Starting phenix.real_space_refine on Sat Oct 11 14:59:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tve_26140/10_2025/7tve_26140_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tve_26140/10_2025/7tve_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_26140/10_2025/7tve_26140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tve_26140/10_2025/7tve_26140.map" model { file = "/net/cci-nas-00/data/ceres_data/7tve_26140/10_2025/7tve_26140_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tve_26140/10_2025/7tve_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-2.0-5842/lib/python3.9/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: 3.75, per 1000 atoms: 0.24 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: 1.12 Conformation dependent library (CDL) restraints added in 612.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.88 Creating SS restraints... Processing helix chain 'C' and resid 13 through 28 removed outlier: 4.182A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 23 " --> pdb=" O LYS C 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 48 removed outlier: 3.949A pdb=" N LEU C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 79 Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.534A pdb=" N LYS C 145 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 146 " --> pdb=" O GLU C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 151 through 171 removed outlier: 3.788A pdb=" N THR C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.824A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 237 removed outlier: 3.508A pdb=" N ILE C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 306 through 316 Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.672A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.987A pdb=" N ASN D 134 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 200 through 212 removed outlier: 4.129A pdb=" N ILE D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.341A pdb=" N THR D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 247 removed outlier: 3.753A pdb=" N LYS D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 295 removed outlier: 3.964A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.199A pdb=" N LYS D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 916 Processing helix chain 'D' and resid 921 through 984 removed outlier: 4.068A pdb=" N LYS D 941 " --> pdb=" O LYS D 937 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN D 963 " --> pdb=" O ALA D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 removed outlier: 3.818A pdb=" N PHE D1026 " --> pdb=" O GLY D1022 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER D1027 " --> pdb=" O GLU D1023 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D1030 " --> pdb=" O PHE D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1072 removed outlier: 3.657A pdb=" N LYS D1059 " --> pdb=" O GLN D1055 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D1060 " --> pdb=" O VAL D1056 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS D1067 " --> pdb=" O THR D1063 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D1070 " --> pdb=" O VAL D1066 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D1071 " --> pdb=" O LYS D1067 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE D1072 " --> pdb=" O LYS D1068 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 98 through 103 removed outlier: 3.696A pdb=" N ASP E 101 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE E 102 " --> pdb=" O VAL E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.797A pdb=" N VAL E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 removed outlier: 4.170A pdb=" N VAL E 185 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU E 186 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE E 188 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 206 through 262 removed outlier: 3.956A pdb=" N ASP E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 878 removed outlier: 4.330A pdb=" N ALA E 878 " --> pdb=" O GLU E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 945 removed outlier: 3.846A pdb=" N GLN E 907 " --> pdb=" O THR E 903 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL E 924 " --> pdb=" O GLU E 920 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 925 " --> pdb=" O ASP E 921 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 926 " --> pdb=" O HIS E 922 " (cutoff:3.500A) Proline residue: E 927 - end of helix removed outlier: 3.832A pdb=" N VAL E 933 " --> pdb=" O LEU E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 1002 removed outlier: 3.639A pdb=" N MET E 999 " --> pdb=" O THR E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1022 through 1037 removed outlier: 3.715A pdb=" N ILE E1027 " --> pdb=" O ARG E1023 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL E1028 " --> pdb=" O ASN E1024 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET E1032 " --> pdb=" O VAL E1028 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN E1035 " --> pdb=" O ALA E1031 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 25 Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.154A pdb=" N ARG F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 59 through 63 removed outlier: 4.223A pdb=" N ASN F 63 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 83 removed outlier: 4.371A pdb=" N MET F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 6.702A pdb=" N PHE F 138 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 200 through 209 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 260 through 265 Processing helix chain 'F' and resid 267 through 279 removed outlier: 4.501A pdb=" N LYS F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET F 279 " --> pdb=" O VAL F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 removed outlier: 4.156A pdb=" N THR F 286 " --> pdb=" O LYS F 283 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS F 287 " --> pdb=" O GLU F 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 283 through 287' Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.659A pdb=" N SER F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 71 removed outlier: 4.424A pdb=" N HIS G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.688A pdb=" N MET G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 119 Processing helix chain 'G' and resid 131 through 143 removed outlier: 4.549A pdb=" N ASN G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER G 138 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 214 through 218 removed outlier: 3.557A pdb=" N GLN G 217 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 246 removed outlier: 3.544A pdb=" N ILE G 246 " --> pdb=" O PRO G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 300 removed outlier: 3.765A pdb=" N PHE G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 334 removed outlier: 3.740A pdb=" N ASN G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 373 Processing helix chain 'G' and resid 385 through 388 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.661A pdb=" N PHE C 133 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 85 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 134 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 173 through 174 removed outlier: 6.277A pdb=" N LYS C 205 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 336 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER C 207 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 333 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 283 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 335 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C 281 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 93 through 99 removed outlier: 6.749A pdb=" N GLU D 94 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 96 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 98 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 85 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 84 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE D 90 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N SER D 149 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 1043 through 1047 Processing sheet with id=AA5, first strand: chain 'D' and resid 990 through 993 removed outlier: 3.517A pdb=" N TYR D1004 " --> pdb=" O ASN D 991 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 993 " --> pdb=" O GLU D1002 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU D1002 " --> pdb=" O SER D 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.734A pdb=" N ILE E 42 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS E 117 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS E 44 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 115 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 112 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 139 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 114 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL E 157 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1010 through 1014 removed outlier: 6.432A pdb=" N ARG E1011 " --> pdb=" O PHE E1045 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E1047 " --> pdb=" O ARG E1011 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E1013 " --> pdb=" O ILE E1047 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 65 " --> pdb=" O TYR E1044 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E1046 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 64 " --> pdb=" O ARG E1062 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 951 through 956 Processing sheet with id=AA9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'F' and resid 240 through 242 Processing sheet with id=AB3, first strand: chain 'G' and resid 305 through 306 592 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.59 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: 1830 0.051 - 0.103: 515 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.940 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15803 Z= 0.266 Angle : 0.861 19.438 21502 Z= 0.535 Chirality : 0.048 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 aren 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 covalent geometry : bond 0.00537 (15803) covalent geometry : angle 0.86134 (21502) hydrogen bonds : bond 0.16899 ( 616) hydrogen bonds : angle 7.10468 ( 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 : 0.564 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: 0.7566 (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: 0.1348 time to fit residues: 67.0798 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 : 0.585 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E 882 HIS E1017 ASN E1018 GLN E1043 GLN F 142 GLN G 67 GLN G 134 ASN G 260 ASN G 353 GLN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.165631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127970 restraints weight = 22284.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130700 restraints weight = 17544.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130868 restraints weight = 15141.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131516 restraints weight = 12275.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131778 restraints weight = 10880.524| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15803 Z= 0.169 Angle : 0.678 12.116 21502 Z= 0.364 Chirality : 0.044 0.216 2441 Planarity : 0.004 0.055 2563 Dihedral : 18.565 84.854 2656 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.28 % Favored : 89.61 % Rotamer: Outliers : 3.70 % Allowed : 18.56 % Favored : 77.74 % 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 aren not related in a simple way. whole: -3.20 (0.18), residues: 1771 helix: -0.92 (0.18), residues: 793 sheet: -2.28 (0.36), residues: 185 loop : -3.42 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1042 TYR 0.017 0.002 TYR F 84 PHE 0.021 0.002 PHE E 78 TRP 0.019 0.002 TRP C 239 HIS 0.009 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00384 (15803) covalent geometry : angle 0.67760 (21502) hydrogen bonds : bond 0.04927 ( 616) hydrogen bonds : angle 5.38205 ( 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 275 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6964 (mm-30) REVERT: C 301 LEU cc_start: 0.9051 (mm) cc_final: 0.8812 (mm) REVERT: D 196 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: D 205 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 211 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6679 (m-10) REVERT: D 251 GLU cc_start: 0.6985 (mp0) cc_final: 0.6699 (mp0) REVERT: D 1009 ASN cc_start: 0.6299 (OUTLIER) cc_final: 0.5960 (p0) REVERT: E 50 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6421 (m-10) REVERT: E 91 GLU cc_start: 0.8303 (pt0) cc_final: 0.7932 (mp0) REVERT: E 101 ASP cc_start: 0.7434 (m-30) cc_final: 0.6951 (t0) REVERT: E 155 TYR cc_start: 0.5146 (m-80) cc_final: 0.3859 (m-80) REVERT: E 169 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6554 (mm) REVERT: E 180 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6896 (pp) REVERT: E 230 ASP cc_start: 0.7776 (m-30) cc_final: 0.7438 (m-30) REVERT: E 1061 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7150 (ptp) REVERT: F 166 SER cc_start: 0.8761 (m) cc_final: 0.8119 (p) REVERT: G 290 LYS cc_start: 0.8347 (mppt) cc_final: 0.8047 (mmtp) outliers start: 59 outliers final: 25 residues processed: 256 average time/residue: 0.1083 time to fit residues: 43.0360 Evaluate side-chains 196 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 1007 THR Chi-restraints excluded: chain D residue 1009 ASN 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 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 246 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 999 MET Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 138 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 94 optimal weight: 0.0970 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 GLN E 71 ASN E1035 ASN E1074 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.164246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.127648 restraints weight = 23272.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129181 restraints weight = 18654.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.129761 restraints weight = 16090.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130360 restraints weight = 13086.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130650 restraints weight = 11870.112| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15803 Z= 0.126 Angle : 0.591 11.765 21502 Z= 0.319 Chirality : 0.041 0.205 2441 Planarity : 0.003 0.051 2563 Dihedral : 18.159 88.699 2615 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 4.20 % Allowed : 20.44 % Favored : 75.36 % 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 aren not related in a simple way. whole: -2.48 (0.19), residues: 1771 helix: -0.33 (0.18), residues: 792 sheet: -1.71 (0.38), residues: 189 loop : -3.09 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 292 TYR 0.017 0.001 TYR E 961 PHE 0.029 0.001 PHE E 256 TRP 0.019 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00263 (15803) covalent geometry : angle 0.59102 (21502) hydrogen bonds : bond 0.04178 ( 616) hydrogen bonds : angle 4.82836 ( 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 285 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 218 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 PRO cc_start: 0.8244 (Cg_endo) cc_final: 0.8037 (Cg_exo) REVERT: D 205 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 211 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: D 1023 GLU cc_start: 0.6881 (pm20) cc_final: 0.6363 (pm20) REVERT: E 50 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: E 91 GLU cc_start: 0.8116 (pt0) cc_final: 0.7807 (mp0) REVERT: E 101 ASP cc_start: 0.7389 (m-30) cc_final: 0.6911 (t0) REVERT: E 112 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7272 (mp) REVERT: E 155 TYR cc_start: 0.5144 (m-80) cc_final: 0.3949 (m-80) REVERT: E 180 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6793 (pp) REVERT: E 1061 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7152 (ptp) REVERT: E 1071 TRP cc_start: 0.5134 (m100) cc_final: 0.4884 (m100) REVERT: F 126 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8610 (pp) REVERT: F 166 SER cc_start: 0.8631 (m) cc_final: 0.7806 (p) REVERT: G 290 LYS cc_start: 0.8318 (mppt) cc_final: 0.7968 (mmtp) outliers start: 67 outliers final: 28 residues processed: 256 average time/residue: 0.1004 time to fit residues: 41.1967 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 MET 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 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER 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 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 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 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 171 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 37 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 GLN F 63 ASN F 142 GLN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.158761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.121356 restraints weight = 23340.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.122441 restraints weight = 19344.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.122745 restraints weight = 17853.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123873 restraints weight = 14413.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124039 restraints weight = 12530.485| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15803 Z= 0.186 Angle : 0.668 11.811 21502 Z= 0.354 Chirality : 0.044 0.224 2441 Planarity : 0.004 0.057 2563 Dihedral : 18.118 86.260 2612 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.56 % Favored : 89.38 % Rotamer: Outliers : 4.39 % Allowed : 22.51 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.19), residues: 1771 helix: -0.32 (0.18), residues: 791 sheet: -1.66 (0.42), residues: 170 loop : -3.04 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 135 TYR 0.021 0.002 TYR C 266 PHE 0.037 0.002 PHE E 256 TRP 0.018 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00433 (15803) covalent geometry : angle 0.66827 (21502) hydrogen bonds : bond 0.04669 ( 616) hydrogen bonds : angle 4.95959 ( 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 251 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ASN cc_start: 0.7422 (t0) cc_final: 0.7133 (t0) REVERT: D 144 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6723 (ttt-90) REVERT: D 196 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: D 205 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7489 (tm-30) REVERT: D 211 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6360 (m-10) REVERT: E 50 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6132 (m-10) REVERT: E 101 ASP cc_start: 0.7372 (m-30) cc_final: 0.6930 (t0) REVERT: E 112 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7061 (mp) REVERT: E 155 TYR cc_start: 0.5435 (m-80) cc_final: 0.3990 (m-80) REVERT: E 169 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6550 (mm) REVERT: E 180 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6802 (pp) REVERT: E 1016 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6620 (pp) REVERT: G 290 LYS cc_start: 0.8504 (mppt) cc_final: 0.8192 (mmtp) outliers start: 70 outliers final: 45 residues processed: 233 average time/residue: 0.0994 time to fit residues: 36.8187 Evaluate side-chains 217 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU 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 1077 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 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 262 GLU 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 931 ASP Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1088 SER 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 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 74 optimal weight: 0.0870 chunk 172 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 161 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 152 optimal weight: 0.0170 chunk 153 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.162544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.125214 restraints weight = 23188.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.125463 restraints weight = 19535.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.126955 restraints weight = 17013.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.127390 restraints weight = 13656.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127667 restraints weight = 12496.022| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15803 Z= 0.115 Angle : 0.583 11.862 21502 Z= 0.308 Chirality : 0.041 0.196 2441 Planarity : 0.003 0.050 2563 Dihedral : 17.870 84.569 2610 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 4.01 % Allowed : 24.14 % 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 aren not related in a simple way. whole: -1.97 (0.20), residues: 1771 helix: 0.07 (0.19), residues: 797 sheet: -1.53 (0.40), residues: 194 loop : -2.78 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 933 TYR 0.013 0.001 TYR E 961 PHE 0.031 0.001 PHE E 256 TRP 0.021 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00252 (15803) covalent geometry : angle 0.58315 (21502) hydrogen bonds : bond 0.03941 ( 616) hydrogen bonds : angle 4.53092 ( 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 251 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 187 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: D 205 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7365 (tm-30) REVERT: E 50 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6371 (m-10) REVERT: E 91 GLU cc_start: 0.8155 (pt0) cc_final: 0.7828 (mp0) REVERT: E 101 ASP cc_start: 0.7390 (m-30) cc_final: 0.6847 (t0) REVERT: E 155 TYR cc_start: 0.5343 (m-80) cc_final: 0.3914 (m-80) REVERT: E 169 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6842 (mm) REVERT: E 180 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6605 (pp) REVERT: E 1061 MET cc_start: 0.7401 (mtp) cc_final: 0.7043 (ptp) REVERT: E 1072 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6670 (mt) REVERT: F 126 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8656 (pp) REVERT: G 129 MET cc_start: 0.8087 (pmm) cc_final: 0.7886 (pmm) REVERT: G 290 LYS cc_start: 0.8394 (mppt) cc_final: 0.8020 (mmtp) REVERT: G 367 ARG cc_start: 0.4969 (tpt-90) cc_final: 0.4574 (mtt180) outliers start: 64 outliers final: 36 residues processed: 234 average time/residue: 0.1102 time to fit residues: 40.4340 Evaluate side-chains 204 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 232 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 175 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 918 LEU 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 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 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 229 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 937 SER Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1088 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 92 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** 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 = 0.4273 r_free = 0.4273 target = 0.156999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119848 restraints weight = 23383.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120470 restraints weight = 19139.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120775 restraints weight = 17659.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.121790 restraints weight = 14716.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121975 restraints weight = 12889.254| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15803 Z= 0.204 Angle : 0.680 11.295 21502 Z= 0.358 Chirality : 0.044 0.185 2441 Planarity : 0.004 0.058 2563 Dihedral : 17.939 84.965 2610 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.01 % Favored : 88.93 % Rotamer: Outliers : 5.33 % Allowed : 24.14 % Favored : 70.53 % 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 aren not related in a simple way. whole: -2.13 (0.19), residues: 1771 helix: -0.14 (0.19), residues: 794 sheet: -1.52 (0.40), residues: 192 loop : -2.79 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 135 TYR 0.019 0.002 TYR F 84 PHE 0.027 0.002 PHE E 256 TRP 0.020 0.002 TRP C 160 HIS 0.009 0.001 HIS G 377 Details of bonding type rmsd covalent geometry : bond 0.00476 (15803) covalent geometry : angle 0.68036 (21502) hydrogen bonds : bond 0.04634 ( 616) hydrogen bonds : angle 4.87351 ( 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 256 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 171 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.6681 (tt) REVERT: D 144 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6986 (ttt180) REVERT: D 205 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 101 ASP cc_start: 0.7415 (m-30) cc_final: 0.6904 (t0) REVERT: E 155 TYR cc_start: 0.5444 (m-80) cc_final: 0.3991 (m-80) REVERT: E 169 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6584 (mm) REVERT: E 180 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6647 (pp) REVERT: E 262 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7005 (pp20) REVERT: E 1016 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6445 (pp) REVERT: E 1058 HIS cc_start: 0.7140 (OUTLIER) cc_final: 0.6719 (t-90) REVERT: F 166 SER cc_start: 0.8828 (m) cc_final: 0.8566 (p) REVERT: F 285 GLN cc_start: 0.8044 (pm20) cc_final: 0.7668 (pm20) REVERT: G 290 LYS cc_start: 0.8447 (mppt) cc_final: 0.8114 (mmtp) outliers start: 85 outliers final: 59 residues processed: 232 average time/residue: 0.1057 time to fit residues: 38.6201 Evaluate side-chains 228 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL 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 918 LEU 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 1077 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain D residue 1079 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 182 GLN Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1088 SER Chi-restraints excluded: chain F residue 31 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 140 ILE Chi-restraints excluded: chain F residue 146 THR 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 Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.155078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118117 restraints weight = 23412.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118771 restraints weight = 20603.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119277 restraints weight = 18368.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.120161 restraints weight = 15077.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120409 restraints weight = 13261.580| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15803 Z= 0.220 Angle : 0.715 11.395 21502 Z= 0.376 Chirality : 0.045 0.234 2441 Planarity : 0.004 0.051 2563 Dihedral : 17.951 85.811 2609 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.86 % Favored : 88.09 % Rotamer: Outliers : 5.45 % Allowed : 24.51 % Favored : 70.03 % 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 aren not related in a simple way. whole: -2.31 (0.19), residues: 1771 helix: -0.35 (0.18), residues: 803 sheet: -1.57 (0.39), residues: 196 loop : -2.84 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 135 TYR 0.019 0.002 TYR F 84 PHE 0.016 0.002 PHE D 973 TRP 0.023 0.003 TRP C 160 HIS 0.009 0.001 HIS G 377 Details of bonding type rmsd covalent geometry : bond 0.00513 (15803) covalent geometry : angle 0.71543 (21502) hydrogen bonds : bond 0.04764 ( 616) hydrogen bonds : angle 4.99483 ( 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 256 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 169 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.6784 (tt) REVERT: C 251 ASP cc_start: 0.7405 (t0) cc_final: 0.7072 (t0) REVERT: D 144 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6768 (ttt180) REVERT: D 205 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 101 ASP cc_start: 0.7418 (m-30) cc_final: 0.7058 (t0) REVERT: E 155 TYR cc_start: 0.5382 (m-80) cc_final: 0.3908 (m-80) REVERT: E 169 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6626 (mm) REVERT: E 262 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: E 1016 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6622 (pp) REVERT: E 1058 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6737 (t-90) REVERT: F 202 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: F 207 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7445 (t80) REVERT: G 290 LYS cc_start: 0.8470 (mppt) cc_final: 0.8162 (mmtp) outliers start: 87 outliers final: 65 residues processed: 235 average time/residue: 0.1010 time to fit residues: 37.5251 Evaluate side-chains 233 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 160 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 175 VAL 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 918 LEU 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 1077 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1046 LEU Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1088 SER Chi-restraints excluded: chain F residue 31 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 140 ILE Chi-restraints excluded: chain F residue 146 THR 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 202 GLN 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 135 ILE Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 84 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 162 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 299 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS G 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.161602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124419 restraints weight = 23257.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125405 restraints weight = 18735.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.126064 restraints weight = 16948.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126658 restraints weight = 13828.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126941 restraints weight = 12469.274| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4417 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= 0.125 Angle : 0.627 11.649 21502 Z= 0.328 Chirality : 0.042 0.226 2441 Planarity : 0.003 0.056 2563 Dihedral : 17.688 86.695 2609 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 3.89 % Allowed : 26.77 % Favored : 69.34 % 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 aren not related in a simple way. whole: -1.83 (0.20), residues: 1771 helix: 0.08 (0.19), residues: 799 sheet: -1.50 (0.39), residues: 192 loop : -2.56 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 933 TYR 0.037 0.001 TYR D 240 PHE 0.012 0.001 PHE D1052 TRP 0.026 0.002 TRP C 160 HIS 0.005 0.001 HIS D 242 Details of bonding type rmsd covalent geometry : bond 0.00278 (15803) covalent geometry : angle 0.62660 (21502) hydrogen bonds : bond 0.04054 ( 616) hydrogen bonds : angle 4.53855 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7028 (tt) REVERT: C 237 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7917 (mm) REVERT: C 251 ASP cc_start: 0.7144 (t0) cc_final: 0.6832 (t0) REVERT: D 144 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6955 (ttt-90) REVERT: D 205 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 290 LEU cc_start: 0.8461 (mt) cc_final: 0.8234 (mt) REVERT: E 91 GLU cc_start: 0.8194 (pt0) cc_final: 0.7804 (mp0) REVERT: E 101 ASP cc_start: 0.7319 (m-30) cc_final: 0.6857 (t0) REVERT: E 155 TYR cc_start: 0.5214 (m-80) cc_final: 0.3903 (m-80) REVERT: E 169 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6815 (mm) REVERT: E 254 ARG cc_start: 0.8072 (tpt-90) cc_final: 0.7740 (tpp80) REVERT: E 262 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6925 (pp20) REVERT: E 1058 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6703 (t-90) REVERT: E 1072 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6729 (mt) REVERT: F 193 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6755 (t80) REVERT: F 207 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7072 (t80) REVERT: G 220 TRP cc_start: 0.7510 (m100) cc_final: 0.7293 (m100) REVERT: G 290 LYS cc_start: 0.8346 (mppt) cc_final: 0.8002 (mmtp) outliers start: 62 outliers final: 42 residues processed: 237 average time/residue: 0.0978 time to fit residues: 36.8826 Evaluate side-chains 221 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL 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 918 LEU 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 50 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 VAL 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 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 937 SER Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 146 THR 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 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 237 THR 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: 2.9990 chunk 179 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 83 optimal weight: 0.0020 chunk 35 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 145 optimal weight: 0.2980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 215 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.163873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.127239 restraints weight = 22951.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129460 restraints weight = 18150.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129811 restraints weight = 17557.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130640 restraints weight = 12293.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.130912 restraints weight = 10833.504| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15803 Z= 0.118 Angle : 0.627 12.770 21502 Z= 0.325 Chirality : 0.041 0.236 2441 Planarity : 0.003 0.051 2563 Dihedral : 17.574 86.934 2609 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.64 % Rotamer: Outliers : 3.45 % Allowed : 27.65 % Favored : 68.90 % 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 aren not related in a simple way. whole: -1.61 (0.20), residues: 1771 helix: 0.28 (0.19), residues: 805 sheet: -1.38 (0.39), residues: 201 loop : -2.50 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 933 TYR 0.019 0.001 TYR D 240 PHE 0.028 0.001 PHE C 310 TRP 0.029 0.002 TRP C 160 HIS 0.004 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00259 (15803) covalent geometry : angle 0.62684 (21502) hydrogen bonds : bond 0.03941 ( 616) hydrogen bonds : angle 4.42596 ( 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 238 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 ASN cc_start: 0.6978 (OUTLIER) cc_final: 0.6618 (t0) REVERT: C 237 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7957 (mm) REVERT: D 94 GLU cc_start: 0.5893 (mm-30) cc_final: 0.5557 (mm-30) REVERT: D 205 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7417 (tm-30) REVERT: D 275 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6788 (tp30) REVERT: E 91 GLU cc_start: 0.8067 (pt0) cc_final: 0.7739 (mp0) REVERT: E 101 ASP cc_start: 0.7250 (m-30) cc_final: 0.6865 (t0) REVERT: E 155 TYR cc_start: 0.5019 (m-80) cc_final: 0.3851 (m-80) REVERT: E 169 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6874 (mm) REVERT: E 254 ARG cc_start: 0.8131 (tpt-90) cc_final: 0.7846 (tpp80) REVERT: E 262 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6917 (pp20) REVERT: E 1058 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6667 (t-90) REVERT: F 193 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6724 (t80) REVERT: F 207 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7088 (t80) REVERT: G 49 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7710 (mmtp) REVERT: G 244 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7288 (tt) REVERT: G 290 LYS cc_start: 0.8346 (mppt) cc_final: 0.7887 (mmmm) outliers start: 55 outliers final: 39 residues processed: 227 average time/residue: 0.1017 time to fit residues: 36.7004 Evaluate side-chains 216 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 215 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 175 VAL 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 918 LEU 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 50 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS 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 146 THR 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 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 244 LEU 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: 1.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.158815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.121675 restraints weight = 23400.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.121841 restraints weight = 22530.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.123464 restraints weight = 18129.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123860 restraints weight = 13807.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.124159 restraints weight = 12896.695| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15803 Z= 0.168 Angle : 0.696 13.512 21502 Z= 0.361 Chirality : 0.044 0.304 2441 Planarity : 0.004 0.057 2563 Dihedral : 17.622 87.294 2609 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 3.26 % Allowed : 28.15 % Favored : 68.59 % 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 aren not related in a simple way. whole: -1.75 (0.20), residues: 1771 helix: 0.13 (0.19), residues: 806 sheet: -1.40 (0.39), residues: 201 loop : -2.55 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 43 TYR 0.025 0.002 TYR D 240 PHE 0.014 0.002 PHE D1052 TRP 0.036 0.003 TRP G 220 HIS 0.006 0.001 HIS G 377 Details of bonding type rmsd covalent geometry : bond 0.00388 (15803) covalent geometry : angle 0.69554 (21502) hydrogen bonds : bond 0.04332 ( 616) hydrogen bonds : angle 4.66500 ( 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 221 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 205 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 275 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6814 (tp30) REVERT: E 91 GLU cc_start: 0.8216 (pt0) cc_final: 0.7759 (mp0) REVERT: E 155 TYR cc_start: 0.5126 (m-80) cc_final: 0.3928 (m-80) REVERT: E 169 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6787 (mm) REVERT: E 254 ARG cc_start: 0.8159 (tpt-90) cc_final: 0.7951 (tpp80) REVERT: E 262 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6958 (pp20) REVERT: E 1058 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6717 (t-90) REVERT: F 207 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7227 (t80) REVERT: G 49 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7749 (mmtp) REVERT: G 290 LYS cc_start: 0.8422 (mppt) cc_final: 0.8045 (mmtp) outliers start: 52 outliers final: 43 residues processed: 210 average time/residue: 0.1068 time to fit residues: 35.1283 Evaluate side-chains 207 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 175 VAL 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 918 LEU 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 50 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1053 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1072 ILE Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1088 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 146 THR 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 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 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 = 0.4340 r_free = 0.4340 target = 0.163255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126474 restraints weight = 23045.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127090 restraints weight = 19671.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128506 restraints weight = 16871.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128927 restraints weight = 13558.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129272 restraints weight = 12341.678| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15803 Z= 0.127 Angle : 0.656 13.522 21502 Z= 0.339 Chirality : 0.042 0.310 2441 Planarity : 0.003 0.051 2563 Dihedral : 17.430 87.748 2609 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 3.01 % Allowed : 28.40 % Favored : 68.59 % 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 aren not related in a simple way. whole: -1.53 (0.20), residues: 1771 helix: 0.31 (0.19), residues: 800 sheet: -1.24 (0.39), residues: 201 loop : -2.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 933 TYR 0.017 0.001 TYR F 84 PHE 0.011 0.001 PHE D1052 TRP 0.025 0.003 TRP G 220 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00281 (15803) covalent geometry : angle 0.65619 (21502) hydrogen bonds : bond 0.03986 ( 616) hydrogen bonds : angle 4.48480 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.48 seconds wall clock time: 46 minutes 59.15 seconds (2819.15 seconds total)