Starting phenix.real_space_refine on Fri Jul 3 18:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tve_26140/07_2026/7tve_26140_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tve_26140/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tve_26140/07_2026/7tve_26140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tve_26140/07_2026/7tve_26140.map" model { file = "/net/cci-nas-00/data/ceres_data/7tve_26140/07_2026/7tve_26140_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tve_26140/07_2026/7tve_26140_neut.cif" } 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-dev-6108/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: 3.37, per 1000 atoms: 0.22 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: 1.21 Conformation dependent library (CDL) restraints added in 681.1 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: 1.65 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: 1.98 Time building geometry restraints manager: 1.67 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: 2.640 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.440 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- 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= 0.265 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 0.84456 / 0.53 (21502) hydrogen bonds : bond 0.16899 / 19.98 ( 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 : 0.506 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: 0.1190 time to fit residues: 59.6148 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 : 0.429 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.165437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128110 restraints weight = 22374.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130112 restraints weight = 17324.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130667 restraints weight = 14439.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131264 restraints weight = 12591.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.131472 restraints weight = 11211.565| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15803 Z= 0.177 Angle : 0.716 10.565 21502 Z= 0.381 Chirality : 0.046 0.233 2441 Planarity : 0.004 0.056 2563 Dihedral : 19.029 88.467 2656 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.41 % Favored : 88.48 % Rotamer: Outliers : 3.76 % Allowed : 18.62 % Favored : 77.62 % 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: -3.38 (0.18), residues: 1771 helix: -1.08 (0.18), residues: 786 sheet: -2.43 (0.35), residues: 187 loop : -3.46 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 127 TYR 0.015 0.002 TYR D 161 PHE 0.025 0.002 PHE C 165 TRP 0.019 0.002 TRP C 239 HIS 0.009 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (15803) covalent geometry : angle 0.71553 / 0.38 (21502) hydrogen bonds : bond 0.05541 / 6.11 ( 616) hydrogen bonds : angle 5.65913 / 7.01 ( 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: 60 poor density : 202 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 ASP cc_start: 0.7741 (t0) cc_final: 0.7425 (t0) REVERT: D 205 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 1023 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: D 1053 MET cc_start: 0.6894 (ptt) cc_final: 0.6689 (ptm) REVERT: E 50 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: E 75 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6594 (pttm) REVERT: E 91 GLU cc_start: 0.8331 (pt0) cc_final: 0.7991 (mp0) REVERT: E 101 ASP cc_start: 0.7419 (m-30) cc_final: 0.6975 (t0) REVERT: E 155 TYR cc_start: 0.5127 (m-80) cc_final: 0.3813 (m-80) REVERT: E 169 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6626 (mm) REVERT: E 180 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6998 (pp) REVERT: E 230 ASP cc_start: 0.7801 (m-30) cc_final: 0.7418 (m-30) REVERT: E 1061 MET cc_start: 0.7550 (mtp) cc_final: 0.7145 (ptp) REVERT: F 166 SER cc_start: 0.8655 (m) cc_final: 0.7921 (p) REVERT: F 207 PHE cc_start: 0.7710 (t80) cc_final: 0.7355 (t80) REVERT: F 252 GLU cc_start: 0.6824 (mp0) cc_final: 0.6339 (mp0) REVERT: G 285 THR cc_start: 0.6722 (p) cc_final: 0.6366 (t) REVERT: G 290 LYS cc_start: 0.8373 (mppt) cc_final: 0.8084 (mmtp) REVERT: G 393 LYS cc_start: 0.6563 (tptm) cc_final: 0.6081 (tptm) outliers start: 60 outliers final: 27 residues processed: 245 average time/residue: 0.1061 time to fit residues: 40.4392 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 1023 GLU 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 169 LEU 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 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: 0.9990 chunk 144 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 96 optimal weight: 0.0020 chunk 105 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 94 optimal weight: 0.0370 overall best weight: 0.5466 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.161902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125022 restraints weight = 23306.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126540 restraints weight = 19002.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127425 restraints weight = 16375.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127939 restraints weight = 13179.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.128172 restraints weight = 12013.276| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2168 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= 0.135 Angle : 0.650 11.722 21502 Z= 0.346 Chirality : 0.044 0.364 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.768 89.657 2625 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.77 % Favored : 90.18 % Rotamer: Outliers : 3.45 % Allowed : 20.13 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.91 (0.19), residues: 1771 helix: -0.69 (0.18), residues: 791 sheet: -2.13 (0.38), residues: 175 loop : -3.23 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 189 TYR 0.017 0.002 TYR E1044 PHE 0.039 0.002 PHE E 256 TRP 0.017 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15803) covalent geometry : angle 0.64974 / 0.35 (21502) hydrogen bonds : bond 0.04950 / 5.45 ( 616) hydrogen bonds : angle 5.24524 / 6.62 ( 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 254 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.375 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: 0.9008 (mm) cc_final: 0.8765 (mm) REVERT: D 205 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 211 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: E 50 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: E 71 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7718 (m110) REVERT: E 91 GLU cc_start: 0.8294 (pt0) cc_final: 0.7917 (mp0) REVERT: E 101 ASP cc_start: 0.7439 (m-30) cc_final: 0.7007 (t0) REVERT: E 155 TYR cc_start: 0.4920 (m-80) cc_final: 0.3639 (m-80) REVERT: E 169 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6457 (mm) REVERT: E 180 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6828 (pp) REVERT: E 1061 MET cc_start: 0.7466 (mtp) cc_final: 0.7145 (ptp) REVERT: F 126 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8574 (pp) REVERT: F 166 SER cc_start: 0.8671 (m) cc_final: 0.7257 (p) REVERT: G 290 LYS cc_start: 0.8338 (mppt) cc_final: 0.8068 (mmtp) outliers start: 55 outliers final: 28 residues processed: 237 average time/residue: 0.1031 time to fit residues: 38.9133 Evaluate side-chains 205 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 169 LEU 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: 0.0060 chunk 80 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 8 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.161621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124712 restraints weight = 23293.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126291 restraints weight = 18931.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126836 restraints weight = 17244.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127494 restraints weight = 13426.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.127796 restraints weight = 11877.282| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15803 Z= 0.133 Angle : 0.627 11.860 21502 Z= 0.332 Chirality : 0.043 0.254 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.560 89.664 2615 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.37 % Favored : 90.57 % Rotamer: Outliers : 3.76 % Allowed : 22.19 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.19), residues: 1771 helix: -0.45 (0.18), residues: 792 sheet: -1.96 (0.39), residues: 175 loop : -3.08 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 960 TYR 0.014 0.001 TYR C 261 PHE 0.018 0.001 PHE G 88 TRP 0.019 0.002 TRP C 160 HIS 0.008 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15803) covalent geometry : angle 0.62678 / 0.33 (21502) hydrogen bonds : bond 0.04652 / 5.10 ( 616) hydrogen bonds : angle 5.08031 / 6.40 ( 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 250 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.516 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: 0.9043 (mm) cc_final: 0.8819 (mm) REVERT: D 144 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6869 (ttt-90) REVERT: D 205 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 211 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: E 50 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: E 91 GLU cc_start: 0.8156 (pt0) cc_final: 0.7891 (mp0) REVERT: E 101 ASP cc_start: 0.7380 (m-30) cc_final: 0.6983 (t0) REVERT: E 155 TYR cc_start: 0.5074 (m-80) cc_final: 0.3839 (m-80) REVERT: E 180 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6781 (pp) REVERT: E 1061 MET cc_start: 0.7445 (mtp) cc_final: 0.7151 (ptp) REVERT: F 126 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8568 (pp) REVERT: F 279 MET cc_start: 0.7701 (mtm) cc_final: 0.7485 (mpp) REVERT: G 290 LYS cc_start: 0.8343 (mppt) cc_final: 0.8047 (mmtp) REVERT: G 346 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4821 (pp) REVERT: G 393 LYS cc_start: 0.6578 (tptm) cc_final: 0.6293 (tptp) outliers start: 60 outliers final: 37 residues processed: 231 average time/residue: 0.1007 time to fit residues: 37.0415 Evaluate side-chains 213 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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 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 185 LEU Chi-restraints excluded: chain F residue 226 THR 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: 0.8980 chunk 172 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 3 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 152 optimal weight: 0.1980 chunk 153 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 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 = 0.4339 r_free = 0.4339 target = 0.163168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.126203 restraints weight = 23206.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127870 restraints weight = 18833.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128431 restraints weight = 16264.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129056 restraints weight = 12978.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129331 restraints weight = 11611.006| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15803 Z= 0.122 Angle : 0.601 11.850 21502 Z= 0.318 Chirality : 0.042 0.242 2441 Planarity : 0.003 0.053 2563 Dihedral : 18.337 89.585 2612 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 3.82 % Allowed : 22.63 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.19), residues: 1771 helix: -0.22 (0.18), residues: 788 sheet: -1.75 (0.39), residues: 185 loop : -2.95 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 43 TYR 0.013 0.001 TYR D 161 PHE 0.016 0.001 PHE G 309 TRP 0.023 0.002 TRP C 160 HIS 0.004 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15803) covalent geometry : angle 0.60123 / 0.32 (21502) hydrogen bonds : bond 0.04462 / 4.87 ( 616) hydrogen bonds : angle 4.89859 / 6.23 ( 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 252 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 301 LEU cc_start: 0.9067 (mm) cc_final: 0.8860 (mm) REVERT: D 205 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 211 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: E 50 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6206 (m-10) REVERT: E 91 GLU cc_start: 0.8140 (pt0) cc_final: 0.7804 (mp0) REVERT: E 101 ASP cc_start: 0.7462 (m-30) cc_final: 0.6959 (t0) REVERT: E 155 TYR cc_start: 0.4932 (m-80) cc_final: 0.3840 (m-80) REVERT: E 169 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6428 (mm) REVERT: E 180 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6480 (pp) REVERT: E 999 MET cc_start: 0.6378 (ttt) cc_final: 0.6067 (ttt) REVERT: E 1061 MET cc_start: 0.7361 (mtp) cc_final: 0.7128 (ptp) REVERT: F 126 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8630 (pp) REVERT: G 290 LYS cc_start: 0.8305 (mppt) cc_final: 0.8004 (mmtp) REVERT: G 393 LYS cc_start: 0.6443 (tptm) cc_final: 0.6156 (tptp) outliers start: 61 outliers final: 33 residues processed: 232 average time/residue: 0.1014 time to fit residues: 38.2926 Evaluate side-chains 207 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain C residue 279 ILE 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 1016 VAL 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 169 LEU 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 870 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 92 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.160584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123559 restraints weight = 23306.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.124629 restraints weight = 19178.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125451 restraints weight = 17653.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125924 restraints weight = 14006.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.126257 restraints weight = 12417.004| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15803 Z= 0.153 Angle : 0.634 11.923 21502 Z= 0.333 Chirality : 0.043 0.157 2441 Planarity : 0.003 0.055 2563 Dihedral : 18.288 88.850 2612 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.66 % Favored : 90.29 % Rotamer: Outliers : 4.01 % Allowed : 23.95 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.19), residues: 1771 helix: -0.18 (0.18), residues: 787 sheet: -1.79 (0.40), residues: 184 loop : -2.94 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 135 TYR 0.015 0.001 TYR F 84 PHE 0.021 0.002 PHE C 310 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 0.63390 / 0.33 (21502) hydrogen bonds : bond 0.04528 / 4.93 ( 616) hydrogen bonds : angle 4.92106 / 6.26 ( 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 240 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 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: symmetry clash REVERT: C 301 LEU cc_start: 0.9067 (mm) cc_final: 0.8857 (mm) REVERT: D 184 PRO cc_start: 0.8224 (Cg_endo) cc_final: 0.8008 (Cg_exo) REVERT: D 205 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7450 (tm-30) REVERT: D 211 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: E 50 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6389 (m-10) REVERT: E 91 GLU cc_start: 0.8128 (pt0) cc_final: 0.7816 (mp0) REVERT: E 101 ASP cc_start: 0.7435 (m-30) cc_final: 0.6892 (t0) REVERT: E 155 TYR cc_start: 0.5289 (m-80) cc_final: 0.4089 (m-80) REVERT: E 169 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6493 (mm) REVERT: E 180 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6587 (pp) REVERT: E 1061 MET cc_start: 0.7432 (mtp) cc_final: 0.7165 (ptp) REVERT: F 50 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7576 (tppt) REVERT: F 126 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8493 (pp) REVERT: F 279 MET cc_start: 0.7622 (mtm) cc_final: 0.7409 (mpp) REVERT: G 290 LYS cc_start: 0.8233 (mppt) cc_final: 0.7939 (mmtp) REVERT: G 367 ARG cc_start: 0.4693 (tpt-90) cc_final: 0.4098 (ptt180) REVERT: G 393 LYS cc_start: 0.6613 (tptm) cc_final: 0.6325 (tptp) outliers start: 64 outliers final: 41 residues processed: 222 average time/residue: 0.1013 time to fit residues: 35.3102 Evaluate side-chains 208 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 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 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 181 SER 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 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 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: 3.9990 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 166 optimal weight: 0.3980 chunk 44 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.163035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.126132 restraints weight = 22993.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127064 restraints weight = 19145.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.128076 restraints weight = 16903.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.128684 restraints weight = 13219.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.128972 restraints weight = 11945.420| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3161 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= 0.122 Angle : 0.598 12.324 21502 Z= 0.316 Chirality : 0.042 0.178 2441 Planarity : 0.003 0.051 2563 Dihedral : 18.164 87.711 2610 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.42 % Rotamer: Outliers : 3.89 % Allowed : 24.26 % Favored : 71.85 % 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: -2.07 (0.19), residues: 1771 helix: 0.02 (0.19), residues: 789 sheet: -1.71 (0.40), residues: 184 loop : -2.81 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.025 0.001 TYR D 240 PHE 0.018 0.001 PHE G 380 TRP 0.024 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15803) covalent geometry : angle 0.59827 / 0.32 (21502) hydrogen bonds : bond 0.04344 / 4.71 ( 616) hydrogen bonds : angle 4.71810 / 6.06 ( 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 242 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.614 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: 0.7569 (OUTLIER) cc_final: 0.6659 (tt) REVERT: C 237 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (mp) REVERT: D 205 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 211 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: D 245 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7708 (tttm) REVERT: E 50 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6320 (m-10) REVERT: E 91 GLU cc_start: 0.8174 (pt0) cc_final: 0.7794 (mp0) REVERT: E 101 ASP cc_start: 0.7442 (m-30) cc_final: 0.6880 (t0) REVERT: E 155 TYR cc_start: 0.5173 (m-80) cc_final: 0.3977 (m-80) REVERT: E 169 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6486 (mm) REVERT: E 177 CYS cc_start: 0.5587 (t) cc_final: 0.5041 (t) REVERT: E 180 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6684 (pp) REVERT: E 1061 MET cc_start: 0.7369 (mtp) cc_final: 0.7104 (ptp) REVERT: F 31 MET cc_start: 0.7558 (tpt) cc_final: 0.7156 (mmt) REVERT: F 126 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8559 (pp) REVERT: G 290 LYS cc_start: 0.8204 (mppt) cc_final: 0.7901 (mmtp) REVERT: G 367 ARG cc_start: 0.4814 (tpt-90) cc_final: 0.4538 (mtt180) outliers start: 62 outliers final: 40 residues processed: 222 average time/residue: 0.1088 time to fit residues: 37.8674 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 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 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 66 MET 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 169 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 84 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 0.0270 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 121 optimal weight: 0.0000 chunk 162 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 overall best weight: 0.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 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 = 0.4342 r_free = 0.4342 target = 0.163459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126768 restraints weight = 23193.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127519 restraints weight = 18763.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128693 restraints weight = 17423.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.129353 restraints weight = 13015.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.129640 restraints weight = 11753.211| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15803 Z= 0.114 Angle : 0.617 14.735 21502 Z= 0.317 Chirality : 0.042 0.344 2441 Planarity : 0.003 0.051 2563 Dihedral : 18.073 86.470 2610 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer: Outliers : 3.39 % Allowed : 24.76 % Favored : 71.85 % 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: -1.84 (0.20), residues: 1771 helix: 0.15 (0.19), residues: 797 sheet: -1.36 (0.41), residues: 180 loop : -2.70 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 189 TYR 0.014 0.001 TYR D 240 PHE 0.012 0.001 PHE D1052 TRP 0.028 0.002 TRP C 60 HIS 0.012 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15803) covalent geometry : angle 0.61708 / 0.32 (21502) hydrogen bonds : bond 0.04156 / 4.53 ( 616) hydrogen bonds : angle 4.62643 / 5.97 ( 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 256 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6620 (tt) REVERT: C 237 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7501 (mm) REVERT: C 251 ASP cc_start: 0.7320 (t0) cc_final: 0.6981 (t0) REVERT: D 205 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7370 (tm-30) REVERT: D 211 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6427 (m-10) REVERT: D 245 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7695 (ttpp) REVERT: D 1094 SER cc_start: 0.8303 (t) cc_final: 0.8102 (p) REVERT: E 50 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: E 91 GLU cc_start: 0.8127 (pt0) cc_final: 0.7760 (mp0) REVERT: E 101 ASP cc_start: 0.7380 (m-30) cc_final: 0.6875 (t0) REVERT: E 155 TYR cc_start: 0.4968 (m-80) cc_final: 0.3766 (m-80) REVERT: E 169 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6779 (mm) REVERT: E 180 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6658 (pp) REVERT: E 230 ASP cc_start: 0.7326 (m-30) cc_final: 0.6916 (m-30) REVERT: E 1061 MET cc_start: 0.7354 (mtp) cc_final: 0.7085 (ptp) REVERT: F 31 MET cc_start: 0.7491 (tpt) cc_final: 0.7210 (mmt) REVERT: F 126 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (pp) REVERT: G 290 LYS cc_start: 0.8198 (mppt) cc_final: 0.7792 (mmmm) outliers start: 54 outliers final: 36 residues processed: 236 average time/residue: 0.1010 time to fit residues: 37.5972 Evaluate side-chains 216 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 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 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 1056 VAL 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 135 ILE Chi-restraints excluded: chain E residue 169 LEU 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 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 1081 MET 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 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 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: 2.9990 chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 168 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 157 optimal weight: 0.0470 chunk 145 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 = 0.162196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124984 restraints weight = 23044.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.126171 restraints weight = 18240.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126985 restraints weight = 17558.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127401 restraints weight = 13545.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127733 restraints weight = 12189.284| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15803 Z= 0.154 Angle : 0.655 11.807 21502 Z= 0.340 Chirality : 0.045 0.449 2441 Planarity : 0.003 0.054 2563 Dihedral : 18.074 85.094 2610 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.49 % Favored : 90.46 % Rotamer: Outliers : 3.76 % Allowed : 25.27 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.89 (0.20), residues: 1771 helix: 0.08 (0.19), residues: 797 sheet: -1.57 (0.39), residues: 194 loop : -2.65 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 135 TYR 0.022 0.002 TYR D 240 PHE 0.027 0.002 PHE C 310 TRP 0.027 0.002 TRP C 160 HIS 0.012 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (15803) covalent geometry : angle 0.65549 / 0.34 (21502) hydrogen bonds : bond 0.04362 / 4.74 ( 616) hydrogen bonds : angle 4.73265 / 6.04 ( 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 231 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.6917 (tt) REVERT: C 237 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8089 (mp) REVERT: C 251 ASP cc_start: 0.7336 (t0) cc_final: 0.7017 (t0) REVERT: D 144 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6953 (ttt-90) REVERT: D 205 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7415 (tm-30) REVERT: D 211 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: D 245 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7646 (ttpp) REVERT: E 50 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6300 (m-10) REVERT: E 91 GLU cc_start: 0.8136 (pt0) cc_final: 0.7750 (mp0) REVERT: E 101 ASP cc_start: 0.7334 (m-30) cc_final: 0.6831 (t0) REVERT: E 155 TYR cc_start: 0.5051 (m-80) cc_final: 0.3863 (m-80) REVERT: E 169 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6816 (mm) REVERT: E 180 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6743 (pp) REVERT: E 1061 MET cc_start: 0.7341 (mtp) cc_final: 0.7101 (ptp) REVERT: F 126 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8471 (pp) REVERT: F 207 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7151 (t80) REVERT: G 290 LYS cc_start: 0.8242 (mppt) cc_final: 0.7851 (mmmm) REVERT: G 367 ARG cc_start: 0.6526 (mtt180) cc_final: 0.6280 (ptm160) outliers start: 60 outliers final: 42 residues processed: 211 average time/residue: 0.1053 time to fit residues: 35.2838 Evaluate side-chains 215 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 265 MET 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 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 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 135 ILE Chi-restraints excluded: chain E residue 169 LEU 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 0.2980 chunk 135 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 41 optimal weight: 0.0050 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.4194 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.165336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.128087 restraints weight = 23044.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129213 restraints weight = 18581.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130446 restraints weight = 16164.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.130953 restraints weight = 12699.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131185 restraints weight = 11750.562| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15803 Z= 0.119 Angle : 0.632 13.151 21502 Z= 0.324 Chirality : 0.043 0.296 2441 Planarity : 0.003 0.050 2563 Dihedral : 18.000 84.018 2610 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 3.51 % Allowed : 25.58 % 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: -1.70 (0.20), residues: 1771 helix: 0.26 (0.19), residues: 801 sheet: -1.50 (0.39), residues: 194 loop : -2.56 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.028 0.001 TYR D 240 PHE 0.013 0.001 PHE D1052 TRP 0.030 0.002 TRP C 160 HIS 0.013 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15803) covalent geometry : angle 0.63204 / 0.32 (21502) hydrogen bonds : bond 0.04114 / 4.51 ( 616) hydrogen bonds : angle 4.58960 / 5.88 ( 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 225 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 0.582 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: 0.7447 (OUTLIER) cc_final: 0.6666 (tt) REVERT: C 237 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7808 (mp) REVERT: D 205 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 245 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7589 (ttpp) REVERT: E 50 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: E 91 GLU cc_start: 0.8113 (pt0) cc_final: 0.7720 (mp0) REVERT: E 101 ASP cc_start: 0.7373 (m-30) cc_final: 0.6841 (t0) REVERT: E 155 TYR cc_start: 0.5004 (m-80) cc_final: 0.3774 (m-80) REVERT: E 169 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6766 (mm) REVERT: E 180 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6666 (pp) REVERT: F 126 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8509 (pp) REVERT: F 207 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7185 (t80) REVERT: G 290 LYS cc_start: 0.8230 (mppt) cc_final: 0.7831 (mmmm) outliers start: 56 outliers final: 40 residues processed: 208 average time/residue: 0.1013 time to fit residues: 33.3338 Evaluate side-chains 212 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 125 VAL Chi-restraints excluded: chain C residue 216 LEU 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 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 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 1069 LEU 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 135 ILE Chi-restraints excluded: chain E residue 169 LEU 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 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 1072 ILE Chi-restraints excluded: chain E residue 1081 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** F 63 ASN ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 ASN G 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.164014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126576 restraints weight = 22943.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.127529 restraints weight = 18708.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128509 restraints weight = 17007.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.129073 restraints weight = 13403.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129382 restraints weight = 12067.483| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15803 Z= 0.129 Angle : 0.633 12.768 21502 Z= 0.326 Chirality : 0.043 0.341 2441 Planarity : 0.003 0.054 2563 Dihedral : 17.987 83.235 2610 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.02 % Rotamer: Outliers : 3.26 % Allowed : 25.77 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.67 (0.20), residues: 1771 helix: 0.27 (0.19), residues: 801 sheet: -1.49 (0.39), residues: 194 loop : -2.53 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1040 TYR 0.013 0.001 TYR F 84 PHE 0.016 0.001 PHE G 48 TRP 0.030 0.002 TRP C 160 HIS 0.013 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15803) covalent geometry : angle 0.63267 / 0.33 (21502) hydrogen bonds : bond 0.04163 / 4.56 ( 616) hydrogen bonds : angle 4.63208 / 5.93 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.05 seconds wall clock time: 46 minutes 46.61 seconds (2806.61 seconds total)