality : 0.044 0.155 2074 Planarity : 0.005 0.050 2020 Dihedral : 21.891 89.613 2439 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.79 % Favored : 93.00 % Rotamer: Outliers : 0.90 % Allowed : 9.10 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.22), residues: 1385 helix: -0.15 (0.23), residues: 442 sheet: -0.96 (0.30), residues: 297 loop : -1.40 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 624 HIS 0.009 0.001 HIS A 644 PHE 0.028 0.002 PHE D 144 TYR 0.020 0.002 TYR A 747 ARG 0.007 0.001 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.06639 ( 509) hydrogen bonds : angle 6.70566 ( 1357) SS BOND : bond 0.00381 ( 3) SS BOND : angle 1.04748 ( 6) covalent geometry : bond 0.00388 (13125) covalent geometry : angle 0.70529 (18114) *********************** 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 137 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.206 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 664 TRP cc_start: 0.7830 (t60) cc_final: 0.7354 (t60) REVERT: A 988 MET cc_start: 0.8919 (ttt) cc_final: 0.8595 (ttm) REVERT: B 75 MET cc_start: 0.8412 (mmp) cc_final: 0.8098 (mmp) REVERT: B 229 MET cc_start: 0.7725 (tpt) cc_final: 0.7175 (tpp) REVERT: B 239 TYR cc_start: 0.9289 (m-80) cc_final: 0.8894 (m-80) REVERT: C 23 ILE cc_start: 0.4825 (mm) cc_final: 0.3968 (mm) REVERT: C 68 MET cc_start: 0.8291 (tpt) cc_final: 0.7932 (tpp) REVERT: C 72 LEU cc_start: 0.8732 (mm) cc_final: 0.8445 (mm) REVERT: C 116 MET cc_start: 0.7096 (tpt) cc_final: 0.6424 (tpt) REVERT: C 144 PHE cc_start: 0.9397 (t80) cc_final: 0.9041 (t80) REVERT: C 169 PHE cc_start: 0.9430 (m-80) cc_final: 0.9196 (m-80) REVERT: D 119 MET cc_start: 0.7153 (ppp) cc_final: 0.6948 (ppp) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.2836 time to fit residues: 52.2178 Evaluate side-chains 120 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 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 121 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 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** B 213 ASN C 246 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.078382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.058738 restraints weight = 107937.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.060110 restraints weight = 82949.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.061076 restraints weight = 68609.556| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2364 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= 0.155 Angle : 0.663 9.595 18120 Z= 0.351 Chirality : 0.043 0.208 2074 Planarity : 0.004 0.044 2020 Dihedral : 21.784 88.669 2439 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 1.23 % Allowed : 12.30 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1385 helix: -0.02 (0.23), residues: 448 sheet: -0.79 (0.30), residues: 302 loop : -1.35 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 624 HIS 0.006 0.001 HIS A 485 PHE 0.035 0.002 PHE B 214 TYR 0.021 0.002 TYR D 250 ARG 0.009 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05616 ( 509) hydrogen bonds : angle 6.09395 ( 1357) SS BOND : bond 0.00316 ( 3) SS BOND : angle 0.83426 ( 6) covalent geometry : bond 0.00319 (13125) covalent geometry : angle 0.66277 (18114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.312 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 988 MET cc_start: 0.8821 (ttt) cc_final: 0.8390 (ttt) REVERT: B 75 MET cc_start: 0.8519 (mmp) cc_final: 0.8300 (mmp) REVERT: B 229 MET cc_start: 0.7810 (tpt) cc_final: 0.7381 (tpp) REVERT: B 239 TYR cc_start: 0.9203 (m-80) cc_final: 0.8876 (m-80) REVERT: C 23 ILE cc_start: 0.4650 (mm) cc_final: 0.3728 (mm) REVERT: C 28 TRP cc_start: 0.9087 (t-100) cc_final: 0.8346 (t-100) REVERT: C 68 MET cc_start: 0.8251 (tpt) cc_final: 0.7982 (tpp) REVERT: C 72 LEU cc_start: 0.8765 (mm) cc_final: 0.8474 (mm) REVERT: C 116 MET cc_start: 0.7181 (tpt) cc_final: 0.6430 (tpt) REVERT: C 144 PHE cc_start: 0.9390 (t80) cc_final: 0.9046 (t80) REVERT: D 119 MET cc_start: 0.7222 (ppp) cc_final: 0.6869 (ppp) REVERT: D 139 MET cc_start: 0.9790 (OUTLIER) cc_final: 0.9511 (pmm) REVERT: D 144 PHE cc_start: 0.9622 (t80) cc_final: 0.9421 (t80) outliers start: 15 outliers final: 6 residues processed: 125 average time/residue: 0.2951 time to fit residues: 52.6244 Evaluate side-chains 115 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 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 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 60 optimal weight: 50.0000 chunk 100 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.075620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.056344 restraints weight = 110760.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.057588 restraints weight = 86494.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.058460 restraints weight = 72322.801| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13128 Z= 0.189 Angle : 0.669 11.591 18120 Z= 0.354 Chirality : 0.043 0.204 2074 Planarity : 0.004 0.057 2020 Dihedral : 21.771 86.125 2439 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.64 % Favored : 93.14 % Rotamer: Outliers : 2.13 % Allowed : 13.44 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1385 helix: -0.14 (0.23), residues: 442 sheet: -0.99 (0.29), residues: 296 loop : -1.38 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 28 HIS 0.007 0.001 HIS A 485 PHE 0.052 0.002 PHE A 407 TYR 0.024 0.002 TYR D 250 ARG 0.005 0.001 ARG A 721 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 509) hydrogen bonds : angle 5.91495 ( 1357) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.10662 ( 6) covalent geometry : bond 0.00388 (13125) covalent geometry : angle 0.66868 (18114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.339 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 605 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (t80) REVERT: A 988 MET cc_start: 0.8950 (ttt) cc_final: 0.8620 (ttt) REVERT: B 1 MET cc_start: 0.9168 (tpp) cc_final: 0.8949 (tpp) REVERT: B 28 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.6483 (m-90) REVERT: B 75 MET cc_start: 0.8685 (mmp) cc_final: 0.8437 (mmp) REVERT: B 199 MET cc_start: 0.8052 (mmm) cc_final: 0.7541 (tpp) REVERT: B 229 MET cc_start: 0.7908 (tpt) cc_final: 0.7594 (tpp) REVERT: B 239 TYR cc_start: 0.9255 (m-80) cc_final: 0.8907 (m-80) REVERT: C 28 TRP cc_start: 0.9161 (t-100) cc_final: 0.8350 (t-100) REVERT: C 68 MET cc_start: 0.8422 (tpt) cc_final: 0.8166 (tpp) REVERT: C 72 LEU cc_start: 0.8848 (mm) cc_final: 0.8578 (mm) REVERT: C 144 PHE cc_start: 0.9388 (t80) cc_final: 0.9042 (t80) REVERT: D 40 MET cc_start: 0.5044 (tpp) cc_final: 0.4756 (tpp) REVERT: D 68 MET cc_start: 0.9160 (tmm) cc_final: 0.8949 (tmm) REVERT: D 119 MET cc_start: 0.7391 (ppp) cc_final: 0.7050 (ppp) REVERT: D 139 MET cc_start: 0.9800 (OUTLIER) cc_final: 0.9517 (pmm) REVERT: D 144 PHE cc_start: 0.9659 (t80) cc_final: 0.9414 (t80) REVERT: D 244 MET cc_start: 0.9279 (tpt) cc_final: 0.8765 (tpt) outliers start: 26 outliers final: 13 residues processed: 127 average time/residue: 0.2833 time to fit residues: 50.8335 Evaluate side-chains 122 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 591 ARG 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 637 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 940 LEU 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 D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 48 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 65 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 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 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.075751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.056334 restraints weight = 111774.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.057644 restraints weight = 85950.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.058603 restraints weight = 71119.620| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13128 Z= 0.149 Angle : 0.653 11.203 18120 Z= 0.340 Chirality : 0.042 0.215 2074 Planarity : 0.004 0.050 2020 Dihedral : 21.727 87.766 2439 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.43 % Favored : 93.36 % Rotamer: Outliers : 2.70 % Allowed : 14.92 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1385 helix: -0.11 (0.23), residues: 446 sheet: -0.72 (0.30), residues: 290 loop : -1.32 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 28 HIS 0.006 0.001 HIS A 485 PHE 0.049 0.002 PHE A 407 TYR 0.024 0.002 TYR D 250 ARG 0.005 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 509) hydrogen bonds : angle 5.68501 ( 1357) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.86663 ( 6) covalent geometry : bond 0.00321 (13125) covalent geometry : angle 0.65317 (18114) *********************** 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 149 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: A 717 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8790 (tt0) REVERT: A 988 MET cc_start: 0.8912 (ttt) cc_final: 0.8645 (ttt) REVERT: B 28 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6450 (m-90) REVERT: B 40 MET cc_start: 0.8935 (tmm) cc_final: 0.8707 (tpt) REVERT: B 75 MET cc_start: 0.8751 (mmp) cc_final: 0.8512 (mmp) REVERT: B 199 MET cc_start: 0.7929 (mmm) cc_final: 0.7494 (tpp) REVERT: B 239 TYR cc_start: 0.9170 (m-80) cc_final: 0.8847 (m-80) REVERT: C 28 TRP cc_start: 0.9076 (t-100) cc_final: 0.8337 (t-100) REVERT: C 40 MET cc_start: 0.7938 (tpp) cc_final: 0.7674 (tpp) REVERT: C 68 MET cc_start: 0.8392 (tpt) cc_final: 0.8136 (tpp) REVERT: C 72 LEU cc_start: 0.8886 (mm) cc_final: 0.8611 (mm) REVERT: C 116 MET cc_start: 0.7402 (tpt) cc_final: 0.6722 (tpt) REVERT: C 144 PHE cc_start: 0.9375 (t80) cc_final: 0.9012 (t80) REVERT: C 195 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (t) REVERT: C 229 MET cc_start: 0.6816 (mmm) cc_final: 0.6597 (mmm) REVERT: D 2 PHE cc_start: 0.8016 (t80) cc_final: 0.7193 (t80) REVERT: D 40 MET cc_start: 0.4932 (tpp) cc_final: 0.4644 (tpp) REVERT: D 119 MET cc_start: 0.7357 (ppp) cc_final: 0.7010 (ppp) REVERT: D 139 MET cc_start: 0.9815 (OUTLIER) cc_final: 0.9545 (pmm) REVERT: D 144 PHE cc_start: 0.9688 (t80) cc_final: 0.9415 (t80) outliers start: 33 outliers final: 14 residues processed: 139 average time/residue: 0.2783 time to fit residues: 55.1904 Evaluate side-chains 124 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 717 GLN Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 85 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- 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 639 ASN A 696 GLN ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN C 44 HIS D 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.071310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.051355 restraints weight = 114765.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.052467 restraints weight = 90591.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.053264 restraints weight = 76834.328| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13128 Z= 0.237 Angle : 0.756 14.844 18120 Z= 0.396 Chirality : 0.045 0.219 2074 Planarity : 0.005 0.074 2020 Dihedral : 21.842 86.428 2439 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.15 % Favored : 92.64 % Rotamer: Outliers : 2.62 % Allowed : 17.54 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1385 helix: -0.27 (0.24), residues: 435 sheet: -1.00 (0.28), residues: 320 loop : -1.46 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.009 0.002 HIS A 485 PHE 0.065 0.003 PHE A 407 TYR 0.033 0.003 TYR A 408 ARG 0.007 0.001 ARG A 969 Details of bonding type rmsd hydrogen bonds : bond 0.06898 ( 509) hydrogen bonds : angle 6.09480 ( 1357) SS BOND : bond 0.00426 ( 3) SS BOND : angle 1.07646 ( 6) covalent geometry : bond 0.00507 (13125) covalent geometry : angle 0.75635 (18114) *********************** 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 142 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: B 229 MET cc_start: 0.8459 (mmm) cc_final: 0.7633 (ttt) REVERT: B 239 TYR cc_start: 0.9230 (m-80) cc_final: 0.8884 (m-80) REVERT: C 28 TRP cc_start: 0.9205 (t-100) cc_final: 0.8446 (t-100) REVERT: C 68 MET cc_start: 0.8660 (tpt) cc_final: 0.8402 (tpp) REVERT: C 116 MET cc_start: 0.7777 (tpt) cc_final: 0.7018 (tpt) REVERT: C 144 PHE cc_start: 0.9381 (t80) cc_final: 0.8980 (t80) REVERT: C 195 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8497 (t) REVERT: D 2 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7431 (t80) REVERT: D 119 MET cc_start: 0.7676 (ppp) cc_final: 0.7201 (ppp) REVERT: D 139 MET cc_start: 0.9837 (OUTLIER) cc_final: 0.9579 (pmm) REVERT: D 144 PHE cc_start: 0.9708 (t80) cc_final: 0.9412 (t80) outliers start: 32 outliers final: 18 residues processed: 132 average time/residue: 0.2594 time to fit residues: 49.5928 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 : 1.296 ------------------------------------------------------------------------------- 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 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 B residue 19 LEU Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 169 PHE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 249 TYR Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 138 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 chunk 19 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.072707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.053319 restraints weight = 114403.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.054451 restraints weight = 90725.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.055232 restraints weight = 76998.215| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13128 Z= 0.188 Angle : 0.723 11.366 18120 Z= 0.373 Chirality : 0.044 0.259 2074 Planarity : 0.004 0.049 2020 Dihedral : 21.858 86.528 2439 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 19.51 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.22), residues: 1385 helix: -0.23 (0.24), residues: 445 sheet: -0.97 (0.28), residues: 316 loop : -1.47 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 28 HIS 0.007 0.001 HIS A 716 PHE 0.053 0.002 PHE A 407 TYR 0.049 0.002 TYR A 408 ARG 0.006 0.001 ARG B 61 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 509) hydrogen bonds : angle 5.81055 ( 1357) SS BOND : bond 0.00682 ( 3) SS BOND : angle 1.98565 ( 6) covalent geometry : bond 0.00401 (13125) covalent geometry : angle 0.72196 (18114) *********************** 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 129 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.366 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 853 ASP cc_start: 0.8167 (p0) cc_final: 0.7139 (m-30) REVERT: B 28 TRP cc_start: 0.6675 (OUTLIER) cc_final: 0.6177 (m-90) REVERT: B 211 TYR cc_start: 0.9640 (m-80) cc_final: 0.9405 (m-80) REVERT: B 229 MET cc_start: 0.8534 (mmm) cc_final: 0.7717 (ttt) REVERT: B 239 TYR cc_start: 0.9218 (m-80) cc_final: 0.8932 (m-80) REVERT: C 28 TRP cc_start: 0.9249 (t-100) cc_final: 0.8541 (t-100) REVERT: C 68 MET cc_start: 0.8583 (tpt) cc_final: 0.8300 (tpp) REVERT: C 116 MET cc_start: 0.7656 (tpt) cc_final: 0.6857 (tpt) REVERT: C 144 PHE cc_start: 0.9406 (t80) cc_final: 0.8995 (t80) REVERT: C 229 MET cc_start: 0.7089 (mmm) cc_final: 0.6286 (mmp) REVERT: C 235 LEU cc_start: 0.9477 (tp) cc_final: 0.8783 (pp) REVERT: D 2 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7273 (t80) REVERT: D 68 MET cc_start: 0.9129 (tmm) cc_final: 0.8818 (tmm) REVERT: D 116 MET cc_start: 0.7898 (tpp) cc_final: 0.6765 (tmm) REVERT: D 119 MET cc_start: 0.7841 (ppp) cc_final: 0.7438 (ppp) REVERT: D 139 MET cc_start: 0.9848 (OUTLIER) cc_final: 0.9628 (pmm) REVERT: D 144 PHE cc_start: 0.9705 (t80) cc_final: 0.9381 (t80) outliers start: 28 outliers final: 21 residues processed: 117 average time/residue: 0.2588 time to fit residues: 44.5364 Evaluate side-chains 119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 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 209 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 49 GLN Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- 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 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.069143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.050140 restraints weight = 119606.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.051216 restraints weight = 94188.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.052001 restraints weight = 79878.038| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5614 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= 0.246 Angle : 0.793 13.477 18120 Z= 0.414 Chirality : 0.046 0.214 2074 Planarity : 0.005 0.078 2020 Dihedral : 22.052 84.365 2439 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 29.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 2.70 % Allowed : 19.75 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.21), residues: 1385 helix: -0.53 (0.23), residues: 450 sheet: -1.20 (0.28), residues: 314 loop : -1.72 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 664 HIS 0.010 0.002 HIS A 485 PHE 0.069 0.003 PHE A 407 TYR 0.043 0.003 TYR A 408 ARG 0.008 0.001 ARG A 860 Details of bonding type rmsd hydrogen bonds : bond 0.07242 ( 509) hydrogen bonds : angle 6.12260 ( 1357) SS BOND : bond 0.00597 ( 3) SS BOND : angle 0.96635 ( 6) covalent geometry : bond 0.00528 (13125) covalent geometry : angle 0.79292 (18114) *********************** 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 135 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.259 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 834 GLU cc_start: 0.3960 (OUTLIER) cc_final: 0.2372 (tt0) REVERT: A 988 MET cc_start: 0.8967 (ttt) cc_final: 0.8545 (tmm) REVERT: B 211 TYR cc_start: 0.9647 (m-80) cc_final: 0.9406 (m-80) REVERT: B 229 MET cc_start: 0.8520 (mmm) cc_final: 0.7780 (ttt) REVERT: B 239 TYR cc_start: 0.9197 (m-80) cc_final: 0.8948 (m-80) REVERT: C 28 TRP cc_start: 0.9252 (t-100) cc_final: 0.8645 (t-100) REVERT: C 116 MET cc_start: 0.7704 (tpt) cc_final: 0.6954 (tpt) REVERT: C 121 LEU cc_start: 0.3931 (OUTLIER) cc_final: 0.3148 (mm) REVERT: C 144 PHE cc_start: 0.9405 (t80) cc_final: 0.9079 (t80) REVERT: C 229 MET cc_start: 0.7491 (mmm) cc_final: 0.7253 (mmm) REVERT: D 2 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7403 (t80) REVERT: D 119 MET cc_start: 0.7915 (ppp) cc_final: 0.7465 (ppp) REVERT: D 139 MET cc_start: 0.9855 (OUTLIER) cc_final: 0.9634 (pmm) REVERT: D 144 PHE cc_start: 0.9732 (t80) cc_final: 0.9415 (t80) REVERT: D 229 MET cc_start: 0.7649 (tpt) cc_final: 0.6830 (tpp) outliers start: 33 outliers final: 24 residues processed: 124 average time/residue: 0.2613 time to fit residues: 49.6707 Evaluate side-chains 124 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 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 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 139 MET 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 72 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 108 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 0.0670 overall best weight: 3.1724 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.071423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.052210 restraints weight = 115253.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.053349 restraints weight = 89648.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.054142 restraints weight = 75707.951| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13128 Z= 0.156 Angle : 0.741 12.973 18120 Z= 0.375 Chirality : 0.044 0.205 2074 Planarity : 0.004 0.051 2020 Dihedral : 22.003 84.849 2439 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.06 % Favored : 93.72 % Rotamer: Outliers : 2.38 % Allowed : 20.66 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1385 helix: -0.16 (0.24), residues: 455 sheet: -1.04 (0.28), residues: 320 loop : -1.63 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 28 HIS 0.007 0.001 HIS A 485 PHE 0.056 0.002 PHE A 407 TYR 0.050 0.002 TYR A 408 ARG 0.008 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 509) hydrogen bonds : angle 5.74473 ( 1357) SS BOND : bond 0.00387 ( 3) SS BOND : angle 1.18567 ( 6) covalent geometry : bond 0.00339 (13125) covalent geometry : angle 0.74120 (18114) *********************** 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 127 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.350 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 988 MET cc_start: 0.8972 (ttt) cc_final: 0.8675 (tmm) REVERT: B 211 TYR cc_start: 0.9657 (m-80) cc_final: 0.9425 (m-80) REVERT: B 229 MET cc_start: 0.8534 (mmm) cc_final: 0.7843 (ttt) REVERT: B 239 TYR cc_start: 0.9151 (m-80) cc_final: 0.8943 (m-80) REVERT: C 28 TRP cc_start: 0.9299 (t-100) cc_final: 0.8574 (t-100) REVERT: C 75 MET cc_start: 0.9233 (mmm) cc_final: 0.8821 (mmp) REVERT: C 116 MET cc_start: 0.7585 (tpt) cc_final: 0.6658 (tpt) REVERT: C 121 LEU cc_start: 0.3664 (OUTLIER) cc_final: 0.2901 (mm) REVERT: C 144 PHE cc_start: 0.9478 (t80) cc_final: 0.9083 (t80) REVERT: C 229 MET cc_start: 0.7582 (mmm) cc_final: 0.6918 (mmm) REVERT: C 235 LEU cc_start: 0.9489 (tp) cc_final: 0.8850 (pp) REVERT: D 2 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7212 (t80) REVERT: D 68 MET cc_start: 0.9001 (tmm) cc_final: 0.8658 (tmm) REVERT: D 119 MET cc_start: 0.7892 (ppp) cc_final: 0.7473 (ppp) REVERT: D 139 MET cc_start: 0.9854 (OUTLIER) cc_final: 0.9637 (pmm) REVERT: D 144 PHE cc_start: 0.9726 (t80) cc_final: 0.9402 (t80) REVERT: D 229 MET cc_start: 0.7726 (tpt) cc_final: 0.6959 (tpp) outliers start: 29 outliers final: 22 residues processed: 115 average time/residue: 0.2940 time to fit residues: 50.0825 Evaluate side-chains 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 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 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 49 GLN Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 139 MET 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 13 optimal weight: 0.0570 chunk 146 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 117 optimal weight: 0.0980 chunk 68 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 overall best weight: 2.7902 ------------------------------------------------------------------------------- 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 597 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 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.071640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.052509 restraints weight = 113181.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.053710 restraints weight = 88194.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.054561 restraints weight = 73833.801| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13128 Z= 0.150 Angle : 0.736 13.046 18120 Z= 0.370 Chirality : 0.044 0.244 2074 Planarity : 0.004 0.052 2020 Dihedral : 21.847 84.276 2439 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 1.97 % Allowed : 21.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1385 helix: -0.03 (0.24), residues: 455 sheet: -0.93 (0.28), residues: 323 loop : -1.57 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 28 HIS 0.006 0.001 HIS A 485 PHE 0.037 0.002 PHE B 214 TYR 0.051 0.002 TYR A 408 ARG 0.007 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.05034 ( 509) hydrogen bonds : angle 5.62532 ( 1357) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.13693 ( 6) covalent geometry : bond 0.00328 (13125) covalent geometry : angle 0.73624 (18114) ********************** 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 127 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.335 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 393 MET cc_start: 0.9385 (pmm) cc_final: 0.9080 (pmm) REVERT: A 853 ASP cc_start: 0.8522 (p0) cc_final: 0.7652 (m-30) REVERT: A 988 MET cc_start: 0.8874 (ttt) cc_final: 0.8374 (pmm) REVERT: B 28 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.6173 (m-90) REVERT: B 211 TYR cc_start: 0.9654 (m-80) cc_final: 0.9435 (m-80) REVERT: B 229 MET cc_start: 0.8570 (mmm) cc_final: 0.7966 (ttt) REVERT: C 28 TRP cc_start: 0.9284 (t-100) cc_final: 0.8554 (t-100) REVERT: C 75 MET cc_start: 0.9237 (mmm) cc_final: 0.8817 (mmp) REVERT: C 116 MET cc_start: 0.7549 (tpt) cc_final: 0.6612 (tpt) REVERT: C 121 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.2972 (mm) REVERT: C 144 PHE cc_start: 0.9474 (t80) cc_final: 0.9100 (t80) REVERT: C 229 MET cc_start: 0.7752 (mmm) cc_final: 0.7099 (mmm) REVERT: C 235 LEU cc_start: 0.9496 (tp) cc_final: 0.8861 (pp) REVERT: D 2 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7104 (t80) REVERT: D 68 MET cc_start: 0.9015 (tmm) cc_final: 0.8674 (tmm) REVERT: D 119 MET cc_start: 0.7893 (ppp) cc_final: 0.7471 (ppp) REVERT: D 139 MET cc_start: 0.9857 (OUTLIER) cc_final: 0.9642 (pmm) REVERT: D 144 PHE cc_start: 0.9719 (t80) cc_final: 0.9394 (t80) REVERT: D 229 MET cc_start: 0.7708 (tpt) cc_final: 0.6919 (tpp) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.3070 time to fit residues: 54.9064 Evaluate side-chains 122 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 772 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 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 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 139 MET 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 127 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 40 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- 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 597 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 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.070590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.051679 restraints weight = 115206.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.052808 restraints weight = 89534.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.053619 restraints weight = 75253.452| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13128 Z= 0.166 Angle : 0.732 13.238 18120 Z= 0.371 Chirality : 0.043 0.215 2074 Planarity : 0.004 0.051 2020 Dihedral : 21.825 83.873 2439 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.43 % Rotamer: Outliers : 2.21 % Allowed : 20.98 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1385 helix: -0.06 (0.24), residues: 457 sheet: -0.85 (0.29), residues: 321 loop : -1.63 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 28 HIS 0.008 0.001 HIS B 246 PHE 0.037 0.002 PHE B 214 TYR 0.033 0.002 TYR A 408 ARG 0.007 0.001 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 509) hydrogen bonds : angle 5.63489 ( 1357) SS BOND : bond 0.00408 ( 3) SS BOND : angle 1.10751 ( 6) covalent geometry : bond 0.00361 (13125) covalent geometry : angle 0.73207 (18114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.42 seconds wall clock time: 104 minutes 20.13 seconds (6260.13 seconds total)