Starting phenix.real_space_refine on Sat Sep 12 11:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tve_26140/09_2026/7tve_26140.map" } resolution = 3.8 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 59 5.16 5 C 9572 2.51 5 N 2692 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2489 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3512 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3661 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2150 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 1 Chain: "G" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2506 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.71, per 1000 atoms: 0.18 Number of scatterers: 15456 At special positions: 0 Unit cell: (98.348, 148.591, 169.971, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 57 15.00 O 3076 8.00 N 2692 7.00 C 9572 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: 1.10 Conformation dependent library (CDL) restraints added in 515.0 milliseconds 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 45.9% alpha, 7.8% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 13 through 28 removed outlier: 4.182A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 48 removed outlier: 3.949A pdb=" N LEU C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 79 Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.534A pdb=" N LYS C 145 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 146 " --> pdb=" O GLU C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 151 through 171 removed outlier: 3.788A pdb=" N THR C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.824A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 237 removed outlier: 3.508A pdb=" N ILE C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.672A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.987A pdb=" N ASN D 134 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 200 through 212 removed outlier: 4.129A pdb=" N ILE D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.341A pdb=" N THR D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.753A pdb=" N LYS D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 295 removed outlier: 3.964A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.199A pdb=" N LYS D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 916 Processing helix chain 'D' and resid 921 through 984 removed outlier: 4.068A pdb=" N LYS D 941 " --> pdb=" O LYS D 937 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D 963 " --> pdb=" O ALA D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 removed outlier: 3.818A pdb=" N PHE D1026 " --> pdb=" O GLY D1022 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER D1027 " --> pdb=" O GLU D1023 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D1030 " --> pdb=" O PHE D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1072 removed outlier: 3.657A pdb=" N LYS D1059 " --> pdb=" O GLN D1055 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D1060 " --> pdb=" O VAL D1056 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS D1067 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D1070 " --> pdb=" O VAL D1066 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D1071 " --> pdb=" O LYS D1067 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE D1072 " --> pdb=" O LYS D1068 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 98 through 103 removed outlier: 3.696A pdb=" N ASP E 101 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE E 102 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.797A pdb=" N VAL E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 removed outlier: 4.170A pdb=" N VAL E 185 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU E 186 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE E 188 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 206 through 262 removed outlier: 3.956A pdb=" N ASP E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 878 removed outlier: 4.330A pdb=" N ALA E 878 " --> pdb=" O GLU E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 945 removed outlier: 3.846A pdb=" N GLN E 907 " --> pdb=" O THR E 903 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL E 924 " --> pdb=" O GLU E 920 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 925 " --> pdb=" O ASP E 921 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 926 " --> pdb=" O HIS E 922 " (cutoff:3.500A) Proline residue: E 927 - end of helix removed outlier: 3.832A pdb=" N VAL E 933 " --> pdb=" O LEU E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 1002 removed outlier: 3.639A pdb=" N MET E 999 " --> pdb=" O THR E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1022 through 1037 removed outlier: 3.715A pdb=" N ILE E1027 " --> pdb=" O ARG E1023 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL E1028 " --> pdb=" O ASN E1024 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET E1032 " --> pdb=" O VAL E1028 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN E1035 " --> pdb=" O ALA E1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 25 Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.154A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 59 through 63 removed outlier: 4.223A pdb=" N ASN F 63 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 83 removed outlier: 4.371A pdb=" N MET F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 6.702A pdb=" N PHE F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 260 through 265 Processing helix chain 'F' and resid 267 through 279 removed outlier: 4.501A pdb=" N LYS F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET F 279 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 removed outlier: 4.156A pdb=" N THR F 286 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 283 through 287' Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.659A pdb=" N SER F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 71 removed outlier: 4.424A pdb=" N HIS G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.688A pdb=" N MET G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 119 Processing helix chain 'G' and resid 131 through 143 removed outlier: 4.549A pdb=" N ASN G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER G 138 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 214 through 218 removed outlier: 3.557A pdb=" N GLN G 217 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 246 removed outlier: 3.544A pdb=" N ILE G 246 " --> pdb=" O PRO G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 300 removed outlier: 3.765A pdb=" N PHE G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 334 removed outlier: 3.740A pdb=" N ASN G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 373 Processing helix chain 'G' and resid 385 through 388 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.661A pdb=" N PHE C 133 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 85 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 134 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.277A pdb=" N LYS C 205 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 336 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER C 207 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 333 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 283 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 335 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C 281 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 93 through 99 removed outlier: 6.749A pdb=" N GLU D 94 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 96 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 98 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 85 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 84 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE D 90 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N SER D 149 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 1043 through 1047 Processing sheet with id=AA5, first strand: chain 'D' and resid 990 through 993 removed outlier: 3.517A pdb=" N TYR D1004 " --> pdb=" O ASN D 991 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 993 " --> pdb=" O GLU D1002 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU D1002 " --> pdb=" O SER D 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.734A pdb=" N ILE E 42 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS E 117 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS E 44 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 115 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 112 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 139 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 114 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL E 157 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1010 through 1014 removed outlier: 6.432A pdb=" N ARG E1011 " --> pdb=" O PHE E1045 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E1047 " --> pdb=" O ARG E1011 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E1013 " --> pdb=" O ILE E1047 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 65 " --> pdb=" O TYR E1044 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E1046 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 64 " --> pdb=" O ARG E1062 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 951 through 956 Processing sheet with id=AA9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'F' and resid 240 through 242 Processing sheet with id=AB3, first strand: chain 'G' and resid 305 through 306 592 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4958 1.34 - 1.46: 3515 1.46 - 1.58: 7122 1.58 - 1.70: 111 1.70 - 1.83: 97 Bond restraints: 15803 Sorted by residual: bond pdb=" C4 ATP E1101 " pdb=" C5 ATP E1101 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.77e+01 bond pdb=" C5 ATP E1101 " pdb=" C6 ATP E1101 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP E1101 " pdb=" N7 ATP E1101 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP E1101 " pdb=" N7 ATP E1101 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.80e+01 bond pdb=" C4 ATP E1101 " pdb=" N9 ATP E1101 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.49e+01 ... (remaining 15798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 21389 3.89 - 7.78: 105 7.78 - 11.66: 5 11.66 - 15.55: 1 15.55 - 19.44: 2 Bond angle restraints: 21502 Sorted by residual: angle pdb=" PB ATP E1101 " pdb=" O3B ATP E1101 " pdb=" PG ATP E1101 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP E1101 " pdb=" O3A ATP E1101 " pdb=" PB ATP E1101 " ideal model delta sigma weight residual 136.83 120.36 16.47 1.00e+00 1.00e+00 2.71e+02 angle pdb=" C5 ATP E1101 " pdb=" C4 ATP E1101 " pdb=" N3 ATP E1101 " ideal model delta sigma weight residual 126.80 118.72 8.08 1.00e+00 1.00e+00 6.53e+01 angle pdb=" N3 ATP E1101 " pdb=" C4 ATP E1101 " pdb=" N9 ATP E1101 " ideal model delta sigma weight residual 127.04 134.94 -7.90 1.15e+00 7.59e-01 4.74e+01 angle pdb=" N1 ATP E1101 " pdb=" C2 ATP E1101 " pdb=" N3 ATP E1101 " ideal model delta sigma weight residual 128.69 123.73 4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 21497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8029 17.92 - 35.85: 1092 35.85 - 53.77: 393 53.77 - 71.70: 100 71.70 - 89.62: 18 Dihedral angle restraints: 9632 sinusoidal: 4388 harmonic: 5244 Sorted by residual: dihedral pdb=" CA ASN G 376 " pdb=" C ASN G 376 " pdb=" N HIS G 377 " pdb=" CA HIS G 377 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ALA G 373 " pdb=" C ALA G 373 " pdb=" N HIS G 374 " pdb=" CA HIS G 374 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS G 392 " pdb=" C LYS G 392 " pdb=" N LYS G 393 " pdb=" CA LYS G 393 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 9629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1811 0.051 - 0.103: 534 0.103 - 0.154: 76 0.154 - 0.205: 18 0.205 - 0.257: 2 Chirality restraints: 2441 Sorted by residual: chirality pdb=" CA SER E 193 " pdb=" N SER E 193 " pdb=" C SER E 193 " pdb=" CB SER E 193 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE G 153 " pdb=" CA ILE G 153 " pdb=" CG1 ILE G 153 " pdb=" CG2 ILE G 153 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE E 263 " pdb=" CA ILE E 263 " pdb=" CG1 ILE E 263 " pdb=" CG2 ILE E 263 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 2438 not shown) Planarity restraints: 2563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 239 " 0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP C 239 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 239 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 239 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 239 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 239 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 239 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 239 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 239 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 239 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 957 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO E 958 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 958 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 958 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 192 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C LYS E 192 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS E 192 " -0.011 2.00e-02 2.50e+03 pdb=" N SER E 193 " -0.010 2.00e-02 2.50e+03 ... (remaining 2560 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2177 2.75 - 3.29: 15441 3.29 - 3.83: 25091 3.83 - 4.36: 28962 4.36 - 4.90: 47720 Nonbonded interactions: 119391 Sorted by model distance: nonbonded pdb=" OE1 GLN E1003 " pdb=" OH TYR E1044 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS E 971 " pdb=" O ALA E 976 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR C 270 " pdb=" O LYS C 276 " model vdw 2.221 3.040 nonbonded pdb=" O ARG G 65 " pdb=" OG1 THR G 69 " model vdw 2.229 3.040 nonbonded pdb=" ND2 ASN G 134 " pdb=" O ARG G 202 " model vdw 2.242 3.120 ... (remaining 119386 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.005 0.082 15803 Z= 0.266 Angle : 0.845 19.438 21502 Z= 0.527 Chirality : 0.049 0.257 2441 Planarity : 0.004 0.056 2563 Dihedral : 19.049 89.620 6218 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.44 % Favored : 86.28 % Rotamer: Outliers : 3.26 % Allowed : 11.97 % Favored : 84.76 % 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: -4.24 (0.16), residues: 1771 helix: -1.83 (0.16), residues: 777 sheet: -2.76 (0.34), residues: 172 loop : -3.89 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 361 TYR 0.020 0.002 TYR F 181 PHE 0.025 0.002 PHE E 50 TRP 0.039 0.003 TRP C 239 HIS 0.008 0.001 HIS G 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.27 (15803) covalent geometry : angle 0.84495 / 0.53 (21502) hydrogen bonds : bond 0.16899 / 20.08 ( 616) hydrogen bonds : angle 7.10468 / 8.52 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 0.619 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: C 43 ARG cc_start: 0.6480 (ttp80) cc_final: 0.5934 (ttt180) REVERT: D 205 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7498 (tm-30) REVERT: D 1023 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6022 (pm20) REVERT: E 50 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: E 75 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6604 (pttm) REVERT: E 91 GLU cc_start: 0.8511 (pt0) cc_final: 0.8140 (pm20) REVERT: E 101 ASP cc_start: 0.7432 (m-30) cc_final: 0.6911 (t0) REVERT: E 155 TYR cc_start: 0.5281 (m-80) cc_final: 0.3908 (m-80) REVERT: E 230 ASP cc_start: 0.7739 (m-30) cc_final: 0.7415 (m-30) REVERT: E 875 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7787 (p) REVERT: F 50 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7618 (tppt) REVERT: F 166 SER cc_start: 0.7824 (m) cc_final: 0.7433 (p) REVERT: F 207 PHE cc_start: 0.7781 (t80) cc_final: 0.7567 (t80) REVERT: F 252 GLU cc_start: 0.6792 (mp0) cc_final: 0.6468 (mp0) REVERT: G 290 LYS cc_start: 0.8425 (mppt) cc_final: 0.8167 (mmtp) REVERT: G 393 LYS cc_start: 0.6599 (tptm) cc_final: 0.6060 (tptm) outliers start: 52 outliers final: 20 residues processed: 343 average time/residue: 0.1252 time to fit residues: 62.9976 Evaluate side-chains 203 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 184 ARG Chi-restraints excluded: chain E residue 875 SER Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 884 GLU Chi-restraints excluded: chain E residue 891 ASP Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN C 52 ASN C 87 HIS C 152 GLN C 188 ASN C 215 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 166 GLN D 263 HIS D1009 ASN D1048 GLN E 71 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E 882 HIS E1017 ASN E1018 GLN E1035 ASN E1043 GLN E1074 ASN F 142 GLN G 67 GLN G 134 ASN G 260 ASN ** G 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.165505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128226 restraints weight = 22368.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130361 restraints weight = 17274.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.130845 restraints weight = 14425.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131399 restraints weight = 12386.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.131612 restraints weight = 11062.714| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15803 Z= 0.176 Angle : 0.715 11.169 21502 Z= 0.381 Chirality : 0.046 0.232 2441 Planarity : 0.004 0.055 2563 Dihedral : 19.012 88.716 2656 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.18 % Favored : 88.71 % Rotamer: Outliers : 3.82 % Allowed : 18.62 % Favored : 77.55 % 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: -3.39 (0.18), residues: 1771 helix: -1.08 (0.18), residues: 786 sheet: -2.44 (0.35), residues: 187 loop : -3.46 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 127 TYR 0.016 0.002 TYR D 161 PHE 0.026 0.002 PHE C 165 TRP 0.019 0.002 TRP C 239 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (15803) covalent geometry : angle 0.71479 / 0.38 (21502) hydrogen bonds : bond 0.05483 / 6.06 ( 616) hydrogen bonds : angle 5.66974 / 7.02 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 ASP cc_start: 0.7755 (t0) cc_final: 0.7377 (t0) REVERT: D 205 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7519 (tm-30) REVERT: D 1053 MET cc_start: 0.6806 (ptt) cc_final: 0.6598 (ptm) REVERT: E 50 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: E 75 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6596 (pttm) REVERT: E 91 GLU cc_start: 0.8289 (pt0) cc_final: 0.8004 (mp0) REVERT: E 101 ASP cc_start: 0.7360 (m-30) cc_final: 0.6933 (t0) REVERT: E 155 TYR cc_start: 0.5201 (m-80) cc_final: 0.3821 (m-80) REVERT: E 180 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7026 (pp) REVERT: E 230 ASP cc_start: 0.7801 (m-30) cc_final: 0.7427 (m-30) REVERT: E 1061 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (ptp) REVERT: F 166 SER cc_start: 0.8624 (m) cc_final: 0.7114 (p) REVERT: F 207 PHE cc_start: 0.7659 (t80) cc_final: 0.7311 (t80) REVERT: F 252 GLU cc_start: 0.6806 (mp0) cc_final: 0.6347 (mp0) REVERT: G 285 THR cc_start: 0.6737 (p) cc_final: 0.6401 (t) REVERT: G 290 LYS cc_start: 0.8381 (mppt) cc_final: 0.8098 (mmtp) REVERT: G 393 LYS cc_start: 0.6556 (tptm) cc_final: 0.6072 (tptm) outliers start: 61 outliers final: 27 residues processed: 244 average time/residue: 0.1080 time to fit residues: 41.1170 Evaluate side-chains 209 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1009 ASN Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 884 GLU Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 138 optimal weight: 0.0370 chunk 127 optimal weight: 0.7980 chunk 94 optimal weight: 0.0040 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN G 208 GLN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.161662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.124760 restraints weight = 23285.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126284 restraints weight = 19073.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.127020 restraints weight = 16490.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127562 restraints weight = 13376.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127843 restraints weight = 12109.220| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15803 Z= 0.136 Angle : 0.653 11.768 21502 Z= 0.347 Chirality : 0.044 0.348 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.735 89.770 2622 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.88 % Favored : 90.06 % Rotamer: Outliers : 3.45 % Allowed : 20.25 % Favored : 76.30 % 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: -2.92 (0.19), residues: 1771 helix: -0.71 (0.18), residues: 794 sheet: -2.14 (0.38), residues: 175 loop : -3.24 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 189 TYR 0.017 0.002 TYR E1044 PHE 0.043 0.002 PHE E 256 TRP 0.018 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (15803) covalent geometry : angle 0.65312 / 0.35 (21502) hydrogen bonds : bond 0.04960 / 5.48 ( 616) hydrogen bonds : angle 5.25905 / 6.63 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 301 LEU cc_start: 0.8993 (mm) cc_final: 0.8757 (mm) REVERT: D 205 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 211 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6277 (m-10) REVERT: E 50 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: E 71 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7694 (m110) REVERT: E 91 GLU cc_start: 0.8254 (pt0) cc_final: 0.7934 (mp0) REVERT: E 101 ASP cc_start: 0.7352 (m-30) cc_final: 0.6980 (t0) REVERT: E 155 TYR cc_start: 0.5039 (m-80) cc_final: 0.3714 (m-80) REVERT: E 180 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6854 (pp) REVERT: E 230 ASP cc_start: 0.7782 (m-30) cc_final: 0.7375 (m-30) REVERT: E 1061 MET cc_start: 0.7309 (mtp) cc_final: 0.7043 (ptp) REVERT: F 126 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8582 (pp) REVERT: G 290 LYS cc_start: 0.8354 (mppt) cc_final: 0.8087 (mmtp) outliers start: 55 outliers final: 28 residues processed: 239 average time/residue: 0.0976 time to fit residues: 37.7001 Evaluate side-chains 200 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 884 GLU Chi-restraints excluded: chain E residue 891 ASP Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 171 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 162 optimal weight: 0.0370 chunk 173 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 119 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.161670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124923 restraints weight = 23301.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126147 restraints weight = 19154.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126873 restraints weight = 17059.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127402 restraints weight = 13625.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127761 restraints weight = 12148.476| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15803 Z= 0.132 Angle : 0.626 11.665 21502 Z= 0.331 Chirality : 0.043 0.274 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.484 89.753 2615 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.80 % Rotamer: Outliers : 4.08 % Allowed : 22.01 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.19), residues: 1771 helix: -0.46 (0.18), residues: 792 sheet: -1.95 (0.39), residues: 175 loop : -3.06 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 960 TYR 0.014 0.001 TYR C 261 PHE 0.016 0.001 PHE G 88 TRP 0.019 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15803) covalent geometry : angle 0.62597 / 0.33 (21502) hydrogen bonds : bond 0.04629 / 5.12 ( 616) hydrogen bonds : angle 5.08406 / 6.43 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 0.460 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: C 301 LEU cc_start: 0.9040 (mm) cc_final: 0.8810 (mm) REVERT: D 144 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6873 (ttt-90) REVERT: D 205 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7494 (tm-30) REVERT: D 211 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: E 50 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6148 (m-10) REVERT: E 91 GLU cc_start: 0.8159 (pt0) cc_final: 0.7887 (mp0) REVERT: E 101 ASP cc_start: 0.7370 (m-30) cc_final: 0.6970 (t0) REVERT: E 155 TYR cc_start: 0.5092 (m-80) cc_final: 0.3845 (m-80) REVERT: E 180 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6723 (pp) REVERT: E 1061 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7072 (ptp) REVERT: F 126 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8576 (pp) REVERT: F 281 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8349 (pp) REVERT: G 290 LYS cc_start: 0.8341 (mppt) cc_final: 0.8044 (mmtp) REVERT: G 346 LEU cc_start: 0.5029 (OUTLIER) cc_final: 0.4789 (pp) REVERT: G 393 LYS cc_start: 0.6543 (tptm) cc_final: 0.6260 (tptp) outliers start: 65 outliers final: 39 residues processed: 238 average time/residue: 0.0959 time to fit residues: 36.4396 Evaluate side-chains 218 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain G residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 74 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 3 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.162386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126151 restraints weight = 23265.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128277 restraints weight = 18720.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129022 restraints weight = 16258.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.129410 restraints weight = 12362.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129753 restraints weight = 11231.319| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15803 Z= 0.127 Angle : 0.610 11.995 21502 Z= 0.321 Chirality : 0.043 0.243 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.326 89.650 2612 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.32 % Favored : 90.63 % Rotamer: Outliers : 4.01 % Allowed : 22.63 % Favored : 73.35 % 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: -2.39 (0.19), residues: 1771 helix: -0.27 (0.18), residues: 789 sheet: -1.76 (0.40), residues: 175 loop : -2.96 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 189 TYR 0.013 0.001 TYR C 261 PHE 0.015 0.002 PHE G 380 TRP 0.021 0.002 TRP C 160 HIS 0.004 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (15803) covalent geometry : angle 0.61002 / 0.32 (21502) hydrogen bonds : bond 0.04520 / 4.96 ( 616) hydrogen bonds : angle 4.93890 / 6.27 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 205 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 211 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: E 50 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6274 (m-10) REVERT: E 91 GLU cc_start: 0.8082 (pt0) cc_final: 0.7827 (mp0) REVERT: E 101 ASP cc_start: 0.7445 (m-30) cc_final: 0.6961 (t0) REVERT: E 155 TYR cc_start: 0.5024 (m-80) cc_final: 0.3822 (m-80) REVERT: E 180 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6472 (pp) REVERT: E 230 ASP cc_start: 0.7446 (m-30) cc_final: 0.7133 (m-30) REVERT: E 1061 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7083 (ptp) REVERT: F 126 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (pp) REVERT: G 290 LYS cc_start: 0.8352 (mppt) cc_final: 0.8046 (mmtp) REVERT: G 393 LYS cc_start: 0.6464 (tptm) cc_final: 0.6198 (tptp) outliers start: 64 outliers final: 36 residues processed: 229 average time/residue: 0.0925 time to fit residues: 34.5207 Evaluate side-chains 204 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.159555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.122768 restraints weight = 23303.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123697 restraints weight = 19780.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.124563 restraints weight = 17643.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125215 restraints weight = 13807.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125491 restraints weight = 12351.271| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15803 Z= 0.152 Angle : 0.630 12.029 21502 Z= 0.330 Chirality : 0.044 0.245 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.257 88.886 2612 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.77 % Favored : 90.18 % Rotamer: Outliers : 4.45 % Allowed : 23.45 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.19), residues: 1771 helix: -0.15 (0.18), residues: 786 sheet: -1.79 (0.40), residues: 184 loop : -2.93 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.023 0.002 TYR C 261 PHE 0.040 0.002 PHE E 256 TRP 0.020 0.002 TRP C 160 HIS 0.005 0.001 HIS G 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (15803) covalent geometry : angle 0.62986 / 0.33 (21502) hydrogen bonds : bond 0.04510 / 4.94 ( 616) hydrogen bonds : angle 4.97146 / 6.32 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 174 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: D 205 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7430 (tm-30) REVERT: D 211 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: E 50 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: E 71 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: E 91 GLU cc_start: 0.8223 (pt0) cc_final: 0.7805 (mp0) REVERT: E 101 ASP cc_start: 0.7483 (m-30) cc_final: 0.6911 (t0) REVERT: E 155 TYR cc_start: 0.4989 (m-80) cc_final: 0.3804 (m-80) REVERT: E 180 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6582 (pp) REVERT: E 1061 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7117 (ptp) REVERT: F 50 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7495 (tppt) REVERT: F 126 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8503 (pp) REVERT: G 290 LYS cc_start: 0.8343 (mppt) cc_final: 0.8027 (mmtp) REVERT: G 367 ARG cc_start: 0.4766 (tpt-90) cc_final: 0.4125 (ptt180) REVERT: G 393 LYS cc_start: 0.6555 (tptm) cc_final: 0.6266 (tptp) outliers start: 71 outliers final: 47 residues processed: 223 average time/residue: 0.1141 time to fit residues: 40.4424 Evaluate side-chains 213 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN G 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.160857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124487 restraints weight = 23021.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125169 restraints weight = 19836.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.126377 restraints weight = 17162.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126919 restraints weight = 13354.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127219 restraints weight = 12107.708| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15803 Z= 0.133 Angle : 0.610 12.157 21502 Z= 0.321 Chirality : 0.043 0.173 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.173 87.814 2612 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.32 % Favored : 90.63 % Rotamer: Outliers : 4.39 % Allowed : 24.33 % Favored : 71.29 % 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: -2.12 (0.19), residues: 1771 helix: -0.03 (0.19), residues: 789 sheet: -1.75 (0.39), residues: 184 loop : -2.83 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.017 0.001 TYR D 240 PHE 0.047 0.002 PHE E 256 TRP 0.023 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15803) covalent geometry : angle 0.61038 / 0.32 (21502) hydrogen bonds : bond 0.04429 / 4.83 ( 616) hydrogen bonds : angle 4.84575 / 6.18 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.6649 (tt) REVERT: C 237 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8116 (mp) REVERT: D 144 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6931 (ttt-90) REVERT: D 205 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7460 (tm-30) REVERT: D 211 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: D 245 LYS cc_start: 0.8457 (ttpt) cc_final: 0.7796 (tttm) REVERT: E 50 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: E 91 GLU cc_start: 0.8178 (pt0) cc_final: 0.7829 (mp0) REVERT: E 101 ASP cc_start: 0.7375 (m-30) cc_final: 0.6841 (t0) REVERT: E 155 TYR cc_start: 0.5173 (m-80) cc_final: 0.3889 (m-80) REVERT: E 1061 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7042 (ptp) REVERT: F 126 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8513 (pp) REVERT: G 290 LYS cc_start: 0.8362 (mppt) cc_final: 0.8021 (mmtp) REVERT: G 367 ARG cc_start: 0.4733 (tpt-90) cc_final: 0.4531 (mtt180) outliers start: 70 outliers final: 41 residues processed: 222 average time/residue: 0.1088 time to fit residues: 38.4238 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 374 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.160268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123474 restraints weight = 23267.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.124777 restraints weight = 19264.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125601 restraints weight = 16491.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126139 restraints weight = 13161.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126399 restraints weight = 11919.633| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 15803 Z= 0.125 Angle : 0.640 15.239 21502 Z= 0.327 Chirality : 0.043 0.335 2441 Planarity : 0.003 0.052 2563 Dihedral : 18.102 86.582 2610 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.15 % Favored : 90.80 % Rotamer: Outliers : 3.89 % Allowed : 25.20 % Favored : 70.91 % 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 (0.19), residues: 1771 helix: 0.05 (0.19), residues: 792 sheet: -1.56 (0.40), residues: 184 loop : -2.75 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.012 0.001 TYR F 84 PHE 0.044 0.002 PHE E 256 TRP 0.029 0.002 TRP C 60 HIS 0.011 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15803) covalent geometry : angle 0.63990 / 0.33 (21502) hydrogen bonds : bond 0.04293 / 4.73 ( 616) hydrogen bonds : angle 4.75506 / 6.10 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.555 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: C 230 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6718 (tt) REVERT: C 237 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 205 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7470 (tm-30) REVERT: D 211 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: E 50 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6383 (m-10) REVERT: E 91 GLU cc_start: 0.8176 (pt0) cc_final: 0.7806 (mp0) REVERT: E 101 ASP cc_start: 0.7366 (m-30) cc_final: 0.6850 (t0) REVERT: E 155 TYR cc_start: 0.5071 (m-80) cc_final: 0.3864 (m-80) REVERT: F 126 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8500 (pp) REVERT: F 207 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7056 (t80) REVERT: G 290 LYS cc_start: 0.8377 (mppt) cc_final: 0.8041 (mmtp) outliers start: 62 outliers final: 48 residues processed: 224 average time/residue: 0.1154 time to fit residues: 40.5291 Evaluate side-chains 219 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 61 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 21 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.162056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.124689 restraints weight = 23061.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125166 restraints weight = 19265.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126462 restraints weight = 17181.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.126931 restraints weight = 13604.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127275 restraints weight = 12295.713| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15803 Z= 0.124 Angle : 0.639 12.682 21502 Z= 0.327 Chirality : 0.043 0.311 2441 Planarity : 0.003 0.051 2563 Dihedral : 18.053 85.350 2610 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.54 % Favored : 90.40 % Rotamer: Outliers : 3.95 % Allowed : 25.39 % Favored : 70.66 % 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: -1.93 (0.20), residues: 1771 helix: 0.05 (0.19), residues: 798 sheet: -1.51 (0.40), residues: 194 loop : -2.70 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 933 TYR 0.018 0.001 TYR E 961 PHE 0.040 0.002 PHE E 256 TRP 0.028 0.002 TRP C 160 HIS 0.012 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15803) covalent geometry : angle 0.63868 / 0.33 (21502) hydrogen bonds : bond 0.04237 / 4.63 ( 616) hydrogen bonds : angle 4.69396 / 6.00 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.622 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: C 230 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.6774 (tt) REVERT: C 237 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7899 (mp) REVERT: C 251 ASP cc_start: 0.7276 (t0) cc_final: 0.6985 (t0) REVERT: D 205 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7470 (tm-30) REVERT: D 211 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: E 50 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: E 91 GLU cc_start: 0.8207 (pt0) cc_final: 0.7803 (mp0) REVERT: E 101 ASP cc_start: 0.7363 (m-30) cc_final: 0.6829 (t0) REVERT: E 155 TYR cc_start: 0.5007 (m-80) cc_final: 0.3825 (m-80) REVERT: F 31 MET cc_start: 0.7697 (tpt) cc_final: 0.7462 (mmt) REVERT: F 126 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8503 (pp) REVERT: F 207 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7098 (t80) REVERT: G 290 LYS cc_start: 0.8324 (mppt) cc_final: 0.7993 (mmtp) outliers start: 63 outliers final: 51 residues processed: 216 average time/residue: 0.1074 time to fit residues: 37.2910 Evaluate side-chains 223 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN G 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.162877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.125633 restraints weight = 23193.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126047 restraints weight = 19854.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127640 restraints weight = 16865.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128001 restraints weight = 13634.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128316 restraints weight = 12430.151| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15803 Z= 0.133 Angle : 0.651 12.400 21502 Z= 0.333 Chirality : 0.043 0.304 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.023 84.305 2610 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.32 % Favored : 90.63 % Rotamer: Outliers : 3.89 % Allowed : 25.45 % Favored : 70.66 % 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: -1.88 (0.20), residues: 1771 helix: 0.11 (0.19), residues: 799 sheet: -1.49 (0.39), residues: 194 loop : -2.69 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 933 TYR 0.025 0.002 TYR C 266 PHE 0.039 0.001 PHE E 256 TRP 0.029 0.002 TRP C 160 HIS 0.013 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15803) covalent geometry : angle 0.65105 / 0.33 (21502) hydrogen bonds : bond 0.04218 / 4.64 ( 616) hydrogen bonds : angle 4.65107 / 5.96 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.6772 (tt) REVERT: C 237 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7944 (mp) REVERT: C 251 ASP cc_start: 0.7263 (t0) cc_final: 0.6971 (t0) REVERT: D 144 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6949 (ttt-90) REVERT: D 205 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7442 (tm-30) REVERT: D 211 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6401 (m-10) REVERT: E 50 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6347 (m-10) REVERT: E 91 GLU cc_start: 0.8176 (pt0) cc_final: 0.7766 (mp0) REVERT: E 101 ASP cc_start: 0.7355 (m-30) cc_final: 0.6813 (t0) REVERT: E 155 TYR cc_start: 0.5259 (m-80) cc_final: 0.3926 (m-80) REVERT: F 31 MET cc_start: 0.7773 (tpt) cc_final: 0.7518 (mmt) REVERT: F 126 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8484 (pp) REVERT: F 207 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7171 (t80) REVERT: G 290 LYS cc_start: 0.8320 (mppt) cc_final: 0.7984 (mmtp) outliers start: 62 outliers final: 51 residues processed: 212 average time/residue: 0.1073 time to fit residues: 36.7970 Evaluate side-chains 226 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1023 GLU Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 902 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 164 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN G 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.162944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.125630 restraints weight = 23005.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126999 restraints weight = 18402.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127453 restraints weight = 19290.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128735 restraints weight = 13637.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128920 restraints weight = 11622.087| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15803 Z= 0.122 Angle : 0.646 13.033 21502 Z= 0.329 Chirality : 0.042 0.300 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.975 83.390 2610 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 3.82 % Allowed : 26.02 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1771 helix: 0.25 (0.19), residues: 795 sheet: -1.44 (0.39), residues: 194 loop : -2.60 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 933 TYR 0.016 0.001 TYR C 266 PHE 0.038 0.001 PHE E 256 TRP 0.033 0.002 TRP C 160 HIS 0.013 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15803) covalent geometry : angle 0.64592 / 0.33 (21502) hydrogen bonds : bond 0.04134 / 4.54 ( 616) hydrogen bonds : angle 4.59323 / 5.88 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.69 seconds wall clock time: 47 minutes 41.13 seconds (2861.13 seconds total)