Starting phenix.real_space_refine on Sat Aug 23 00:18:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6l_36007/08_2025/8j6l_36007.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5657 2.51 5 N 1505 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8839 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2560 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 383 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2403 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8839 At special positions: 0 Unit cell: (105.472, 110.416, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1610 8.00 N 1505 7.00 C 5657 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: 0.97 Conformation dependent library (CDL) restraints added in 346.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 37.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.947A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.633A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.870A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.809A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.723A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.656A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.591A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.912A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 25 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.124A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.835A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.580A pdb=" N ALA R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 89 removed outlier: 4.279A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 131 Processing helix chain 'R' and resid 140 through 164 removed outlier: 3.569A pdb=" N ALA R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU R 163 " --> pdb=" O THR R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 219 removed outlier: 3.694A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.859A pdb=" N ARG R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 260 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 268 through 280 removed outlier: 4.402A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 298 removed outlier: 3.836A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 3.997A pdb=" N PHE R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.895A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.763A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.564A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.703A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.416A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.818A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.300A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.869A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.796A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.524A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.986A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR H 190 " --> pdb=" O ASN H 194 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.986A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 231 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR H 238 " --> pdb=" O GLN H 231 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2207 1.33 - 1.45: 1828 1.45 - 1.57: 4903 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 9035 Sorted by residual: bond pdb=" N ILE R 139 " pdb=" CA ILE R 139 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ILE G 25 " pdb=" CA ILE G 25 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.19e-02 7.06e+03 8.55e+00 bond pdb=" N LYS G 29 " pdb=" CA LYS G 29 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.53e+00 bond pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.56e+00 bond pdb=" N ILE G 28 " pdb=" CA ILE G 28 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.41e+00 ... (remaining 9030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11822 1.49 - 2.97: 325 2.97 - 4.46: 75 4.46 - 5.95: 16 5.95 - 7.43: 3 Bond angle restraints: 12241 Sorted by residual: angle pdb=" N PHE R 82 " pdb=" CA PHE R 82 " pdb=" C PHE R 82 " ideal model delta sigma weight residual 112.45 105.56 6.89 1.39e+00 5.18e-01 2.45e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 110.42 105.85 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.36 106.32 5.04 1.09e+00 8.42e-01 2.14e+01 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 111.75 105.93 5.82 1.28e+00 6.10e-01 2.07e+01 angle pdb=" N LEU G 15 " pdb=" CA LEU G 15 " pdb=" C LEU G 15 " ideal model delta sigma weight residual 111.07 106.95 4.12 1.07e+00 8.73e-01 1.49e+01 ... (remaining 12236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4681 17.87 - 35.74: 497 35.74 - 53.60: 115 53.60 - 71.47: 8 71.47 - 89.34: 7 Dihedral angle restraints: 5308 sinusoidal: 2012 harmonic: 3296 Sorted by residual: dihedral pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " pdb=" CG ASP A 328 " pdb=" OD1 ASP A 328 " ideal model delta sinusoidal sigma weight residual -30.00 -88.31 58.31 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG B 283 " pdb=" CD ARG B 283 " pdb=" NE ARG B 283 " pdb=" CZ ARG B 283 " ideal model delta sinusoidal sigma weight residual -180.00 -135.11 -44.89 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 -88.43 88.43 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1181 0.054 - 0.108: 147 0.108 - 0.162: 48 0.162 - 0.217: 8 0.217 - 0.271: 3 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA VAL G 16 " pdb=" N VAL G 16 " pdb=" C VAL G 16 " pdb=" CB VAL G 16 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1384 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 137 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN R 137 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN R 137 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS R 138 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO R 81 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 39 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.81e+00 pdb=" C ILE R 39 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 39 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE R 40 " -0.010 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 113 2.63 - 3.20: 8278 3.20 - 3.76: 13582 3.76 - 4.33: 18810 4.33 - 4.90: 30767 Nonbonded interactions: 71550 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.061 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.144 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.176 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 322 " model vdw 2.202 3.040 nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.202 3.040 ... (remaining 71545 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 individual isotropic 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 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 : 0.003 0.044 9035 Z= 0.191 Angle : 0.616 7.433 12241 Z= 0.374 Chirality : 0.045 0.271 1387 Planarity : 0.004 0.060 1545 Dihedral : 15.239 89.338 3176 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 0.21 % Allowed : 24.95 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1120 helix: 1.70 (0.28), residues: 352 sheet: 0.80 (0.32), residues: 261 loop : -0.67 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.008 0.001 TYR H 102 PHE 0.009 0.001 PHE R 25 TRP 0.005 0.001 TRP H 176 HIS 0.006 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9035) covalent geometry : angle 0.61586 (12241) hydrogen bonds : bond 0.17883 ( 421) hydrogen bonds : angle 6.66304 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7019 (m-30) cc_final: 0.6695 (m-30) REVERT: A 28 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5613 (mt-10) REVERT: A 32 ARG cc_start: 0.7420 (mtm180) cc_final: 0.6234 (mpt180) REVERT: A 197 LYS cc_start: 0.7144 (mtpp) cc_final: 0.6902 (mtmt) REVERT: A 207 GLU cc_start: 0.6432 (tt0) cc_final: 0.6192 (tt0) REVERT: A 209 LYS cc_start: 0.7773 (ttmm) cc_final: 0.7521 (tttm) REVERT: A 252 SER cc_start: 0.7862 (m) cc_final: 0.7634 (p) REVERT: A 341 ASP cc_start: 0.7316 (t0) cc_final: 0.6724 (m-30) REVERT: B 150 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7324 (mmt-90) REVERT: B 263 THR cc_start: 0.7533 (t) cc_final: 0.7302 (m) REVERT: B 312 ASP cc_start: 0.7020 (p0) cc_final: 0.6753 (p0) REVERT: H 83 MET cc_start: 0.6363 (mtm) cc_final: 0.6117 (mtm) REVERT: H 186 GLN cc_start: 0.6372 (tt0) cc_final: 0.5978 (tm-30) REVERT: H 230 MET cc_start: 0.7677 (ttm) cc_final: 0.7432 (ttp) REVERT: R 12 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6492 (mp0) REVERT: R 17 ASN cc_start: 0.5803 (m-40) cc_final: 0.5530 (m-40) REVERT: R 52 PHE cc_start: 0.5671 (t80) cc_final: 0.4800 (m-10) REVERT: R 106 MET cc_start: 0.4915 (mmp) cc_final: 0.3813 (ttt) REVERT: R 164 LYS cc_start: 0.4454 (tmmt) cc_final: 0.4110 (mptt) REVERT: R 187 GLN cc_start: 0.5649 (pm20) cc_final: 0.5010 (pm20) REVERT: R 264 GLN cc_start: 0.5296 (pp30) cc_final: 0.4240 (mp10) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1067 time to fit residues: 27.9141 Evaluate side-chains 135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 213 HIS A 294 ASN B 13 GLN B 142 HIS B 220 GLN B 259 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.206974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174932 restraints weight = 10710.221| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.47 r_work: 0.3783 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9035 Z= 0.171 Angle : 0.651 6.999 12241 Z= 0.337 Chirality : 0.045 0.161 1387 Planarity : 0.004 0.066 1545 Dihedral : 4.375 26.297 1220 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.82 % Allowed : 18.90 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1120 helix: 1.89 (0.27), residues: 358 sheet: 0.19 (0.30), residues: 304 loop : -0.62 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.012 0.002 TYR B 59 PHE 0.024 0.002 PHE R 54 TRP 0.014 0.001 TRP B 169 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9035) covalent geometry : angle 0.65074 (12241) hydrogen bonds : bond 0.03990 ( 421) hydrogen bonds : angle 4.93607 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7310 (mtm110) REVERT: A 207 GLU cc_start: 0.6779 (tt0) cc_final: 0.6503 (tp30) REVERT: A 341 ASP cc_start: 0.8411 (t0) cc_final: 0.7987 (m-30) REVERT: B 234 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: H 83 MET cc_start: 0.6360 (mtm) cc_final: 0.6001 (mtm) REVERT: H 138 ILE cc_start: 0.6186 (mm) cc_final: 0.5880 (mm) REVERT: R 17 ASN cc_start: 0.5755 (m-40) cc_final: 0.5496 (m-40) REVERT: R 52 PHE cc_start: 0.5981 (t80) cc_final: 0.4988 (m-80) REVERT: R 106 MET cc_start: 0.5209 (mmp) cc_final: 0.4581 (ttt) REVERT: R 195 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6037 (mp) REVERT: R 264 GLN cc_start: 0.5067 (pp30) cc_final: 0.4347 (mp10) REVERT: R 270 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7998 (mtt-85) REVERT: R 287 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6839 (p) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.1076 time to fit residues: 24.3467 Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 77 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 294 ASN B 16 ASN B 220 GLN B 293 ASN B 295 ASN H 183 GLN H 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.207527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172732 restraints weight = 10668.406| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.33 r_work: 0.3815 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9035 Z= 0.118 Angle : 0.561 6.721 12241 Z= 0.291 Chirality : 0.042 0.172 1387 Planarity : 0.004 0.055 1545 Dihedral : 4.129 24.070 1220 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 3.29 % Allowed : 20.49 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1120 helix: 2.06 (0.27), residues: 357 sheet: 0.24 (0.30), residues: 296 loop : -0.69 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 22 TYR 0.008 0.001 TYR B 59 PHE 0.021 0.001 PHE R 54 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9035) covalent geometry : angle 0.56134 (12241) hydrogen bonds : bond 0.03421 ( 421) hydrogen bonds : angle 4.62945 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7645 (mtm180) cc_final: 0.6946 (mpt180) REVERT: A 207 GLU cc_start: 0.6812 (tt0) cc_final: 0.6413 (tp30) REVERT: A 276 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 341 ASP cc_start: 0.8296 (t0) cc_final: 0.8057 (m-30) REVERT: B 234 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: H 83 MET cc_start: 0.6332 (mtm) cc_final: 0.5991 (mtm) REVERT: H 138 ILE cc_start: 0.6247 (mm) cc_final: 0.5847 (mm) REVERT: R 17 ASN cc_start: 0.5557 (m-40) cc_final: 0.5298 (m-40) REVERT: R 52 PHE cc_start: 0.5975 (t80) cc_final: 0.5009 (m-80) REVERT: R 106 MET cc_start: 0.5097 (mmp) cc_final: 0.4487 (ttt) REVERT: R 195 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5922 (mp) REVERT: R 258 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6043 (mt) REVERT: R 264 GLN cc_start: 0.5008 (pp30) cc_final: 0.4331 (mp10) REVERT: R 287 SER cc_start: 0.7281 (OUTLIER) cc_final: 0.6828 (p) outliers start: 31 outliers final: 20 residues processed: 159 average time/residue: 0.0981 time to fit residues: 21.6322 Evaluate side-chains 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 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 = 0.4458 r_free = 0.4458 target = 0.204989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.169410 restraints weight = 10620.072| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.29 r_work: 0.3773 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9035 Z= 0.137 Angle : 0.585 8.431 12241 Z= 0.302 Chirality : 0.044 0.299 1387 Planarity : 0.004 0.050 1545 Dihedral : 4.280 23.348 1220 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 4.25 % Allowed : 19.85 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1120 helix: 1.87 (0.27), residues: 362 sheet: 0.13 (0.30), residues: 288 loop : -0.73 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 90 TYR 0.018 0.001 TYR R 269 PHE 0.040 0.002 PHE R 255 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9035) covalent geometry : angle 0.58532 (12241) hydrogen bonds : bond 0.03452 ( 421) hydrogen bonds : angle 4.64783 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7607 (mtm180) cc_final: 0.6942 (mpt180) REVERT: A 207 GLU cc_start: 0.6836 (tt0) cc_final: 0.6470 (tp30) REVERT: A 269 ASN cc_start: 0.7884 (m-40) cc_final: 0.7544 (m110) REVERT: A 317 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7304 (mttp) REVERT: B 234 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: H 83 MET cc_start: 0.6410 (mtm) cc_final: 0.6056 (mtm) REVERT: R 17 ASN cc_start: 0.5724 (m-40) cc_final: 0.5443 (m-40) REVERT: R 36 LEU cc_start: 0.5466 (pp) cc_final: 0.5196 (mt) REVERT: R 62 SER cc_start: 0.6382 (OUTLIER) cc_final: 0.5749 (p) REVERT: R 101 ARG cc_start: 0.5398 (mmt180) cc_final: 0.4585 (mmt180) REVERT: R 195 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.5909 (mp) REVERT: R 264 GLN cc_start: 0.5183 (pp30) cc_final: 0.4503 (mp10) REVERT: R 287 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7051 (p) outliers start: 40 outliers final: 23 residues processed: 152 average time/residue: 0.0993 time to fit residues: 20.9924 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 220 GLN H 142 GLN H 194 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.203650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.168476 restraints weight = 10686.924| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.22 r_work: 0.3761 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9035 Z= 0.130 Angle : 0.581 12.026 12241 Z= 0.298 Chirality : 0.043 0.256 1387 Planarity : 0.004 0.049 1545 Dihedral : 4.278 21.632 1220 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 5.10 % Allowed : 19.85 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1120 helix: 1.68 (0.27), residues: 365 sheet: 0.01 (0.29), residues: 293 loop : -0.73 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 90 TYR 0.011 0.001 TYR R 269 PHE 0.046 0.002 PHE R 255 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9035) covalent geometry : angle 0.58143 (12241) hydrogen bonds : bond 0.03367 ( 421) hydrogen bonds : angle 4.57294 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7018 (mpt180) REVERT: A 207 GLU cc_start: 0.6909 (tt0) cc_final: 0.6539 (tp30) REVERT: A 269 ASN cc_start: 0.7902 (m-40) cc_final: 0.7545 (m110) REVERT: A 317 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7421 (mttp) REVERT: B 234 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: H 18 ARG cc_start: 0.4399 (ptm160) cc_final: 0.4190 (ptm160) REVERT: H 83 MET cc_start: 0.6478 (mtm) cc_final: 0.6184 (mtm) REVERT: R 17 ASN cc_start: 0.5640 (m-40) cc_final: 0.5379 (m110) REVERT: R 36 LEU cc_start: 0.5386 (pp) cc_final: 0.5125 (mt) REVERT: R 195 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5861 (mp) REVERT: R 258 LEU cc_start: 0.6944 (tp) cc_final: 0.6569 (tt) REVERT: R 264 GLN cc_start: 0.5165 (pp30) cc_final: 0.4498 (mp10) REVERT: R 287 SER cc_start: 0.7610 (OUTLIER) cc_final: 0.7075 (p) outliers start: 48 outliers final: 33 residues processed: 160 average time/residue: 0.0959 time to fit residues: 21.4190 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN B 295 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.202923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166090 restraints weight = 10542.427| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.22 r_work: 0.3739 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9035 Z= 0.134 Angle : 0.594 11.201 12241 Z= 0.304 Chirality : 0.043 0.225 1387 Planarity : 0.004 0.050 1545 Dihedral : 4.336 22.000 1220 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 4.56 % Allowed : 21.13 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1120 helix: 1.68 (0.27), residues: 366 sheet: -0.08 (0.29), residues: 298 loop : -0.76 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.014 0.001 TYR B 59 PHE 0.047 0.002 PHE R 255 TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9035) covalent geometry : angle 0.59355 (12241) hydrogen bonds : bond 0.03379 ( 421) hydrogen bonds : angle 4.56866 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7553 (mtm180) cc_final: 0.7018 (mpt180) REVERT: A 207 GLU cc_start: 0.7109 (tt0) cc_final: 0.6693 (tp30) REVERT: A 269 ASN cc_start: 0.7934 (m-40) cc_final: 0.7574 (m110) REVERT: B 234 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: H 83 MET cc_start: 0.6546 (mtm) cc_final: 0.6289 (mtm) REVERT: R 36 LEU cc_start: 0.5465 (pp) cc_final: 0.5233 (mt) REVERT: R 101 ARG cc_start: 0.5557 (mmt180) cc_final: 0.4805 (mmt180) REVERT: R 195 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5860 (mp) REVERT: R 258 LEU cc_start: 0.7050 (tp) cc_final: 0.6843 (tt) REVERT: R 264 GLN cc_start: 0.5138 (pp30) cc_final: 0.4429 (mp10) REVERT: R 287 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7179 (p) outliers start: 43 outliers final: 35 residues processed: 153 average time/residue: 0.0964 time to fit residues: 20.7679 Evaluate side-chains 154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.202601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167422 restraints weight = 10575.021| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.16 r_work: 0.3740 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.129 Angle : 0.598 12.155 12241 Z= 0.304 Chirality : 0.043 0.208 1387 Planarity : 0.004 0.049 1545 Dihedral : 4.295 21.106 1220 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 4.88 % Allowed : 21.76 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1120 helix: 1.70 (0.27), residues: 366 sheet: -0.10 (0.29), residues: 296 loop : -0.75 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.010 0.001 TYR B 59 PHE 0.044 0.002 PHE R 255 TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9035) covalent geometry : angle 0.59757 (12241) hydrogen bonds : bond 0.03302 ( 421) hydrogen bonds : angle 4.56023 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7002 (mpt180) REVERT: A 330 LYS cc_start: 0.7133 (ttmm) cc_final: 0.6914 (tptt) REVERT: B 234 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: B 259 GLN cc_start: 0.6881 (mm-40) cc_final: 0.6390 (mm-40) REVERT: B 303 ASP cc_start: 0.6504 (p0) cc_final: 0.6289 (p0) REVERT: H 83 MET cc_start: 0.6517 (mtm) cc_final: 0.6243 (mtm) REVERT: R 195 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5842 (mp) REVERT: R 213 TRP cc_start: 0.6364 (t60) cc_final: 0.5961 (t60) REVERT: R 258 LEU cc_start: 0.6955 (tp) cc_final: 0.6732 (tt) REVERT: R 264 GLN cc_start: 0.5165 (OUTLIER) cc_final: 0.4469 (mp10) outliers start: 46 outliers final: 32 residues processed: 155 average time/residue: 0.1024 time to fit residues: 21.9993 Evaluate side-chains 149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 264 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156309 restraints weight = 10540.667| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.29 r_work: 0.3637 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9035 Z= 0.230 Angle : 0.721 12.584 12241 Z= 0.371 Chirality : 0.048 0.223 1387 Planarity : 0.005 0.050 1545 Dihedral : 5.162 32.692 1220 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 4.14 % Allowed : 22.51 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.25), residues: 1120 helix: 1.29 (0.26), residues: 364 sheet: -0.28 (0.28), residues: 307 loop : -0.96 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 52 TYR 0.017 0.002 TYR H 103 PHE 0.047 0.003 PHE R 255 TRP 0.016 0.002 TRP B 169 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 9035) covalent geometry : angle 0.72105 (12241) hydrogen bonds : bond 0.04308 ( 421) hydrogen bonds : angle 5.07814 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.349 Fit side-chains REVERT: A 32 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7115 (mpt180) REVERT: A 330 LYS cc_start: 0.7050 (ttmm) cc_final: 0.6757 (tptt) REVERT: B 234 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: B 259 GLN cc_start: 0.6777 (mm-40) cc_final: 0.6374 (mm-40) REVERT: R 12 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5526 (mp0) REVERT: R 101 ARG cc_start: 0.5553 (mmt180) cc_final: 0.4833 (mmt180) REVERT: R 195 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5776 (mp) REVERT: R 264 GLN cc_start: 0.5361 (OUTLIER) cc_final: 0.4469 (mp10) outliers start: 39 outliers final: 32 residues processed: 144 average time/residue: 0.1032 time to fit residues: 20.3383 Evaluate side-chains 143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 264 GLN Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 176 GLN G 59 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.199971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.162942 restraints weight = 10532.693| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.19 r_work: 0.3716 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9035 Z= 0.125 Angle : 0.607 11.824 12241 Z= 0.310 Chirality : 0.043 0.201 1387 Planarity : 0.004 0.046 1545 Dihedral : 4.603 28.111 1220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.61 % Allowed : 22.93 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1120 helix: 1.55 (0.27), residues: 364 sheet: -0.26 (0.28), residues: 302 loop : -0.84 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 283 TYR 0.009 0.001 TYR R 269 PHE 0.043 0.002 PHE R 255 TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9035) covalent geometry : angle 0.60679 (12241) hydrogen bonds : bond 0.03410 ( 421) hydrogen bonds : angle 4.70670 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.322 Fit side-chains REVERT: A 32 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6924 (mpt180) REVERT: A 216 GLU cc_start: 0.8159 (tt0) cc_final: 0.7934 (tt0) REVERT: A 318 GLU cc_start: 0.5877 (tp30) cc_final: 0.5499 (tp30) REVERT: A 330 LYS cc_start: 0.7068 (ttmm) cc_final: 0.6789 (tptt) REVERT: B 234 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 259 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6458 (mm-40) REVERT: R 12 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5374 (mp0) REVERT: R 195 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.5799 (mp) REVERT: R 264 GLN cc_start: 0.5278 (OUTLIER) cc_final: 0.4394 (mp10) outliers start: 34 outliers final: 27 residues processed: 141 average time/residue: 0.1011 time to fit residues: 19.5587 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 264 GLN Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 294 ASN B 125 ASN ** H 113 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 = 0.4351 r_free = 0.4351 target = 0.194044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156775 restraints weight = 10497.673| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.24 r_work: 0.3631 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9035 Z= 0.235 Angle : 0.711 11.568 12241 Z= 0.367 Chirality : 0.048 0.213 1387 Planarity : 0.005 0.049 1545 Dihedral : 5.147 36.843 1220 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.93 % Allowed : 23.35 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.25), residues: 1120 helix: 1.26 (0.26), residues: 363 sheet: -0.40 (0.27), residues: 307 loop : -1.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 101 TYR 0.015 0.002 TYR H 103 PHE 0.049 0.003 PHE R 255 TRP 0.015 0.002 TRP B 339 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 9035) covalent geometry : angle 0.71109 (12241) hydrogen bonds : bond 0.04204 ( 421) hydrogen bonds : angle 5.04501 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7136 (mpt180) REVERT: A 216 GLU cc_start: 0.8220 (tt0) cc_final: 0.7939 (tt0) REVERT: A 330 LYS cc_start: 0.7051 (ttmm) cc_final: 0.6744 (tptt) REVERT: B 234 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 259 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6347 (mm-40) REVERT: R 101 ARG cc_start: 0.5194 (mmt180) cc_final: 0.4378 (mmt180) REVERT: R 195 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5780 (mp) REVERT: R 264 GLN cc_start: 0.5323 (OUTLIER) cc_final: 0.4397 (mp10) outliers start: 37 outliers final: 29 residues processed: 141 average time/residue: 0.1029 time to fit residues: 19.8215 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 234 MET Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 264 GLN Chi-restraints excluded: chain R residue 286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN R 17 ASN ** R 110 ASN ** 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 = 0.4403 r_free = 0.4403 target = 0.199472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.163583 restraints weight = 10514.919| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.99 r_work: 0.3738 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9035 Z= 0.124 Angle : 0.612 11.685 12241 Z= 0.314 Chirality : 0.043 0.186 1387 Planarity : 0.004 0.047 1545 Dihedral : 4.612 32.323 1220 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.08 % Allowed : 23.78 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1120 helix: 1.56 (0.27), residues: 364 sheet: -0.28 (0.28), residues: 302 loop : -0.88 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.013 0.001 TYR R 295 PHE 0.045 0.002 PHE R 255 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9035) covalent geometry : angle 0.61201 (12241) hydrogen bonds : bond 0.03366 ( 421) hydrogen bonds : angle 4.69089 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.15 seconds wall clock time: 44 minutes 11.75 seconds (2651.75 seconds total)