Starting phenix.real_space_refine on Thu Mar 5 16:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk2_27481/03_2026/8dk2_27481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk2_27481/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk2_27481/03_2026/8dk2_27481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk2_27481/03_2026/8dk2_27481.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk2_27481/03_2026/8dk2_27481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk2_27481/03_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-dev-5986/lib/python3.9/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: 5.78, per 1000 atoms: 0.24 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 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: 3.12 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: 4.54 Time building geometry restraints manager: 3.07 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=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.32e+00 bond pdb=" CA GLN C 263 " pdb=" C GLN C 263 " ideal model delta sigma weight residual 1.521 1.535 -0.013 1.17e-02 7.31e+03 1.31e+00 bond pdb=" N LEU D 289 " pdb=" CA LEU D 289 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.30e+00 bond pdb=" C LEU D 289 " pdb=" O LEU D 289 " ideal model delta sigma weight residual 1.238 1.251 -0.014 1.28e-02 6.10e+03 1.13e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 32443 1.57 - 3.14: 415 3.14 - 4.71: 53 4.71 - 6.28: 10 6.28 - 7.85: 3 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C ALA C 231 " pdb=" N PHE C 232 " pdb=" CA PHE C 232 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N LEU D 289 " pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 109.81 117.24 -7.43 2.21e+00 2.05e-01 1.13e+01 angle pdb=" N VAL C1073 " pdb=" CA VAL C1073 " pdb=" C VAL C1073 " ideal model delta sigma weight residual 113.20 110.46 2.74 9.60e-01 1.09e+00 8.12e+00 angle pdb=" C SER C 230 " pdb=" N ALA C 231 " pdb=" CA ALA C 231 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.69e+00 angle pdb=" CA LEU D 860 " pdb=" CB LEU D 860 " pdb=" CG LEU D 860 " ideal model delta sigma weight residual 116.30 124.15 -7.85 3.50e+00 8.16e-02 5.02e+00 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 14034 26.56 - 53.12: 625 53.12 - 79.68: 55 79.68 - 106.23: 4 106.23 - 132.79: 1 Dihedral angle restraints: 14719 sinusoidal: 6503 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 14716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2397 0.025 - 0.050: 776 0.050 - 0.075: 337 0.075 - 0.101: 132 0.101 - 0.126: 76 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: 5.490 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 25.180 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.002 0.039 24198 Z= 0.123 Angle : 0.466 7.846 32924 Z= 0.256 Chirality : 0.035 0.126 3718 Planarity : 0.004 0.044 4130 Dihedral : 13.702 132.792 9379 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 covalent geometry : bond 0.00241 (24198) covalent geometry : angle 0.46600 (32924) hydrogen bonds : bond 0.11744 ( 1478) hydrogen bonds : angle 4.94989 ( 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 : 0.823 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: 0.1673 time to fit residues: 59.5575 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 : 0.946 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 276 GLN C 329 GLN C 336 HIS C 775 HIS C 858 GLN C 878 ASN 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 = 0.3844 r_free = 0.3844 target = 0.075368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.049588 restraints weight = 188060.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.049369 restraints weight = 114856.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049311 restraints weight = 77791.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049122 restraints weight = 70288.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049186 restraints weight = 59871.104| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1556 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= 0.169 Angle : 0.567 11.535 32924 Z= 0.299 Chirality : 0.038 0.147 3718 Planarity : 0.004 0.064 4130 Dihedral : 13.292 141.188 3808 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.17 % Allowed : 2.04 % Favored : 97.79 % 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: 2.15 (0.16), residues: 2798 helix: 2.72 (0.12), residues: 1732 sheet: 0.04 (0.33), residues: 270 loop : -1.09 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 109 TYR 0.026 0.002 TYR D 995 PHE 0.049 0.002 PHE D 844 TRP 0.012 0.001 TRP B 290 HIS 0.012 0.001 HIS D 775 Details of bonding type rmsd covalent geometry : bond 0.00362 (24198) covalent geometry : angle 0.56707 (32924) hydrogen bonds : bond 0.04780 ( 1478) hydrogen bonds : angle 4.01666 ( 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 103 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9234 (mtp) cc_final: 0.8704 (mpp) REVERT: B 25 LEU cc_start: 0.9121 (mt) cc_final: 0.8872 (pp) REVERT: B 122 MET cc_start: 0.9537 (mtp) cc_final: 0.9010 (pmm) REVERT: B 144 ASN cc_start: 0.8322 (t0) cc_final: 0.8102 (t0) REVERT: B 176 LEU cc_start: 0.8561 (mt) cc_final: 0.8213 (tp) REVERT: B 317 MET cc_start: 0.8709 (mpp) cc_final: 0.8394 (ptp) REVERT: B 325 HIS cc_start: 0.9106 (m170) cc_final: 0.8827 (t70) REVERT: C 901 HIS cc_start: 0.8121 (p-80) cc_final: 0.7770 (p-80) REVERT: D 171 MET cc_start: 0.9018 (mtp) cc_final: 0.8791 (mtp) REVERT: F 74 TYR cc_start: 0.6415 (t80) cc_final: 0.6004 (t80) REVERT: H 95 MET cc_start: 0.2432 (ttp) cc_final: 0.0916 (mmm) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.1665 time to fit residues: 26.5667 Evaluate side-chains 69 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.0570 chunk 265 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 144 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 163 HIS B 330 GLN C 775 HIS C 858 GLN C 878 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.073763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048655 restraints weight = 188444.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047017 restraints weight = 150308.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047899 restraints weight = 90273.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.047451 restraints weight = 52134.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047384 restraints weight = 53988.462| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24198 Z= 0.276 Angle : 0.672 10.272 32924 Z= 0.355 Chirality : 0.041 0.168 3718 Planarity : 0.005 0.061 4130 Dihedral : 13.420 132.087 3808 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % 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: 1.63 (0.16), residues: 2798 helix: 2.32 (0.12), residues: 1735 sheet: -0.16 (0.33), residues: 268 loop : -1.36 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 75 TYR 0.018 0.002 TYR C 181 PHE 0.036 0.002 PHE D 844 TRP 0.015 0.002 TRP B 290 HIS 0.013 0.002 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00595 (24198) covalent geometry : angle 0.67170 (32924) hydrogen bonds : bond 0.05711 ( 1478) hydrogen bonds : angle 4.30870 ( 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 94 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.897 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: 0.9286 (mtp) cc_final: 0.8880 (mpp) REVERT: A 231 LEU cc_start: 0.8439 (tp) cc_final: 0.8142 (pp) REVERT: A 484 TYR cc_start: 0.8466 (t80) cc_final: 0.8014 (t80) REVERT: B 122 MET cc_start: 0.9504 (mtp) cc_final: 0.9049 (pmm) REVERT: B 144 ASN cc_start: 0.8539 (t0) cc_final: 0.8094 (t0) REVERT: B 176 LEU cc_start: 0.8685 (mt) cc_final: 0.8265 (tp) REVERT: B 288 LEU cc_start: 0.8996 (tp) cc_final: 0.8680 (pp) REVERT: C 171 MET cc_start: 0.8485 (mtp) cc_final: 0.8142 (ttt) REVERT: F 74 TYR cc_start: 0.6095 (t80) cc_final: 0.5695 (t80) REVERT: H 95 MET cc_start: 0.2225 (ttp) cc_final: 0.1241 (ttm) outliers start: 5 outliers final: 1 residues processed: 94 average time/residue: 0.1560 time to fit residues: 24.1539 Evaluate side-chains 67 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 0.5980 chunk 206 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.075390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050609 restraints weight = 187298.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049667 restraints weight = 116647.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049826 restraints weight = 94455.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049166 restraints weight = 93592.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049129 restraints weight = 76376.780| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24198 Z= 0.116 Angle : 0.515 9.244 32924 Z= 0.272 Chirality : 0.037 0.138 3718 Planarity : 0.004 0.049 4130 Dihedral : 13.282 129.712 3808 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 0.04 % Allowed : 1.42 % Favored : 98.54 % 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: 2.08 (0.16), residues: 2798 helix: 2.68 (0.12), residues: 1726 sheet: -0.00 (0.33), residues: 271 loop : -1.15 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1059 TYR 0.023 0.001 TYR C 825 PHE 0.021 0.001 PHE C 242 TRP 0.015 0.001 TRP D 128 HIS 0.007 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00235 (24198) covalent geometry : angle 0.51523 (32924) hydrogen bonds : bond 0.04154 ( 1478) hydrogen bonds : angle 3.88587 ( 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 90 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.872 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: 0.9181 (mtp) cc_final: 0.8838 (mpp) REVERT: A 231 LEU cc_start: 0.8432 (tp) cc_final: 0.8117 (pp) REVERT: A 484 TYR cc_start: 0.8374 (t80) cc_final: 0.7995 (t80) REVERT: B 122 MET cc_start: 0.9509 (mtp) cc_final: 0.8984 (pmm) REVERT: B 144 ASN cc_start: 0.8401 (t0) cc_final: 0.7946 (t0) REVERT: B 176 LEU cc_start: 0.8618 (mt) cc_final: 0.8205 (tp) REVERT: C 171 MET cc_start: 0.8376 (mtp) cc_final: 0.7981 (ttt) REVERT: C 901 HIS cc_start: 0.8319 (p-80) cc_final: 0.7956 (p-80) REVERT: F 74 TYR cc_start: 0.6131 (t80) cc_final: 0.5731 (t80) REVERT: H 95 MET cc_start: 0.2810 (ttp) cc_final: 0.1250 (mmm) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1649 time to fit residues: 24.3013 Evaluate side-chains 70 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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: 0.6980 chunk 188 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 264 optimal weight: 0.3980 chunk 217 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 878 ASN C 947 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.075556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049852 restraints weight = 185166.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.048957 restraints weight = 118184.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049522 restraints weight = 83762.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049062 restraints weight = 56968.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049029 restraints weight = 59242.366| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24198 Z= 0.108 Angle : 0.486 9.164 32924 Z= 0.257 Chirality : 0.037 0.189 3718 Planarity : 0.003 0.042 4130 Dihedral : 13.283 126.201 3808 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % 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: 2.28 (0.16), residues: 2798 helix: 2.83 (0.12), residues: 1726 sheet: 0.17 (0.33), residues: 271 loop : -1.07 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1059 TYR 0.011 0.001 TYR I 62 PHE 0.029 0.001 PHE B 336 TRP 0.014 0.001 TRP D 128 HIS 0.006 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00217 (24198) covalent geometry : angle 0.48629 (32924) hydrogen bonds : bond 0.03891 ( 1478) hydrogen bonds : angle 3.70446 ( 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 93 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8339 (ttm) cc_final: 0.7931 (ttp) REVERT: A 122 MET cc_start: 0.9154 (mtp) cc_final: 0.8686 (mpp) REVERT: A 185 MET cc_start: 0.8414 (mtm) cc_final: 0.8061 (mtm) REVERT: A 231 LEU cc_start: 0.8297 (tp) cc_final: 0.8017 (pp) REVERT: A 452 MET cc_start: 0.8694 (ptp) cc_final: 0.8492 (ptp) REVERT: A 484 TYR cc_start: 0.8392 (t80) cc_final: 0.8035 (t80) REVERT: B 122 MET cc_start: 0.9585 (mtp) cc_final: 0.9059 (pmm) REVERT: B 144 ASN cc_start: 0.7792 (t0) cc_final: 0.7288 (t0) REVERT: B 176 LEU cc_start: 0.8426 (mt) cc_final: 0.8030 (tp) REVERT: B 288 LEU cc_start: 0.8978 (tp) cc_final: 0.8699 (pp) REVERT: C 171 MET cc_start: 0.8352 (mtp) cc_final: 0.7942 (ttt) REVERT: C 901 HIS cc_start: 0.8289 (p-80) cc_final: 0.7851 (p-80) REVERT: F 74 TYR cc_start: 0.5878 (t80) cc_final: 0.5525 (t80) REVERT: H 95 MET cc_start: 0.3703 (ttp) cc_final: 0.2624 (mmm) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1597 time to fit residues: 23.9850 Evaluate side-chains 69 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 3.9990 chunk 258 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 263 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN C 258 GLN C 858 GLN ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.074091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049369 restraints weight = 189608.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048011 restraints weight = 128631.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047758 restraints weight = 85605.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.047791 restraints weight = 74570.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047884 restraints weight = 71129.424| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24198 Z= 0.227 Angle : 0.601 7.900 32924 Z= 0.317 Chirality : 0.039 0.146 3718 Planarity : 0.004 0.050 4130 Dihedral : 13.374 124.779 3808 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % 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: 1.99 (0.16), residues: 2798 helix: 2.62 (0.12), residues: 1735 sheet: -0.00 (0.33), residues: 274 loop : -1.27 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.020 0.002 TYR I 62 PHE 0.021 0.002 PHE B 336 TRP 0.022 0.001 TRP C 23 HIS 0.009 0.001 HIS D1069 Details of bonding type rmsd covalent geometry : bond 0.00491 (24198) covalent geometry : angle 0.60120 (32924) hydrogen bonds : bond 0.05066 ( 1478) hydrogen bonds : angle 4.01769 ( 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 82 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9246 (mtp) cc_final: 0.8763 (mpp) REVERT: A 263 MET cc_start: 0.9368 (ptp) cc_final: 0.9155 (ptm) REVERT: A 452 MET cc_start: 0.8861 (ptp) cc_final: 0.8480 (ptp) REVERT: A 484 TYR cc_start: 0.8589 (t80) cc_final: 0.8180 (t80) REVERT: B 122 MET cc_start: 0.9581 (mtp) cc_final: 0.9097 (pmm) REVERT: B 144 ASN cc_start: 0.7894 (t0) cc_final: 0.7430 (t0) REVERT: B 176 LEU cc_start: 0.8606 (mt) cc_final: 0.8158 (tp) REVERT: F 74 TYR cc_start: 0.6053 (t80) cc_final: 0.5690 (t80) REVERT: H 95 MET cc_start: 0.3344 (ttp) cc_final: 0.1949 (mmm) REVERT: I 143 HIS cc_start: 0.8896 (m-70) cc_final: 0.8686 (m-70) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1634 time to fit residues: 21.7942 Evaluate side-chains 65 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 200 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.073794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048400 restraints weight = 188974.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047293 restraints weight = 141427.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047603 restraints weight = 84812.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.047465 restraints weight = 61757.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.047301 restraints weight = 58807.845| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24198 Z= 0.231 Angle : 0.607 8.806 32924 Z= 0.320 Chirality : 0.040 0.153 3718 Planarity : 0.004 0.040 4130 Dihedral : 13.299 122.250 3808 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % 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: 1.81 (0.16), residues: 2798 helix: 2.48 (0.12), residues: 1739 sheet: -0.09 (0.33), residues: 267 loop : -1.36 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 893 TYR 0.013 0.002 TYR C 862 PHE 0.020 0.002 PHE B 336 TRP 0.020 0.001 TRP C 23 HIS 0.008 0.001 HIS D1069 Details of bonding type rmsd covalent geometry : bond 0.00502 (24198) covalent geometry : angle 0.60651 (32924) hydrogen bonds : bond 0.04823 ( 1478) hydrogen bonds : angle 4.12410 ( 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 80 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8425 (ttm) cc_final: 0.8049 (ttp) REVERT: A 122 MET cc_start: 0.9250 (mtp) cc_final: 0.8679 (mpp) REVERT: A 263 MET cc_start: 0.9354 (ptp) cc_final: 0.9140 (ptm) REVERT: A 452 MET cc_start: 0.9010 (ptp) cc_final: 0.8547 (ptp) REVERT: A 484 TYR cc_start: 0.8390 (t80) cc_final: 0.8152 (t80) REVERT: B 122 MET cc_start: 0.9497 (mtp) cc_final: 0.9061 (pmm) REVERT: B 144 ASN cc_start: 0.8098 (t0) cc_final: 0.7877 (t0) REVERT: B 176 LEU cc_start: 0.8692 (mt) cc_final: 0.8250 (tp) REVERT: B 288 LEU cc_start: 0.9011 (tp) cc_final: 0.8761 (pp) REVERT: F 74 TYR cc_start: 0.5980 (t80) cc_final: 0.5615 (t80) REVERT: H 95 MET cc_start: 0.4210 (ttp) cc_final: 0.2642 (mmm) REVERT: I 143 HIS cc_start: 0.8897 (m-70) cc_final: 0.8682 (m-70) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1660 time to fit residues: 21.9182 Evaluate side-chains 64 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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: 3.9990 chunk 245 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 90 optimal weight: 0.0470 chunk 123 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 858 GLN C 878 ASN C 944 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.074567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048874 restraints weight = 186308.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048531 restraints weight = 119873.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.048219 restraints weight = 82951.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048004 restraints weight = 72321.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048010 restraints weight = 65101.964| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24198 Z= 0.139 Angle : 0.532 11.530 32924 Z= 0.279 Chirality : 0.038 0.145 3718 Planarity : 0.004 0.042 4130 Dihedral : 13.201 119.351 3808 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % 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: 2.01 (0.16), residues: 2798 helix: 2.64 (0.12), residues: 1746 sheet: -0.11 (0.33), residues: 272 loop : -1.30 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 207 TYR 0.010 0.001 TYR C 862 PHE 0.020 0.001 PHE B 336 TRP 0.017 0.001 TRP C 23 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00297 (24198) covalent geometry : angle 0.53182 (32924) hydrogen bonds : bond 0.04248 ( 1478) hydrogen bonds : angle 3.89350 ( 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 80 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9191 (m-10) cc_final: 0.8919 (m-10) REVERT: A 60 MET cc_start: 0.8543 (ttm) cc_final: 0.8168 (ttp) REVERT: A 122 MET cc_start: 0.9210 (mtp) cc_final: 0.8611 (mpp) REVERT: A 263 MET cc_start: 0.9390 (ptp) cc_final: 0.9160 (ptm) REVERT: A 484 TYR cc_start: 0.8471 (t80) cc_final: 0.8154 (t80) REVERT: B 122 MET cc_start: 0.9527 (mtp) cc_final: 0.9047 (pmm) REVERT: B 144 ASN cc_start: 0.7878 (t0) cc_final: 0.7665 (t0) REVERT: B 176 LEU cc_start: 0.8596 (mt) cc_final: 0.8131 (tp) REVERT: F 95 MET cc_start: 0.7246 (mtp) cc_final: 0.6251 (mpp) REVERT: H 95 MET cc_start: 0.4366 (ttp) cc_final: 0.2922 (mmm) REVERT: I 143 HIS cc_start: 0.8930 (m-70) cc_final: 0.8702 (m-70) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1682 time to fit residues: 21.7402 Evaluate side-chains 63 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 147 optimal weight: 0.1980 chunk 275 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 858 GLN C 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.074276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049249 restraints weight = 188169.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047677 restraints weight = 132740.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.047628 restraints weight = 94112.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.047640 restraints weight = 66980.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047643 restraints weight = 65133.404| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24198 Z= 0.162 Angle : 0.542 9.726 32924 Z= 0.286 Chirality : 0.038 0.141 3718 Planarity : 0.004 0.043 4130 Dihedral : 13.226 119.044 3808 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % 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: 2.04 (0.16), residues: 2798 helix: 2.71 (0.12), residues: 1732 sheet: -0.16 (0.33), residues: 272 loop : -1.28 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 750 TYR 0.011 0.001 TYR F 74 PHE 0.024 0.002 PHE B 336 TRP 0.009 0.001 TRP B 290 HIS 0.008 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00351 (24198) covalent geometry : angle 0.54178 (32924) hydrogen bonds : bond 0.04417 ( 1478) hydrogen bonds : angle 3.90908 ( 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 76 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8592 (ttm) cc_final: 0.8202 (ttp) REVERT: A 122 MET cc_start: 0.9207 (mtp) cc_final: 0.8612 (mpp) REVERT: A 263 MET cc_start: 0.9395 (ptp) cc_final: 0.9155 (ptm) REVERT: A 484 TYR cc_start: 0.8510 (t80) cc_final: 0.8199 (t80) REVERT: B 122 MET cc_start: 0.9529 (mtp) cc_final: 0.9048 (pmm) REVERT: B 144 ASN cc_start: 0.7741 (t0) cc_final: 0.7268 (t0) REVERT: B 176 LEU cc_start: 0.8614 (mt) cc_final: 0.8181 (tp) REVERT: F 67 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8074 (tp30) REVERT: F 95 MET cc_start: 0.7220 (mtp) cc_final: 0.6288 (mpp) REVERT: H 95 MET cc_start: 0.4524 (ttp) cc_final: 0.3101 (mmm) REVERT: I 143 HIS cc_start: 0.8929 (m-70) cc_final: 0.8700 (m-70) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1661 time to fit residues: 20.7259 Evaluate side-chains 62 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 2.9990 chunk 137 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 21 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.075206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050251 restraints weight = 187113.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048723 restraints weight = 129135.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.049179 restraints weight = 85672.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048509 restraints weight = 57025.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.048552 restraints weight = 52913.913| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3236 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= 0.106 Angle : 0.495 9.648 32924 Z= 0.260 Chirality : 0.037 0.143 3718 Planarity : 0.003 0.043 4130 Dihedral : 13.176 115.714 3808 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % 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: 2.26 (0.16), residues: 2798 helix: 2.89 (0.12), residues: 1726 sheet: -0.01 (0.33), residues: 274 loop : -1.21 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.010 0.001 TYR C 928 PHE 0.023 0.001 PHE B 336 TRP 0.021 0.001 TRP D 128 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00216 (24198) covalent geometry : angle 0.49510 (32924) hydrogen bonds : bond 0.03763 ( 1478) hydrogen bonds : angle 3.68794 ( 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 76 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.9273 (m-10) cc_final: 0.9052 (m-10) REVERT: A 60 MET cc_start: 0.8521 (ttm) cc_final: 0.8174 (ptm) REVERT: A 122 MET cc_start: 0.9175 (mtp) cc_final: 0.8494 (mpp) REVERT: A 263 MET cc_start: 0.9342 (ptp) cc_final: 0.9131 (ptm) REVERT: A 452 MET cc_start: 0.9050 (ptp) cc_final: 0.8822 (ptm) REVERT: A 484 TYR cc_start: 0.8447 (t80) cc_final: 0.8175 (t80) REVERT: B 122 MET cc_start: 0.9600 (mtp) cc_final: 0.9122 (pmm) REVERT: B 144 ASN cc_start: 0.7714 (t0) cc_final: 0.7196 (t0) REVERT: B 176 LEU cc_start: 0.8576 (mt) cc_final: 0.8171 (tp) REVERT: B 263 MET cc_start: 0.9371 (mmm) cc_final: 0.9171 (mmm) REVERT: F 67 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8042 (tp30) REVERT: H 95 MET cc_start: 0.4675 (ttp) cc_final: 0.3410 (mmm) REVERT: I 59 MET cc_start: 0.5262 (tpt) cc_final: 0.4819 (tpt) REVERT: I 143 HIS cc_start: 0.8933 (m-70) cc_final: 0.8690 (m-70) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1687 time to fit residues: 20.9029 Evaluate side-chains 63 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 2.9990 chunk 139 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 275 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS C 878 ASN ** D 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.075146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050460 restraints weight = 187821.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.048588 restraints weight = 138048.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049544 restraints weight = 85593.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048941 restraints weight = 48268.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.048964 restraints weight = 47775.654| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3313 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 : 0.483 9.288 32924 Z= 0.253 Chirality : 0.037 0.139 3718 Planarity : 0.003 0.043 4130 Dihedral : 13.155 112.397 3808 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.43 % 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: 2.36 (0.17), residues: 2798 helix: 2.97 (0.12), residues: 1729 sheet: 0.08 (0.33), residues: 276 loop : -1.22 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 817 TYR 0.012 0.001 TYR C 825 PHE 0.022 0.001 PHE B 336 TRP 0.013 0.001 TRP D 128 HIS 0.007 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00215 (24198) covalent geometry : angle 0.48275 (32924) hydrogen bonds : bond 0.03787 ( 1478) hydrogen bonds : angle 3.62477 ( 4322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5486.78 seconds wall clock time: 94 minutes 35.08 seconds (5675.08 seconds total)