Starting phenix.real_space_refine on Fri Jun 13 22:16:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tve_26140/06_2025/7tve_26140_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tve_26140/06_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_26140/06_2025/7tve_26140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tve_26140/06_2025/7tve_26140.map" model { file = "/net/cci-nas-00/data/ceres_data/7tve_26140/06_2025/7tve_26140_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tve_26140/06_2025/7tve_26140_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.48, per 1000 atoms: 0.61 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: 4.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.46 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: 4.77 Time building geometry restraints manager: 5.16 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.550 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- 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 : 17.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.003 TRP C 239 HIS 0.008 0.001 HIS G 377 PHE 0.025 0.002 PHE E 50 TYR 0.020 0.002 TYR F 181 ARG 0.007 0.001 ARG G 361 Details of bonding type rmsd hydrogen bonds : bond 0.16899 ( 616) hydrogen bonds : angle 7.10468 ( 1758) covalent geometry : bond 0.00537 (15803) covalent geometry : angle 0.86134 (21502) *********************** 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 : 1.762 Fit side-chains 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: 0.5935 (ttt180) REVERT: C 151 ASN cc_start: 0.7802 (t0) cc_final: 0.7467 (t0) REVERT: D 205 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D 1023 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: E 50 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: E 75 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6606 (pttm) REVERT: E 91 GLU cc_start: 0.8511 (pt0) cc_final: 0.8139 (pm20) REVERT: E 101 ASP cc_start: 0.7432 (m-30) cc_final: 0.6907 (t0) REVERT: E 155 TYR cc_start: 0.5281 (m-80) cc_final: 0.3911 (m-80) REVERT: E 230 ASP cc_start: 0.7739 (m-30) cc_final: 0.7418 (m-30) REVERT: E 875 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7785 (p) REVERT: F 50 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7617 (tppt) REVERT: F 166 SER cc_start: 0.7824 (m) cc_final: 0.7430 (p) REVERT: F 207 PHE cc_start: 0.7781 (t80) cc_final: 0.7568 (t80) REVERT: F 252 GLU cc_start: 0.6792 (mp0) cc_final: 0.6464 (mp0) REVERT: G 290 LYS cc_start: 0.8425 (mppt) cc_final: 0.8171 (mmtp) REVERT: G 393 LYS cc_start: 0.6599 (tptm) cc_final: 0.6057 (tptm) outliers start: 52 outliers final: 20 residues processed: 343 average time/residue: 0.2955 time to fit residues: 145.8765 Evaluate side-chains 205 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 153 optimal weight: 2.9990 chunk 137 optimal weight: 0.0060 chunk 76 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 188 ASN C 215 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 166 GLN D 263 HIS D1009 ASN D1048 GLN E 71 ASN ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN E 882 HIS E1017 ASN E1018 GLN E1035 ASN E1043 GLN F 142 GLN G 67 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.171132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133717 restraints weight = 22120.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.136130 restraints weight = 17811.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.136770 restraints weight = 13955.713| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15803 Z= 0.133 Angle : 0.632 11.060 21502 Z= 0.341 Chirality : 0.042 0.212 2441 Planarity : 0.004 0.053 2563 Dihedral : 18.498 85.294 2656 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 3.45 % Allowed : 16.80 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.18), residues: 1771 helix: -0.75 (0.18), residues: 790 sheet: -2.19 (0.37), residues: 175 loop : -3.33 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 160 HIS 0.009 0.001 HIS G 62 PHE 0.019 0.002 PHE E 78 TYR 0.015 0.001 TYR E 961 ARG 0.004 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 616) hydrogen bonds : angle 5.20611 ( 1758) covalent geometry : bond 0.00284 (15803) covalent geometry : angle 0.63250 (21502) *********************** 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 283 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 301 LEU cc_start: 0.8967 (mm) cc_final: 0.8764 (mm) REVERT: D 90 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7043 (t80) REVERT: D 205 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 1009 ASN cc_start: 0.6074 (OUTLIER) cc_final: 0.5700 (p0) REVERT: E 50 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6262 (m-10) REVERT: E 91 GLU cc_start: 0.8115 (pt0) cc_final: 0.7845 (mp0) REVERT: E 101 ASP cc_start: 0.7480 (m-30) cc_final: 0.6952 (t0) REVERT: E 155 TYR cc_start: 0.5045 (m-80) cc_final: 0.3788 (m-80) REVERT: E 169 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6521 (mm) REVERT: E 180 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6717 (pp) REVERT: E 230 ASP cc_start: 0.7705 (m-30) cc_final: 0.7373 (m-30) REVERT: E 969 MET cc_start: 0.6404 (mtm) cc_final: 0.6131 (mtm) REVERT: E 1061 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7178 (ptp) REVERT: F 166 SER cc_start: 0.8617 (m) cc_final: 0.7918 (p) REVERT: G 290 LYS cc_start: 0.8338 (mppt) cc_final: 0.8039 (mmtp) REVERT: G 393 LYS cc_start: 0.6463 (tptm) cc_final: 0.6180 (tptp) outliers start: 55 outliers final: 20 residues processed: 265 average time/residue: 0.2444 time to fit residues: 99.7986 Evaluate side-chains 203 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 VAL 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 254 GLU 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 E residue 50 PHE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 154 ASP 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 F residue 151 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 ASN D1048 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4251 r_free = 0.4251 target = 0.154792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.116930 restraints weight = 23401.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118805 restraints weight = 19465.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118966 restraints weight = 17008.091| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15803 Z= 0.298 Angle : 0.794 10.499 21502 Z= 0.425 Chirality : 0.049 0.198 2441 Planarity : 0.005 0.058 2563 Dihedral : 18.531 88.442 2615 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.16 % Favored : 86.79 % Rotamer: Outliers : 5.64 % Allowed : 20.56 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.18), residues: 1771 helix: -0.93 (0.18), residues: 796 sheet: -2.00 (0.40), residues: 168 loop : -3.35 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 239 HIS 0.013 0.002 HIS G 377 PHE 0.030 0.003 PHE E 78 TYR 0.029 0.003 TYR F 181 ARG 0.010 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.05675 ( 616) hydrogen bonds : angle 5.66921 ( 1758) covalent geometry : bond 0.00693 (15803) covalent geometry : angle 0.79361 (21502) *********************** 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 270 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 180 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 ASP cc_start: 0.7718 (t0) cc_final: 0.7386 (t0) REVERT: D 196 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: D 205 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7558 (tm-30) REVERT: D 1039 MET cc_start: 0.7804 (mtp) cc_final: 0.7540 (mtp) REVERT: E 71 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8268 (m110) REVERT: E 101 ASP cc_start: 0.7481 (m-30) cc_final: 0.6951 (t0) REVERT: E 155 TYR cc_start: 0.5523 (m-80) cc_final: 0.4228 (m-80) REVERT: E 169 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6665 (mm) REVERT: E 180 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7005 (pp) REVERT: E 894 THR cc_start: 0.6756 (m) cc_final: 0.6551 (m) REVERT: E 1050 LYS cc_start: 0.8268 (mttm) cc_final: 0.8048 (mtmm) REVERT: F 166 SER cc_start: 0.8845 (m) cc_final: 0.7685 (p) REVERT: F 252 GLU cc_start: 0.6432 (mp0) cc_final: 0.6127 (mp0) REVERT: G 54 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: G 112 GLU cc_start: 0.7038 (tp30) cc_final: 0.6804 (tp30) REVERT: G 290 LYS cc_start: 0.8541 (mppt) cc_final: 0.8240 (mmtp) REVERT: G 330 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6360 (m-10) outliers start: 90 outliers final: 52 residues processed: 248 average time/residue: 0.2378 time to fit residues: 92.8211 Evaluate side-chains 210 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 152 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 143 GLU Chi-restraints excluded: chain C residue 192 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 336 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 993 SER Chi-restraints excluded: chain D residue 1016 VAL Chi-restraints excluded: chain D residue 1029 MET Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 209 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 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 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 185 LEU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** D1028 GLN E 71 ASN G 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.159646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122716 restraints weight = 23203.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.123668 restraints weight = 19135.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124501 restraints weight = 17819.326| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15803 Z= 0.144 Angle : 0.635 11.535 21502 Z= 0.338 Chirality : 0.043 0.235 2441 Planarity : 0.003 0.051 2563 Dihedral : 18.182 85.422 2612 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.70 % Favored : 91.25 % Rotamer: Outliers : 4.26 % Allowed : 23.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.19), residues: 1771 helix: -0.39 (0.18), residues: 793 sheet: -1.74 (0.40), residues: 184 loop : -3.08 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 160 HIS 0.010 0.001 HIS G 62 PHE 0.022 0.002 PHE E 78 TYR 0.014 0.001 TYR F 84 ARG 0.004 0.000 ARG D 292 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 616) hydrogen bonds : angle 4.97423 ( 1758) covalent geometry : bond 0.00322 (15803) covalent geometry : angle 0.63474 (21502) *********************** 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 261 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 251 ASP cc_start: 0.7529 (t0) cc_final: 0.7306 (t0) REVERT: D 144 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6909 (ttt-90) REVERT: D 196 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: D 205 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 211 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.6330 (m-10) REVERT: E 91 GLU cc_start: 0.8274 (pt0) cc_final: 0.7661 (mp0) REVERT: E 101 ASP cc_start: 0.7402 (m-30) cc_final: 0.6922 (t0) REVERT: E 155 TYR cc_start: 0.5316 (m-80) cc_final: 0.4158 (m-80) REVERT: E 169 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6925 (mm) REVERT: E 180 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6879 (pp) REVERT: E 1016 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6648 (pp) REVERT: E 1050 LYS cc_start: 0.8161 (mttm) cc_final: 0.7894 (mtmm) REVERT: E 1061 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7041 (ptp) REVERT: G 290 LYS cc_start: 0.8501 (mppt) cc_final: 0.8185 (mmtp) REVERT: G 367 ARG cc_start: 0.4926 (tpt-90) cc_final: 0.4313 (ptt180) outliers start: 68 outliers final: 45 residues processed: 242 average time/residue: 0.2471 time to fit residues: 93.7149 Evaluate side-chains 218 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU 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 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 175 VAL 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 253 THR 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 1029 MET 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 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 GLN 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 999 MET Chi-restraints excluded: chain E residue 1016 ILE Chi-restraints excluded: chain E residue 1061 MET 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 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 G residue 135 ILE Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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** ** 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 = 0.4264 r_free = 0.4264 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.118580 restraints weight = 23616.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.118750 restraints weight = 19492.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.119704 restraints weight = 19151.037| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15803 Z= 0.167 Angle : 0.647 10.941 21502 Z= 0.343 Chirality : 0.043 0.199 2441 Planarity : 0.004 0.057 2563 Dihedral : 18.023 84.451 2610 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.33 % Favored : 89.61 % Rotamer: Outliers : 5.96 % Allowed : 24.39 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.19), residues: 1771 helix: -0.25 (0.18), residues: 794 sheet: -1.56 (0.40), residues: 182 loop : -2.94 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 239 HIS 0.011 0.001 HIS G 62 PHE 0.035 0.002 PHE E 256 TYR 0.016 0.002 TYR F 84 ARG 0.005 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 616) hydrogen bonds : angle 4.85431 ( 1758) covalent geometry : bond 0.00382 (15803) covalent geometry : angle 0.64661 (21502) *********************** 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 272 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 177 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7033 (tt) REVERT: D 144 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6687 (ttt180) REVERT: D 205 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 211 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: E 101 ASP cc_start: 0.7465 (m-30) cc_final: 0.6935 (t0) REVERT: E 155 TYR cc_start: 0.5307 (m-80) cc_final: 0.4026 (m-80) REVERT: E 169 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6927 (mm) REVERT: E 180 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6870 (pp) REVERT: E 1058 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6634 (t-90) REVERT: F 202 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: G 290 LYS cc_start: 0.8532 (mppt) cc_final: 0.8205 (mmtp) outliers start: 95 outliers final: 61 residues processed: 246 average time/residue: 0.2317 time to fit residues: 88.8431 Evaluate side-chains 234 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 143 GLU 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 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 97 GLU 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 189 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 253 THR 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 1029 MET Chi-restraints excluded: chain D residue 1069 LEU Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 CYS 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 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 999 MET 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 1088 SER Chi-restraints excluded: chain F residue 31 MET 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 205 ILE 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 306 ILE Chi-restraints excluded: chain G residue 308 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 60 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 ASN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN ** E 71 ASN ** 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 = 0.4327 r_free = 0.4327 target = 0.161527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.124632 restraints weight = 23211.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.125916 restraints weight = 18538.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126683 restraints weight = 17161.782| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15803 Z= 0.125 Angle : 0.597 11.245 21502 Z= 0.317 Chirality : 0.041 0.242 2441 Planarity : 0.003 0.051 2563 Dihedral : 17.838 85.547 2609 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.93 % Rotamer: Outliers : 5.02 % Allowed : 25.71 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1771 helix: 0.10 (0.19), residues: 790 sheet: -1.41 (0.40), residues: 184 loop : -2.69 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 160 HIS 0.009 0.001 HIS G 62 PHE 0.035 0.001 PHE E 256 TYR 0.012 0.001 TYR F 84 ARG 0.008 0.000 ARG D 933 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 616) hydrogen bonds : angle 4.58888 ( 1758) covalent geometry : bond 0.00282 (15803) covalent geometry : angle 0.59704 (21502) *********************** 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 268 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 188 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ILE cc_start: 0.5822 (mt) cc_final: 0.5362 (mt) REVERT: D 144 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6911 (ttt-90) REVERT: D 205 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7453 (tm-30) REVERT: E 91 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 101 ASP cc_start: 0.7390 (m-30) cc_final: 0.6889 (t0) REVERT: E 180 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6632 (pp) REVERT: E 1058 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6659 (t-90) REVERT: G 290 LYS cc_start: 0.8457 (mppt) cc_final: 0.8017 (mmmm) outliers start: 80 outliers final: 53 residues processed: 245 average time/residue: 0.2301 time to fit residues: 88.4809 Evaluate side-chains 219 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 143 GLU 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 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 253 THR 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 1029 MET 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 91 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 177 CYS 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 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 999 MET 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 1081 MET Chi-restraints excluded: chain E residue 1088 SER Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 150 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 178 optimal weight: 0.0070 chunk 47 optimal weight: 0.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 ASN ** 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** F 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.164814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.127942 restraints weight = 23157.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.129465 restraints weight = 17882.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.130023 restraints weight = 17278.652| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15803 Z= 0.112 Angle : 0.590 11.346 21502 Z= 0.310 Chirality : 0.041 0.247 2441 Planarity : 0.003 0.051 2563 Dihedral : 17.690 86.268 2609 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.04 % Rotamer: Outliers : 3.89 % Allowed : 27.08 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1771 helix: 0.39 (0.19), residues: 788 sheet: -1.36 (0.39), residues: 196 loop : -2.48 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 305 HIS 0.003 0.001 HIS G 147 PHE 0.045 0.001 PHE E 256 TYR 0.010 0.001 TYR F 84 ARG 0.004 0.000 ARG D 933 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 616) hydrogen bonds : angle 4.33423 ( 1758) covalent geometry : bond 0.00238 (15803) covalent geometry : angle 0.58965 (21502) *********************** 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 252 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 205 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7367 (tm-30) REVERT: E 91 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: E 101 ASP cc_start: 0.7266 (m-30) cc_final: 0.6780 (t0) REVERT: E 201 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.5995 (tp) REVERT: E 254 ARG cc_start: 0.7916 (tpt-90) cc_final: 0.7615 (tpp80) REVERT: E 1058 HIS cc_start: 0.6875 (OUTLIER) cc_final: 0.6612 (t-90) REVERT: F 166 SER cc_start: 0.8774 (m) cc_final: 0.8497 (p) REVERT: G 49 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7710 (mmtp) REVERT: G 265 GLU cc_start: 0.6733 (pt0) cc_final: 0.6479 (pt0) REVERT: G 393 LYS cc_start: 0.6183 (tptm) cc_final: 0.5653 (mmmt) outliers start: 62 outliers final: 46 residues processed: 235 average time/residue: 0.2502 time to fit residues: 92.9882 Evaluate side-chains 221 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 143 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 90 PHE 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 1029 MET Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 91 GLU 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 127 TYR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 201 ILE 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 999 MET Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1058 HIS Chi-restraints excluded: chain E residue 1061 MET Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 193 PHE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 313 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 148 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 117 optimal weight: 0.0040 chunk 147 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.162743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.125643 restraints weight = 23097.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126340 restraints weight = 17991.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.127138 restraints weight = 18899.872| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15803 Z= 0.124 Angle : 0.618 11.286 21502 Z= 0.320 Chirality : 0.042 0.252 2441 Planarity : 0.003 0.053 2563 Dihedral : 17.630 86.474 2609 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.58 % Favored : 91.36 % Rotamer: Outliers : 4.20 % Allowed : 27.34 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1771 helix: 0.39 (0.19), residues: 792 sheet: -1.30 (0.39), residues: 198 loop : -2.50 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 60 HIS 0.003 0.001 HIS C 33 PHE 0.043 0.001 PHE E 256 TYR 0.012 0.001 TYR F 84 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 616) hydrogen bonds : angle 4.42744 ( 1758) covalent geometry : bond 0.00279 (15803) covalent geometry : angle 0.61805 (21502) *********************** 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 254 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.5162 (tmm-80) REVERT: D 144 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6890 (ttt180) REVERT: D 205 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 91 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: E 101 ASP cc_start: 0.7329 (m-30) cc_final: 0.6853 (t0) REVERT: E 201 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.5820 (tp) REVERT: E 262 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: E 1058 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6153 (t-90) REVERT: F 166 SER cc_start: 0.8817 (m) cc_final: 0.8544 (p) REVERT: F 202 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: F 207 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7184 (t80) REVERT: G 49 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7762 (mmtp) REVERT: G 265 GLU cc_start: 0.6762 (pt0) cc_final: 0.6561 (pt0) REVERT: G 384 MET cc_start: 0.7885 (tpp) cc_final: 0.7580 (ttt) outliers start: 67 outliers final: 49 residues processed: 235 average time/residue: 0.2735 time to fit residues: 101.7294 Evaluate side-chains 225 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 ARG 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 143 GLU Chi-restraints excluded: chain C residue 277 LEU 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 256 LEU 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 1029 MET 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 91 GLU 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 127 TYR Chi-restraints excluded: chain E residue 135 ILE 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 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 999 MET 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 1081 MET 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 146 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 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 205 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 166 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 177 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.164735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127774 restraints weight = 22982.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128736 restraints weight = 18502.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129684 restraints weight = 16279.173| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4645 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= 0.122 Angle : 0.611 11.191 21502 Z= 0.320 Chirality : 0.042 0.247 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.502 87.082 2609 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 4.08 % Allowed : 27.90 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1771 helix: 0.42 (0.19), residues: 793 sheet: -1.12 (0.40), residues: 188 loop : -2.45 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 160 HIS 0.011 0.001 HIS G 62 PHE 0.041 0.002 PHE E 256 TYR 0.018 0.001 TYR F 84 ARG 0.004 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 616) hydrogen bonds : angle 4.39189 ( 1758) covalent geometry : bond 0.00270 (15803) covalent geometry : angle 0.61078 (21502) *********************** 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 242 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 177 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5120 (mm-30) REVERT: D 205 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 91 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: E 101 ASP cc_start: 0.7278 (m-30) cc_final: 0.6797 (t0) REVERT: E 201 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.5781 (tp) REVERT: E 262 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6668 (pp20) REVERT: E 1058 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6214 (t-90) REVERT: F 166 SER cc_start: 0.8789 (m) cc_final: 0.8498 (p) REVERT: F 207 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7058 (t80) REVERT: G 49 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7727 (mmtp) REVERT: G 384 MET cc_start: 0.7796 (tpp) cc_final: 0.7471 (ttt) REVERT: G 393 LYS cc_start: 0.6112 (tptm) cc_final: 0.5088 (ptmm) outliers start: 65 outliers final: 49 residues processed: 225 average time/residue: 0.2488 time to fit residues: 88.2187 Evaluate side-chains 222 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU 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 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 256 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 1029 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 91 GLU 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 127 TYR Chi-restraints excluded: chain E residue 135 ILE 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 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 904 VAL Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 953 VAL Chi-restraints excluded: chain E residue 999 MET 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 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 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 205 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 330 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 162 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 0.0670 chunk 166 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.165133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.128472 restraints weight = 23174.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.129548 restraints weight = 17858.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.130271 restraints weight = 17854.727| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4809 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= 0.123 Angle : 0.620 11.086 21502 Z= 0.324 Chirality : 0.042 0.249 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.427 87.685 2609 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.59 % Rotamer: Outliers : 3.64 % Allowed : 28.34 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.20), residues: 1771 helix: 0.49 (0.19), residues: 792 sheet: -1.18 (0.39), residues: 198 loop : -2.41 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 160 HIS 0.004 0.001 HIS G 374 PHE 0.040 0.002 PHE E 256 TYR 0.018 0.001 TYR C 135 ARG 0.003 0.000 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 616) hydrogen bonds : angle 4.35994 ( 1758) covalent geometry : bond 0.00275 (15803) covalent geometry : angle 0.62003 (21502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 205 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7369 (tm-30) REVERT: E 91 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: E 101 ASP cc_start: 0.7271 (m-30) cc_final: 0.6794 (t0) REVERT: E 201 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.5631 (tp) REVERT: E 228 ASP cc_start: 0.5923 (OUTLIER) cc_final: 0.5581 (t0) REVERT: E 262 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6750 (pp20) REVERT: E 1058 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6671 (t-90) REVERT: F 166 SER cc_start: 0.8785 (m) cc_final: 0.8499 (p) REVERT: F 193 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6772 (t80) REVERT: F 202 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: G 49 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7816 (mmtp) REVERT: G 393 LYS cc_start: 0.6190 (tptm) cc_final: 0.5150 (ptmm) outliers start: 58 outliers final: 49 residues processed: 216 average time/residue: 0.2201 time to fit residues: 75.8180 Evaluate side-chains 218 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 143 GLU 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 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 256 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 1029 MET 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 91 GLU 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 127 TYR Chi-restraints excluded: chain E residue 135 ILE 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 246 LEU Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 882 HIS Chi-restraints excluded: chain E residue 904 VAL Chi-restraints excluded: chain E residue 931 ASP Chi-restraints excluded: chain E residue 953 VAL 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 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 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 205 ILE 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 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.162817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.125632 restraints weight = 23116.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126260 restraints weight = 18968.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127325 restraints weight = 17917.687| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4889 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= 0.136 Angle : 0.626 11.009 21502 Z= 0.329 Chirality : 0.042 0.240 2441 Planarity : 0.003 0.052 2563 Dihedral : 17.413 88.286 2609 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.09 % Favored : 90.85 % Rotamer: Outliers : 3.64 % Allowed : 28.65 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1771 helix: 0.44 (0.19), residues: 791 sheet: -1.17 (0.39), residues: 198 loop : -2.41 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 160 HIS 0.004 0.001 HIS G 377 PHE 0.043 0.002 PHE E 256 TYR 0.021 0.002 TYR C 266 ARG 0.003 0.000 ARG G 370 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 616) hydrogen bonds : angle 4.43774 ( 1758) covalent geometry : bond 0.00310 (15803) covalent geometry : angle 0.62569 (21502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5882.30 seconds wall clock time: 103 minutes 52.04 seconds (6232.04 seconds total)