Starting phenix.real_space_refine on Sun Sep 13 14:15:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk2_27481/09_2026/8dk2_27481.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 14634 2.51 5 N 4387 2.21 5 O 4595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3527 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2738 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5720 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 17, 'TRANS': 705} Chain breaks: 2 Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5680 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 17, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "G" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "I" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.69, per 1000 atoms: 0.20 Number of scatterers: 23727 At special positions: 0 Unit cell: (168.67, 145.203, 288.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 58 15.00 Mg 2 11.99 O 4595 8.00 N 4387 7.00 C 14634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 16 sheets defined 65.9% alpha, 8.5% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.513A pdb=" N SER A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.174A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.844A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.829A pdb=" N SER A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.666A pdb=" N VAL A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.907A pdb=" N VAL A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 272 removed outlier: 4.064A pdb=" N LEU A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.603A pdb=" N ALA A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.727A pdb=" N TRP A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.517A pdb=" N ARG A 294 " --> pdb=" O TRP A 290 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 409 through 425 removed outlier: 4.176A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.170A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.630A pdb=" N ARG B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.553A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.603A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.645A pdb=" N SER B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 220 removed outlier: 4.093A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.806A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.815A pdb=" N LEU B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.534A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.510A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 removed outlier: 3.547A pdb=" N TYR C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.517A pdb=" N LEU C 139 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 164 through 175 removed outlier: 4.014A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.516A pdb=" N PHE C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.872A pdb=" N ILE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.973A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 342 removed outlier: 4.530A pdb=" N LEU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Proline residue: C 264 - end of helix Proline residue: C 290 - end of helix removed outlier: 3.637A pdb=" N ARG C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 741 removed outlier: 3.774A pdb=" N LYS C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.604A pdb=" N ALA C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 808 Processing helix chain 'C' and resid 820 through 848 removed outlier: 4.313A pdb=" N ARG C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix removed outlier: 4.248A pdb=" N GLU C 846 " --> pdb=" O LYS C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 881 removed outlier: 3.768A pdb=" N VAL C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 880 " --> pdb=" O ASP C 876 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 918 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 947 through 955 Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 985 through 1005 removed outlier: 3.704A pdb=" N LYS C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1010 Processing helix chain 'C' and resid 1028 through 1042 Processing helix chain 'C' and resid 1055 through 1062 Processing helix chain 'C' and resid 1082 through 1087 removed outlier: 3.694A pdb=" N GLU C1087 " --> pdb=" O GLU C1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 79 through 86 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 209 removed outlier: 3.570A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.550A pdb=" N ILE D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 242 through 341 removed outlier: 4.358A pdb=" N THR D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix removed outlier: 4.121A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 290 - end of helix Processing helix chain 'D' and resid 692 through 741 Processing helix chain 'D' and resid 748 through 757 removed outlier: 3.586A pdb=" N LEU D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 763 No H-bonds generated for 'chain 'D' and resid 761 through 763' Processing helix chain 'D' and resid 764 through 808 Processing helix chain 'D' and resid 820 through 835 removed outlier: 4.220A pdb=" N ARG D 824 " --> pdb=" O VAL D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 848 removed outlier: 4.152A pdb=" N GLU D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 882 removed outlier: 4.303A pdb=" N VAL D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR D 880 " --> pdb=" O ASP D 876 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 882 " --> pdb=" O ASN D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 918 removed outlier: 3.550A pdb=" N ARG D 918 " --> pdb=" O LEU D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 944 removed outlier: 3.718A pdb=" N HIS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 955 Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 985 through 1005 Processing helix chain 'D' and resid 1028 through 1042 removed outlier: 3.672A pdb=" N PHE D1042 " --> pdb=" O ALA D1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1061 removed outlier: 3.784A pdb=" N HIS D1060 " --> pdb=" O ARG D1056 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 130 through 150 removed outlier: 3.705A pdb=" N GLU G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 Proline residue: G 167 - end of helix removed outlier: 3.850A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 195 Processing helix chain 'G' and resid 212 through 218 removed outlier: 4.140A pdb=" N HIS G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 235 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 130 through 150 removed outlier: 4.204A pdb=" N LEU H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 174 removed outlier: 3.646A pdb=" N ILE H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 4.278A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 196 removed outlier: 3.590A pdb=" N HIS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 219 through 236 Processing helix chain 'I' and resid 49 through 63 Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 130 through 150 removed outlier: 3.825A pdb=" N GLU I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 174 Proline residue: I 167 - end of helix removed outlier: 3.831A pdb=" N TYR I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 195 removed outlier: 3.516A pdb=" N GLU I 182 " --> pdb=" O SER I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 218 removed outlier: 4.114A pdb=" N HIS I 216 " --> pdb=" O PRO I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 460 through 472 removed outlier: 7.897A pdb=" N GLU A 463 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N LEU A 482 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ARG A 465 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N PHE A 480 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N PHE A 467 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N TRP A 478 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU A 469 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N GLN A 476 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 29 through 33 removed outlier: 7.232A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 112 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 116 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 124 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1018 through 1021 removed outlier: 3.528A pdb=" N LEU C1020 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C1049 " --> pdb=" O LEU C1020 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR C 39 " --> pdb=" O PHE C1048 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 890 through 898 removed outlier: 3.754A pdb=" N GLU C 976 " --> pdb=" O VAL C 966 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 968 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 974 " --> pdb=" O ASP C 968 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 33 removed outlier: 7.001A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1017 through 1019 removed outlier: 7.025A pdb=" N THR D 39 " --> pdb=" O PHE D1048 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR D1050 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL D 41 " --> pdb=" O THR D1050 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 40 " --> pdb=" O SER D1064 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D1068 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D1065 " --> pdb=" O LEU D1080 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 890 through 898 removed outlier: 3.980A pdb=" N GLU D 976 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 968 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 974 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.746A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.164A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'I' and resid 159 through 161 1426 hydrogen bonds defined for protein. 4218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8289 1.36 - 1.51: 5987 1.51 - 1.65: 9836 1.65 - 1.80: 49 1.80 - 1.95: 37 Bond restraints: 24198 Sorted by residual: bond pdb=" C3' DT P 13 " pdb=" C2' DT P 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT P 21 " pdb=" C2' DT P 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.68e+00 bond pdb=" C3' DT P 23 " pdb=" C2' DT P 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C3' DT P 8 " pdb=" C2' DT P 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.11e+00 bond pdb=" C3' DT P 17 " pdb=" C2' DT P 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.98e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 32332 1.57 - 3.14: 526 3.14 - 4.71: 53 4.71 - 6.28: 10 6.28 - 7.85: 3 Bond angle restraints: 32924 Sorted by residual: angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT P 19 " pdb=" C4 DT P 19 " pdb=" O4 DT P 19 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT P 26 " pdb=" C4 DT P 26 " pdb=" O4 DT P 26 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT P 6 " pdb=" C4 DT P 6 " pdb=" O4 DT P 6 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT P 24 " pdb=" C4 DT P 24 " pdb=" O4 DT P 24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 14026 26.56 - 53.12: 613 53.12 - 79.68: 53 79.68 - 106.23: 4 106.23 - 132.79: 1 Dihedral angle restraints: 14697 sinusoidal: 6481 harmonic: 8216 Sorted by residual: dihedral pdb=" O1A AGS C1201 " pdb=" O3A AGS C1201 " pdb=" PA AGS C1201 " pdb=" PB AGS C1201 " ideal model delta sinusoidal sigma weight residual -67.73 65.06 -132.79 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA THR C1050 " pdb=" C THR C1050 " pdb=" N PRO C1051 " pdb=" CA PRO C1051 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN A 18 " pdb=" C GLN A 18 " pdb=" N HIS A 19 " pdb=" CA HIS A 19 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 14694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2316 0.025 - 0.050: 802 0.050 - 0.075: 349 0.075 - 0.101: 156 0.101 - 0.126: 95 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CA ILE D1049 " pdb=" N ILE D1049 " pdb=" C ILE D1049 " pdb=" CB ILE D1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE C1049 " pdb=" N ILE C1049 " pdb=" C ILE C1049 " pdb=" CB ILE C1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL A 485 " pdb=" N VAL A 485 " pdb=" C VAL A 485 " pdb=" CB VAL A 485 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 3715 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 780 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C GLN D 780 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN D 780 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 781 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 783 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LEU D 783 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 783 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 784 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 782 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLN D 782 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN D 782 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 783 " 0.010 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 193 2.57 - 3.15: 19087 3.15 - 3.74: 37455 3.74 - 4.32: 47077 4.32 - 4.90: 77901 Nonbonded interactions: 181713 Sorted by model distance: nonbonded pdb=" NH2 ARG D 78 " pdb="MG MG D1202 " model vdw 1.988 2.250 nonbonded pdb=" N ALA C 69 " pdb="MG MG C1202 " model vdw 2.030 2.250 nonbonded pdb=" NE ARG D 78 " pdb="MG MG D1202 " model vdw 2.047 2.250 nonbonded pdb=" N SER C 70 " pdb="MG MG C1202 " model vdw 2.098 2.250 nonbonded pdb=" O ASN C 67 " pdb="MG MG C1202 " model vdw 2.102 2.170 ... (remaining 181708 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 'C' and (resid 10 through 1083 or resid 1201 through 1202)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'H' selection = (chain 'I' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.230 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.039 24198 Z= 0.194 Angle : 0.492 7.846 32924 Z= 0.323 Chirality : 0.037 0.126 3718 Planarity : 0.004 0.044 4130 Dihedral : 13.632 132.792 9357 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 5.42 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.17), residues: 2798 helix: 2.62 (0.13), residues: 1708 sheet: -0.02 (0.33), residues: 279 loop : -0.97 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 307 TYR 0.011 0.001 TYR C 272 PHE 0.010 0.001 PHE D 187 TRP 0.009 0.001 TRP D 128 HIS 0.003 0.001 HIS D 901 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.19 (24198) covalent geometry : angle 0.49230 / 0.32 (32924) hydrogen bonds : bond 0.11744 / 8.07 ( 1478) hydrogen bonds : angle 4.94989 / 3.74 ( 4322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 162 time to evaluate : 0.929 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 12 TYR cc_start: 0.9158 (m-10) cc_final: 0.8925 (m-10) REVERT: A 60 MET cc_start: 0.8359 (mtp) cc_final: 0.8068 (ttm) REVERT: A 122 MET cc_start: 0.9243 (mtp) cc_final: 0.8740 (mpp) REVERT: A 260 LEU cc_start: 0.9278 (mt) cc_final: 0.8719 (mt) REVERT: A 484 TYR cc_start: 0.8502 (t80) cc_final: 0.8034 (t80) REVERT: B 25 LEU cc_start: 0.9134 (mt) cc_final: 0.8865 (pp) REVERT: B 122 MET cc_start: 0.9512 (mtp) cc_final: 0.9122 (pmm) REVERT: B 144 ASN cc_start: 0.8270 (t0) cc_final: 0.7827 (t0) REVERT: B 176 LEU cc_start: 0.8383 (mt) cc_final: 0.8046 (tp) REVERT: B 325 HIS cc_start: 0.9065 (m170) cc_final: 0.8814 (t-170) REVERT: C 801 MET cc_start: 0.7573 (tmm) cc_final: 0.7187 (tmm) REVERT: C 901 HIS cc_start: 0.8159 (p-80) cc_final: 0.7805 (p-80) REVERT: C 953 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9361 (tt) REVERT: D 19 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: D 227 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8176 (t70) REVERT: D 1060 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7864 (m170) REVERT: F 74 TYR cc_start: 0.6652 (t80) cc_final: 0.6069 (t80) REVERT: H 95 MET cc_start: 0.1587 (ttp) cc_final: -0.0359 (mmm) outliers start: 69 outliers final: 23 residues processed: 229 average time/residue: 0.1739 time to fit residues: 62.2143 Evaluate side-chains 111 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 163 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN B 133 GLN B 163 HIS B 240 ASN C 97 GLN C 99 HIS C 103 GLN C 258 GLN C 276 GLN C 329 GLN C 336 HIS C 775 HIS C 858 GLN C1060 HIS D 312 HIS D 712 GLN D 726 GLN D 775 HIS F 57 GLN G 57 GLN G 80 ASN G 110 GLN G 116 GLN G 127 GLN G 149 GLN G 157 GLN G 196 HIS G 216 HIS H 57 GLN H 69 HIS H 205 HIS I 57 GLN I 80 ASN I 110 GLN I 127 GLN I 142 GLN I 149 GLN I 157 GLN I 168 GLN I 224 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.075508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.050297 restraints weight = 188135.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.049513 restraints weight = 128115.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049134 restraints weight = 97862.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049004 restraints weight = 71358.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048879 restraints weight = 64942.903| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24198 Z= 0.169 Angle : 0.578 11.432 32924 Z= 0.307 Chirality : 0.039 0.186 3718 Planarity : 0.004 0.059 4130 Dihedral : 13.331 142.375 3786 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.13 % Allowed : 1.92 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.16), residues: 2798 helix: 2.68 (0.12), residues: 1732 sheet: 0.21 (0.35), residues: 242 loop : -1.06 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 109 TYR 0.022 0.001 TYR D 995 PHE 0.055 0.002 PHE D 844 TRP 0.012 0.001 TRP B 290 HIS 0.013 0.001 HIS D 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (24198) covalent geometry : angle 0.57799 / 0.31 (32924) hydrogen bonds : bond 0.04937 / 3.38 ( 1478) hydrogen bonds : angle 4.07230 / 3.05 ( 4322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9220 (mtp) cc_final: 0.8696 (mpp) REVERT: B 25 LEU cc_start: 0.9126 (mt) cc_final: 0.8882 (pp) REVERT: B 122 MET cc_start: 0.9516 (mtp) cc_final: 0.8992 (pmm) REVERT: B 144 ASN cc_start: 0.8337 (t0) cc_final: 0.8115 (t0) REVERT: B 176 LEU cc_start: 0.8519 (mt) cc_final: 0.8177 (tp) REVERT: B 317 MET cc_start: 0.8692 (mpp) cc_final: 0.8405 (ptp) REVERT: B 325 HIS cc_start: 0.9124 (m170) cc_final: 0.8812 (t70) REVERT: C 801 MET cc_start: 0.7670 (tmm) cc_final: 0.7448 (tpp) REVERT: C 901 HIS cc_start: 0.8188 (p-80) cc_final: 0.7812 (p-80) REVERT: D 171 MET cc_start: 0.9018 (mtp) cc_final: 0.8766 (mtp) REVERT: F 74 TYR cc_start: 0.6335 (t80) cc_final: 0.5952 (t80) REVERT: H 95 MET cc_start: 0.2706 (ttp) cc_final: 0.1175 (mmm) REVERT: I 72 ASN cc_start: 0.8476 (p0) cc_final: 0.8262 (p0) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.1803 time to fit residues: 28.7572 Evaluate side-chains 72 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 265 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 187 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 HIS A 144 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 133 GLN B 330 GLN ** C 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 944 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS D1022 GLN F 69 HIS G 205 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.073719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048907 restraints weight = 188508.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047442 restraints weight = 132919.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047539 restraints weight = 89460.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047472 restraints weight = 73692.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047458 restraints weight = 71367.525| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24198 Z= 0.316 Angle : 0.722 11.166 32924 Z= 0.378 Chirality : 0.042 0.209 3718 Planarity : 0.005 0.058 4130 Dihedral : 13.504 133.910 3786 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.16), residues: 2798 helix: 2.28 (0.12), residues: 1728 sheet: -0.35 (0.32), residues: 274 loop : -1.35 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 109 TYR 0.022 0.002 TYR C 181 PHE 0.035 0.003 PHE D 844 TRP 0.025 0.002 TRP C 23 HIS 0.017 0.002 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.32 (24198) covalent geometry : angle 0.72233 / 0.38 (32924) hydrogen bonds : bond 0.05969 / 4.06 ( 1478) hydrogen bonds : angle 4.40378 / 3.30 ( 4322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9240 (mtp) cc_final: 0.8800 (mpp) REVERT: A 260 LEU cc_start: 0.9419 (mt) cc_final: 0.8831 (mt) REVERT: A 484 TYR cc_start: 0.8506 (t80) cc_final: 0.8096 (t80) REVERT: B 122 MET cc_start: 0.9543 (mtp) cc_final: 0.9085 (pmm) REVERT: B 144 ASN cc_start: 0.8069 (t0) cc_final: 0.7670 (t0) REVERT: B 176 LEU cc_start: 0.8676 (mt) cc_final: 0.8275 (tp) REVERT: C 901 HIS cc_start: 0.8308 (p-80) cc_final: 0.7881 (p-80) REVERT: F 74 TYR cc_start: 0.6392 (t80) cc_final: 0.6033 (t80) REVERT: H 95 MET cc_start: 0.2393 (ttp) cc_final: 0.1152 (ttm) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1585 time to fit residues: 23.1620 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 167 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 280 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 138 ASN ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 HIS C 858 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.075237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050091 restraints weight = 188880.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.048711 restraints weight = 109053.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.049095 restraints weight = 80716.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.048813 restraints weight = 56624.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.048921 restraints weight = 60965.329| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24198 Z= 0.129 Angle : 0.536 9.124 32924 Z= 0.287 Chirality : 0.038 0.143 3718 Planarity : 0.004 0.056 4130 Dihedral : 13.396 136.265 3786 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.16), residues: 2798 helix: 2.66 (0.12), residues: 1729 sheet: 0.01 (0.32), residues: 271 loop : -1.16 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1059 TYR 0.013 0.001 TYR C 928 PHE 0.025 0.002 PHE D 844 TRP 0.016 0.001 TRP D 128 HIS 0.009 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (24198) covalent geometry : angle 0.53565 / 0.29 (32924) hydrogen bonds : bond 0.04328 / 2.95 ( 1478) hydrogen bonds : angle 3.97478 / 2.97 ( 4322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9261 (mtp) cc_final: 0.8848 (mpp) REVERT: A 260 LEU cc_start: 0.9390 (mt) cc_final: 0.9151 (mt) REVERT: A 452 MET cc_start: 0.8985 (mtp) cc_final: 0.8594 (mtt) REVERT: A 484 TYR cc_start: 0.8403 (t80) cc_final: 0.8006 (t80) REVERT: B 122 MET cc_start: 0.9534 (mtp) cc_final: 0.8989 (pmm) REVERT: B 144 ASN cc_start: 0.8337 (t0) cc_final: 0.7917 (t0) REVERT: B 176 LEU cc_start: 0.8559 (mt) cc_final: 0.8158 (tp) REVERT: C 901 HIS cc_start: 0.8256 (p-80) cc_final: 0.7873 (p-80) REVERT: F 74 TYR cc_start: 0.6087 (t80) cc_final: 0.5714 (t80) REVERT: H 95 MET cc_start: 0.2843 (ttp) cc_final: 0.1673 (mmm) REVERT: I 59 MET cc_start: 0.4143 (tpt) cc_final: 0.3680 (tpt) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1699 time to fit residues: 25.4386 Evaluate side-chains 71 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 167 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 25 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN C 858 GLN C 947 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.075426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.049882 restraints weight = 186524.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.049942 restraints weight = 116228.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049257 restraints weight = 81977.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049256 restraints weight = 83704.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049135 restraints weight = 67664.975| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24198 Z= 0.112 Angle : 0.500 9.064 32924 Z= 0.268 Chirality : 0.037 0.274 3718 Planarity : 0.003 0.043 4130 Dihedral : 13.403 133.527 3786 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.04 % Allowed : 1.04 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.16), residues: 2798 helix: 2.77 (0.12), residues: 1734 sheet: 0.09 (0.33), residues: 271 loop : -1.09 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1059 TYR 0.012 0.001 TYR I 62 PHE 0.022 0.001 PHE C 242 TRP 0.014 0.001 TRP D 128 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (24198) covalent geometry : angle 0.49986 / 0.27 (32924) hydrogen bonds : bond 0.04067 / 2.76 ( 1478) hydrogen bonds : angle 3.80675 / 2.85 ( 4322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9188 (m-10) cc_final: 0.8936 (m-10) REVERT: A 122 MET cc_start: 0.9224 (mtp) cc_final: 0.8782 (mpp) REVERT: A 484 TYR cc_start: 0.8480 (t80) cc_final: 0.8091 (t80) REVERT: B 122 MET cc_start: 0.9606 (mtp) cc_final: 0.9055 (pmm) REVERT: B 144 ASN cc_start: 0.7935 (t0) cc_final: 0.7455 (t0) REVERT: B 176 LEU cc_start: 0.8487 (mt) cc_final: 0.8041 (tp) REVERT: C 901 HIS cc_start: 0.8404 (p-80) cc_final: 0.8006 (p-80) REVERT: F 74 TYR cc_start: 0.6047 (t80) cc_final: 0.5681 (t80) REVERT: H 95 MET cc_start: 0.3257 (ttp) cc_final: 0.1910 (mmm) REVERT: I 59 MET cc_start: 0.4416 (tpt) cc_final: 0.3929 (tpt) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1658 time to fit residues: 24.8194 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 28 optimal weight: 4.9990 chunk 258 optimal weight: 0.2980 chunk 172 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN C 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049868 restraints weight = 186543.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050129 restraints weight = 110448.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.049267 restraints weight = 72816.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.049029 restraints weight = 65456.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.049000 restraints weight = 60306.479| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24198 Z= 0.116 Angle : 0.497 9.331 32924 Z= 0.267 Chirality : 0.037 0.151 3718 Planarity : 0.003 0.043 4130 Dihedral : 13.464 131.132 3786 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 0.04 % Allowed : 1.17 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.16), residues: 2798 helix: 2.80 (0.12), residues: 1733 sheet: 0.18 (0.33), residues: 271 loop : -1.06 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 750 TYR 0.013 0.001 TYR I 62 PHE 0.023 0.001 PHE C 242 TRP 0.020 0.001 TRP D 292 HIS 0.006 0.001 HIS I 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (24198) covalent geometry : angle 0.49743 / 0.27 (32924) hydrogen bonds : bond 0.04041 / 2.75 ( 1478) hydrogen bonds : angle 3.76321 / 2.83 ( 4322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9253 (mtp) cc_final: 0.8561 (mpp) REVERT: A 185 MET cc_start: 0.8610 (mtm) cc_final: 0.8240 (mtm) REVERT: A 484 TYR cc_start: 0.8433 (t80) cc_final: 0.8070 (t80) REVERT: B 122 MET cc_start: 0.9572 (mtp) cc_final: 0.9046 (pmm) REVERT: B 144 ASN cc_start: 0.8035 (t0) cc_final: 0.7510 (t0) REVERT: B 176 LEU cc_start: 0.8554 (mt) cc_final: 0.8138 (tp) REVERT: C 801 MET cc_start: 0.7208 (tpp) cc_final: 0.6879 (tpp) REVERT: C 901 HIS cc_start: 0.8391 (p-80) cc_final: 0.8001 (p-80) REVERT: F 74 TYR cc_start: 0.6046 (t80) cc_final: 0.5669 (t80) REVERT: H 95 MET cc_start: 0.3286 (ttp) cc_final: 0.1965 (mmm) REVERT: I 59 MET cc_start: 0.4390 (tpt) cc_final: 0.3979 (tpt) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1608 time to fit residues: 23.0899 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 245 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 281 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN C 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.075220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049744 restraints weight = 185822.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049511 restraints weight = 116568.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.049375 restraints weight = 89771.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.048746 restraints weight = 79480.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048590 restraints weight = 71857.704| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24198 Z= 0.126 Angle : 0.501 9.376 32924 Z= 0.267 Chirality : 0.037 0.135 3718 Planarity : 0.003 0.040 4130 Dihedral : 13.505 128.952 3786 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 0.04 % Allowed : 0.96 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.17), residues: 2798 helix: 2.89 (0.12), residues: 1725 sheet: 0.20 (0.33), residues: 271 loop : -1.01 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 85 TYR 0.015 0.001 TYR C 862 PHE 0.022 0.001 PHE C 242 TRP 0.013 0.001 TRP D 128 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (24198) covalent geometry : angle 0.50097 / 0.27 (32924) hydrogen bonds : bond 0.04054 / 2.76 ( 1478) hydrogen bonds : angle 3.73293 / 2.81 ( 4322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9145 (m-10) cc_final: 0.8913 (m-10) REVERT: A 60 MET cc_start: 0.8353 (ttm) cc_final: 0.7976 (ttp) REVERT: A 122 MET cc_start: 0.9236 (mtp) cc_final: 0.8653 (mpp) REVERT: A 231 LEU cc_start: 0.8592 (tp) cc_final: 0.8256 (pp) REVERT: A 452 MET cc_start: 0.8819 (ptp) cc_final: 0.8568 (ptp) REVERT: A 484 TYR cc_start: 0.8392 (t80) cc_final: 0.8051 (t80) REVERT: B 122 MET cc_start: 0.9538 (mtp) cc_final: 0.9063 (pmm) REVERT: B 144 ASN cc_start: 0.7957 (t0) cc_final: 0.7442 (t0) REVERT: B 176 LEU cc_start: 0.8539 (mt) cc_final: 0.8069 (tp) REVERT: B 288 LEU cc_start: 0.8982 (tp) cc_final: 0.8705 (pp) REVERT: C 801 MET cc_start: 0.7173 (tpp) cc_final: 0.6835 (tpp) REVERT: C 901 HIS cc_start: 0.8407 (p-80) cc_final: 0.7993 (p-80) REVERT: F 74 TYR cc_start: 0.6007 (t80) cc_final: 0.5633 (t80) REVERT: H 95 MET cc_start: 0.3388 (ttp) cc_final: 0.2480 (mtm) REVERT: I 59 MET cc_start: 0.4720 (tpt) cc_final: 0.4190 (tpt) REVERT: I 143 HIS cc_start: 0.8870 (m-70) cc_final: 0.8639 (m-70) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1603 time to fit residues: 21.6421 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 281 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 123 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 256 GLN ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.074361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.049889 restraints weight = 188697.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.048166 restraints weight = 115604.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.047894 restraints weight = 91356.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047712 restraints weight = 68545.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.047716 restraints weight = 62392.979| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24198 Z= 0.192 Angle : 0.574 8.887 32924 Z= 0.305 Chirality : 0.038 0.151 3718 Planarity : 0.004 0.041 4130 Dihedral : 13.553 126.778 3786 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 0.04 % Allowed : 0.83 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 2798 helix: 2.74 (0.12), residues: 1738 sheet: 0.18 (0.33), residues: 267 loop : -1.23 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 817 TYR 0.012 0.002 TYR I 62 PHE 0.020 0.002 PHE C 242 TRP 0.024 0.001 TRP C 23 HIS 0.008 0.001 HIS G 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (24198) covalent geometry : angle 0.57442 / 0.30 (32924) hydrogen bonds : bond 0.04635 / 3.14 ( 1478) hydrogen bonds : angle 3.92437 / 2.95 ( 4322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8268 (ttm) cc_final: 0.7909 (ttp) REVERT: A 122 MET cc_start: 0.9233 (mtp) cc_final: 0.8657 (mpp) REVERT: A 231 LEU cc_start: 0.8497 (tp) cc_final: 0.8152 (pp) REVERT: A 452 MET cc_start: 0.8763 (ptp) cc_final: 0.8441 (ptp) REVERT: A 484 TYR cc_start: 0.8356 (t80) cc_final: 0.8020 (t80) REVERT: B 122 MET cc_start: 0.9523 (mtp) cc_final: 0.9055 (pmm) REVERT: B 144 ASN cc_start: 0.8148 (t0) cc_final: 0.7636 (t0) REVERT: B 176 LEU cc_start: 0.8710 (mt) cc_final: 0.8301 (tp) REVERT: B 288 LEU cc_start: 0.9026 (tp) cc_final: 0.8705 (pp) REVERT: C 801 MET cc_start: 0.7398 (tpp) cc_final: 0.7049 (tpp) REVERT: F 74 TYR cc_start: 0.5983 (t80) cc_final: 0.5615 (t80) REVERT: H 95 MET cc_start: 0.3761 (ttp) cc_final: 0.2888 (mtm) REVERT: I 59 MET cc_start: 0.4736 (tpt) cc_final: 0.4109 (tpt) REVERT: I 143 HIS cc_start: 0.8913 (m-70) cc_final: 0.8682 (m-70) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1755 time to fit residues: 22.8718 Evaluate side-chains 66 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 152 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 275 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 273 optimal weight: 0.0030 chunk 179 optimal weight: 6.9990 chunk 272 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN C 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.075609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050728 restraints weight = 186865.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049481 restraints weight = 135522.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049476 restraints weight = 90212.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.049419 restraints weight = 68945.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049415 restraints weight = 65888.950| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.105 Angle : 0.500 9.587 32924 Z= 0.266 Chirality : 0.037 0.146 3718 Planarity : 0.003 0.041 4130 Dihedral : 13.448 126.916 3786 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 0.04 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.16), residues: 2798 helix: 2.88 (0.12), residues: 1729 sheet: 0.35 (0.34), residues: 266 loop : -1.09 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 800 TYR 0.012 0.001 TYR I 62 PHE 0.022 0.001 PHE C 242 TRP 0.023 0.001 TRP D 128 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.11 (24198) covalent geometry : angle 0.50019 / 0.27 (32924) hydrogen bonds : bond 0.03856 / 2.63 ( 1478) hydrogen bonds : angle 3.71451 / 2.79 ( 4322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9154 (m-10) cc_final: 0.8883 (m-10) REVERT: A 122 MET cc_start: 0.9196 (mtp) cc_final: 0.8613 (mpp) REVERT: A 231 LEU cc_start: 0.8391 (tp) cc_final: 0.8085 (pp) REVERT: A 452 MET cc_start: 0.8811 (ptp) cc_final: 0.8437 (ptp) REVERT: A 484 TYR cc_start: 0.8475 (t80) cc_final: 0.8099 (t80) REVERT: B 122 MET cc_start: 0.9599 (mtp) cc_final: 0.9073 (pmm) REVERT: B 144 ASN cc_start: 0.7604 (t0) cc_final: 0.7152 (t0) REVERT: B 176 LEU cc_start: 0.8524 (mt) cc_final: 0.8102 (tp) REVERT: C 801 MET cc_start: 0.7079 (tpp) cc_final: 0.6743 (tpp) REVERT: C 901 HIS cc_start: 0.8340 (p-80) cc_final: 0.7874 (p-80) REVERT: F 74 TYR cc_start: 0.5912 (t80) cc_final: 0.5574 (t80) REVERT: H 95 MET cc_start: 0.3998 (ttp) cc_final: 0.2906 (mmm) REVERT: I 59 MET cc_start: 0.5080 (tpt) cc_final: 0.4340 (tpt) REVERT: I 143 HIS cc_start: 0.8858 (m-70) cc_final: 0.8634 (m-70) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1687 time to fit residues: 23.3437 Evaluate side-chains 66 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.0270 chunk 216 optimal weight: 0.9990 chunk 274 optimal weight: 0.1980 chunk 207 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051753 restraints weight = 187215.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049676 restraints weight = 148698.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.049688 restraints weight = 96583.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049645 restraints weight = 68647.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049764 restraints weight = 63345.871| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24198 Z= 0.103 Angle : 0.486 9.435 32924 Z= 0.260 Chirality : 0.037 0.135 3718 Planarity : 0.003 0.042 4130 Dihedral : 13.438 124.104 3786 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.17), residues: 2798 helix: 2.92 (0.12), residues: 1733 sheet: 0.33 (0.33), residues: 276 loop : -1.11 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 134 TYR 0.011 0.001 TYR I 62 PHE 0.021 0.001 PHE C 242 TRP 0.013 0.001 TRP B 290 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (24198) covalent geometry : angle 0.48578 / 0.26 (32924) hydrogen bonds : bond 0.03797 / 2.59 ( 1478) hydrogen bonds : angle 3.65807 / 2.74 ( 4322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9008 (m-10) cc_final: 0.8791 (m-10) REVERT: A 60 MET cc_start: 0.8407 (ttm) cc_final: 0.7985 (ttp) REVERT: A 122 MET cc_start: 0.9217 (mtp) cc_final: 0.8733 (mpp) REVERT: A 231 LEU cc_start: 0.8498 (tp) cc_final: 0.8129 (pp) REVERT: A 452 MET cc_start: 0.8808 (ptp) cc_final: 0.8392 (ptp) REVERT: A 484 TYR cc_start: 0.8340 (t80) cc_final: 0.8021 (t80) REVERT: B 122 MET cc_start: 0.9504 (mtp) cc_final: 0.9063 (pmm) REVERT: B 144 ASN cc_start: 0.8078 (t0) cc_final: 0.7550 (t0) REVERT: B 176 LEU cc_start: 0.8691 (mt) cc_final: 0.8237 (tp) REVERT: C 801 MET cc_start: 0.7439 (tpp) cc_final: 0.7053 (tpp) REVERT: C 901 HIS cc_start: 0.8383 (p-80) cc_final: 0.7882 (p-80) REVERT: F 74 TYR cc_start: 0.5999 (t80) cc_final: 0.5654 (t80) REVERT: H 95 MET cc_start: 0.2950 (ttp) cc_final: 0.1148 (mmm) REVERT: I 59 MET cc_start: 0.3963 (tpt) cc_final: 0.3717 (tpt) REVERT: I 143 HIS cc_start: 0.8887 (m-70) cc_final: 0.8608 (m-70) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1700 time to fit residues: 22.4739 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 28 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN B 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.075149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049136 restraints weight = 186981.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.049016 restraints weight = 114096.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048984 restraints weight = 72369.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.048891 restraints weight = 81427.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.048908 restraints weight = 65375.769| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24198 Z= 0.134 Angle : 0.505 9.054 32924 Z= 0.270 Chirality : 0.037 0.143 3718 Planarity : 0.003 0.041 4130 Dihedral : 13.485 122.339 3786 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2798 helix: 2.94 (0.12), residues: 1735 sheet: 0.27 (0.33), residues: 278 loop : -1.12 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 750 TYR 0.011 0.001 TYR I 62 PHE 0.019 0.001 PHE C 242 TRP 0.008 0.001 TRP B 290 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (24198) covalent geometry : angle 0.50533 / 0.27 (32924) hydrogen bonds : bond 0.04031 / 2.74 ( 1478) hydrogen bonds : angle 3.72017 / 2.79 ( 4322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.10 seconds wall clock time: 93 minutes 56.92 seconds (5636.92 seconds total)