Starting phenix.real_space_refine on Mon May 12 04:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6l_36007/05_2025/8j6l_36007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6l_36007/05_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_36007/05_2025/8j6l_36007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6l_36007/05_2025/8j6l_36007.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6l_36007/05_2025/8j6l_36007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6l_36007/05_2025/8j6l_36007.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, '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: {'GLU:plan': 3, 'ARG: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, 'ARG:plan': 2, 'ASP: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: 5.41, per 1000 atoms: 0.61 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 2.42 Time building geometry restraints manager: 2.76 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: 0.810 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.830 Find NCS groups from input model: 0.100 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- 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 : 8.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP H 176 HIS 0.006 0.001 HIS R 131 PHE 0.009 0.001 PHE R 25 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.17883 ( 421) hydrogen bonds : angle 6.66304 ( 1197) covalent geometry : bond 0.00307 ( 9035) covalent geometry : angle 0.61586 (12241) *********************** 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 : 1.011 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: 0.5977 (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: 0.5529 (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: 0.2171 time to fit residues: 56.4977 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 213 HIS A 294 ASN B 13 GLN B 142 HIS B 259 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.207568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172597 restraints weight = 10626.176| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.29 r_work: 0.3811 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9035 Z= 0.168 Angle : 0.643 7.367 12241 Z= 0.332 Chirality : 0.045 0.159 1387 Planarity : 0.004 0.066 1545 Dihedral : 4.390 26.066 1220 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 3.93 % Allowed : 19.00 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1120 helix: 1.98 (0.27), residues: 352 sheet: 0.28 (0.30), residues: 296 loop : -0.62 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.008 0.001 HIS B 54 PHE 0.026 0.002 PHE R 54 TYR 0.013 0.001 TYR B 59 ARG 0.005 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 421) hydrogen bonds : angle 4.84944 ( 1197) covalent geometry : bond 0.00343 ( 9035) covalent geometry : angle 0.64311 (12241) *********************** 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 183 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7281 (mtm110) REVERT: A 341 ASP cc_start: 0.8374 (t0) cc_final: 0.7939 (m-30) REVERT: B 234 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: H 83 MET cc_start: 0.6389 (mtm) cc_final: 0.6027 (mtm) REVERT: H 138 ILE cc_start: 0.6121 (mm) cc_final: 0.5820 (mm) REVERT: R 12 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6499 (mp0) REVERT: R 17 ASN cc_start: 0.5662 (m-40) cc_final: 0.5404 (m-40) REVERT: R 52 PHE cc_start: 0.6012 (t80) cc_final: 0.5012 (m-80) REVERT: R 106 MET cc_start: 0.5116 (mmp) cc_final: 0.4506 (ttt) REVERT: R 162 LEU cc_start: 0.5935 (tp) cc_final: 0.5545 (mt) REVERT: R 195 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.5998 (mp) REVERT: R 264 GLN cc_start: 0.5074 (pp30) cc_final: 0.4392 (mp10) REVERT: R 270 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7985 (mtt-85) REVERT: R 287 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6786 (p) outliers start: 37 outliers final: 18 residues processed: 170 average time/residue: 0.2324 time to fit residues: 53.9629 Evaluate side-chains 141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 294 ASN 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 29 VAL 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 38 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 87 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 16 ASN B 293 ASN B 295 ASN H 183 GLN H 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.207892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.173370 restraints weight = 10713.804| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.49 r_work: 0.3812 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9035 Z= 0.118 Angle : 0.560 6.721 12241 Z= 0.290 Chirality : 0.043 0.295 1387 Planarity : 0.004 0.054 1545 Dihedral : 4.119 23.278 1220 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1120 helix: 2.07 (0.27), residues: 358 sheet: 0.29 (0.30), residues: 291 loop : -0.69 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 161 PHE 0.021 0.001 PHE R 54 TYR 0.017 0.001 TYR R 269 ARG 0.003 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 421) hydrogen bonds : angle 4.59757 ( 1197) covalent geometry : bond 0.00252 ( 9035) covalent geometry : angle 0.55961 (12241) *********************** 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 167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7667 (mtm180) cc_final: 0.6959 (mpt180) REVERT: A 306 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7545 (mm110) REVERT: A 341 ASP cc_start: 0.8303 (t0) cc_final: 0.8064 (m-30) REVERT: B 234 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: H 83 MET cc_start: 0.6345 (mtm) cc_final: 0.5970 (mtm) REVERT: H 138 ILE cc_start: 0.6237 (mm) cc_final: 0.5836 (mm) REVERT: R 17 ASN cc_start: 0.5428 (m-40) cc_final: 0.5170 (m-40) REVERT: R 52 PHE cc_start: 0.5975 (t80) cc_final: 0.5024 (m-80) REVERT: R 106 MET cc_start: 0.5083 (mmp) cc_final: 0.4495 (ttt) REVERT: R 195 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.5920 (mp) REVERT: R 258 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6025 (mt) REVERT: R 264 GLN cc_start: 0.5171 (pp30) cc_final: 0.4448 (mp10) REVERT: R 287 SER cc_start: 0.7274 (OUTLIER) cc_final: 0.6815 (p) outliers start: 31 outliers final: 18 residues processed: 158 average time/residue: 0.2026 time to fit residues: 44.4963 Evaluate side-chains 142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 58 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 269 ASN B 110 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.204808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.168429 restraints weight = 10531.666| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.25 r_work: 0.3784 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3241 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= 0.132 Angle : 0.579 9.263 12241 Z= 0.297 Chirality : 0.043 0.238 1387 Planarity : 0.004 0.049 1545 Dihedral : 4.192 23.449 1220 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 4.14 % Allowed : 19.85 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1120 helix: 1.93 (0.27), residues: 365 sheet: 0.10 (0.29), residues: 293 loop : -0.65 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 161 PHE 0.039 0.002 PHE R 255 TYR 0.016 0.001 TYR R 269 ARG 0.003 0.000 ARG R 251 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 421) hydrogen bonds : angle 4.65507 ( 1197) covalent geometry : bond 0.00293 ( 9035) covalent geometry : angle 0.57924 (12241) *********************** 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 163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7620 (mtm180) cc_final: 0.6948 (mpt180) REVERT: A 269 ASN cc_start: 0.7771 (m110) cc_final: 0.7479 (m110) REVERT: A 317 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7372 (mttp) REVERT: B 234 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: H 83 MET cc_start: 0.6457 (mtm) cc_final: 0.6149 (mtm) REVERT: H 186 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: R 12 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6352 (mp0) REVERT: R 17 ASN cc_start: 0.5519 (m-40) cc_final: 0.5246 (m-40) REVERT: R 36 LEU cc_start: 0.5651 (pp) cc_final: 0.5382 (mt) REVERT: R 52 PHE cc_start: 0.5981 (t80) cc_final: 0.5011 (m-80) REVERT: R 62 SER cc_start: 0.6380 (OUTLIER) cc_final: 0.5775 (p) REVERT: R 195 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.5893 (mp) REVERT: R 258 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6001 (mt) REVERT: R 264 GLN cc_start: 0.5207 (pp30) cc_final: 0.4513 (mp10) REVERT: R 287 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7003 (p) outliers start: 39 outliers final: 26 residues processed: 150 average time/residue: 0.2061 time to fit residues: 42.7215 Evaluate side-chains 149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET 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 186 GLN 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 34 LEU 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 258 LEU 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 14 optimal weight: 0.0670 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 306 GLN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4457 r_free = 0.4457 target = 0.204980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.169831 restraints weight = 10561.599| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.15 r_work: 0.3789 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9035 Z= 0.117 Angle : 0.570 11.902 12241 Z= 0.289 Chirality : 0.042 0.210 1387 Planarity : 0.004 0.046 1545 Dihedral : 4.123 21.351 1220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 4.14 % Allowed : 20.70 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1120 helix: 1.93 (0.27), residues: 366 sheet: 0.14 (0.30), residues: 288 loop : -0.71 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 161 PHE 0.047 0.001 PHE R 255 TYR 0.013 0.001 TYR R 269 ARG 0.004 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 421) hydrogen bonds : angle 4.51069 ( 1197) covalent geometry : bond 0.00250 ( 9035) covalent geometry : angle 0.57000 (12241) *********************** 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 158 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7551 (mtm180) cc_final: 0.6987 (mpt180) REVERT: A 317 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7328 (mttp) REVERT: B 30 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.4721 (mp) REVERT: B 234 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: H 83 MET cc_start: 0.6402 (mtm) cc_final: 0.6106 (mtm) REVERT: R 12 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6220 (mp0) REVERT: R 17 ASN cc_start: 0.5506 (m-40) cc_final: 0.5267 (m-40) REVERT: R 36 LEU cc_start: 0.5615 (pp) cc_final: 0.5377 (mt) REVERT: R 62 SER cc_start: 0.6369 (OUTLIER) cc_final: 0.5688 (p) REVERT: R 195 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.5846 (mp) REVERT: R 258 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.6098 (mp) REVERT: R 264 GLN cc_start: 0.5139 (pp30) cc_final: 0.4510 (mp10) REVERT: R 287 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7054 (p) outliers start: 39 outliers final: 26 residues processed: 149 average time/residue: 0.1933 time to fit residues: 41.2593 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 30 LEU 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 279 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET 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 213 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.202506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165648 restraints weight = 10465.466| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.32 r_work: 0.3749 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3893 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= 0.132 Angle : 0.580 11.455 12241 Z= 0.297 Chirality : 0.043 0.195 1387 Planarity : 0.004 0.047 1545 Dihedral : 4.246 21.463 1220 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 4.88 % Allowed : 21.02 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1120 helix: 1.90 (0.27), residues: 366 sheet: 0.00 (0.29), residues: 293 loop : -0.72 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS R 161 PHE 0.047 0.002 PHE R 255 TYR 0.013 0.001 TYR R 269 ARG 0.003 0.000 ARG R 270 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 421) hydrogen bonds : angle 4.54847 ( 1197) covalent geometry : bond 0.00294 ( 9035) covalent geometry : angle 0.58045 (12241) *********************** 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 167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7592 (mtm180) cc_final: 0.6945 (mpt180) REVERT: A 269 ASN cc_start: 0.7974 (m-40) cc_final: 0.7611 (m110) REVERT: A 317 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7388 (mttp) REVERT: B 234 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: H 18 ARG cc_start: 0.4374 (ptm160) cc_final: 0.4172 (ptm160) REVERT: H 83 MET cc_start: 0.6558 (mtm) cc_final: 0.6254 (mtm) REVERT: R 12 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6182 (mp0) REVERT: R 36 LEU cc_start: 0.5505 (pp) cc_final: 0.5238 (mt) REVERT: R 101 ARG cc_start: 0.5357 (mmt180) cc_final: 0.4653 (mmt180) REVERT: R 109 MET cc_start: 0.6523 (ttp) cc_final: 0.5887 (ttp) REVERT: R 195 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.5804 (mp) REVERT: R 213 TRP cc_start: 0.6386 (t60) cc_final: 0.5971 (t60) REVERT: R 258 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5852 (mm) REVERT: R 264 GLN cc_start: 0.5229 (pp30) cc_final: 0.4418 (mp10) REVERT: R 287 SER cc_start: 0.7643 (OUTLIER) cc_final: 0.7005 (p) outliers start: 46 outliers final: 35 residues processed: 159 average time/residue: 0.2044 time to fit residues: 45.3765 Evaluate side-chains 154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 295 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.0070 chunk 91 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4473 r_free = 0.4473 target = 0.206822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.171704 restraints weight = 10616.753| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.27 r_work: 0.3800 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9035 Z= 0.105 Angle : 0.567 12.304 12241 Z= 0.286 Chirality : 0.042 0.202 1387 Planarity : 0.004 0.047 1545 Dihedral : 4.037 20.668 1220 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 3.72 % Allowed : 22.61 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1120 helix: 1.92 (0.27), residues: 366 sheet: 0.08 (0.30), residues: 290 loop : -0.67 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.005 0.001 HIS R 161 PHE 0.045 0.001 PHE R 255 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 421) hydrogen bonds : angle 4.37043 ( 1197) covalent geometry : bond 0.00224 ( 9035) covalent geometry : angle 0.56715 (12241) *********************** 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 158 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6872 (mpt180) REVERT: A 269 ASN cc_start: 0.7922 (m-40) cc_final: 0.7715 (m110) REVERT: B 234 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: H 38 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.7323 (ptt90) REVERT: H 46 GLU cc_start: 0.6803 (pt0) cc_final: 0.6590 (pt0) REVERT: H 83 MET cc_start: 0.6483 (mtm) cc_final: 0.6194 (mtm) REVERT: H 144 THR cc_start: 0.6079 (t) cc_final: 0.5832 (t) REVERT: R 12 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6156 (mp0) REVERT: R 36 LEU cc_start: 0.5451 (pp) cc_final: 0.5214 (mt) REVERT: R 195 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5774 (mp) REVERT: R 264 GLN cc_start: 0.5317 (OUTLIER) cc_final: 0.4736 (mp10) REVERT: R 287 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7109 (p) outliers start: 35 outliers final: 28 residues processed: 151 average time/residue: 0.2051 time to fit residues: 43.2593 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET 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 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 176 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 264 GLN Chi-restraints excluded: chain R residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.0070 chunk 22 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.205936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.169892 restraints weight = 10695.411| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.34 r_work: 0.3775 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9035 Z= 0.114 Angle : 0.571 13.229 12241 Z= 0.289 Chirality : 0.042 0.191 1387 Planarity : 0.004 0.046 1545 Dihedral : 4.049 20.590 1220 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 3.82 % Allowed : 22.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1120 helix: 1.82 (0.27), residues: 367 sheet: -0.00 (0.29), residues: 298 loop : -0.67 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 93 HIS 0.010 0.001 HIS R 161 PHE 0.047 0.001 PHE R 255 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03069 ( 421) hydrogen bonds : angle 4.41035 ( 1197) covalent geometry : bond 0.00250 ( 9035) covalent geometry : angle 0.57051 (12241) *********************** 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 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6966 (mpt180) REVERT: A 269 ASN cc_start: 0.7914 (m-40) cc_final: 0.7511 (m110) REVERT: A 330 LYS cc_start: 0.7161 (ttmm) cc_final: 0.6918 (tptt) REVERT: B 234 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: B 259 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6396 (mm-40) REVERT: H 83 MET cc_start: 0.6557 (mtm) cc_final: 0.6275 (mtm) REVERT: H 144 THR cc_start: 0.6066 (t) cc_final: 0.5847 (t) REVERT: R 12 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6102 (mp0) REVERT: R 195 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5844 (mp) REVERT: R 264 GLN cc_start: 0.5457 (OUTLIER) cc_final: 0.4759 (mp10) outliers start: 36 outliers final: 28 residues processed: 144 average time/residue: 0.1950 time to fit residues: 39.7097 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET 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 213 THR Chi-restraints excluded: chain H residue 243 THR 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 236 VAL Chi-restraints excluded: chain R residue 264 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4465 r_free = 0.4465 target = 0.206206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.171186 restraints weight = 10640.593| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.94 r_work: 0.3812 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9035 Z= 0.112 Angle : 0.569 12.610 12241 Z= 0.288 Chirality : 0.042 0.183 1387 Planarity : 0.004 0.045 1545 Dihedral : 4.017 20.014 1220 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 3.61 % Allowed : 22.72 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1120 helix: 1.77 (0.27), residues: 367 sheet: 0.10 (0.29), residues: 295 loop : -0.72 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.006 0.001 HIS R 161 PHE 0.045 0.001 PHE R 255 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 421) hydrogen bonds : angle 4.39894 ( 1197) covalent geometry : bond 0.00246 ( 9035) covalent geometry : angle 0.56916 (12241) *********************** 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 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6932 (mpt180) REVERT: B 169 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.8275 (m100) REVERT: B 234 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: B 259 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6558 (mm-40) REVERT: B 262 MET cc_start: 0.7056 (mtp) cc_final: 0.6842 (mtt) REVERT: H 83 MET cc_start: 0.6494 (mtm) cc_final: 0.6223 (mtm) REVERT: H 144 THR cc_start: 0.5956 (OUTLIER) cc_final: 0.5742 (t) REVERT: R 12 GLU cc_start: 0.6727 (mt-10) cc_final: 0.5981 (mp0) REVERT: R 195 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.5804 (mp) REVERT: R 264 GLN cc_start: 0.5328 (OUTLIER) cc_final: 0.4728 (mp10) outliers start: 34 outliers final: 26 residues processed: 142 average time/residue: 0.2129 time to fit residues: 42.6350 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 169 TRP 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 G residue 21 MET 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 29 VAL Chi-restraints excluded: chain R residue 34 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 12 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4422 r_free = 0.4422 target = 0.201796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166264 restraints weight = 10679.324| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.26 r_work: 0.3721 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9035 Z= 0.147 Angle : 0.612 14.224 12241 Z= 0.312 Chirality : 0.044 0.212 1387 Planarity : 0.004 0.045 1545 Dihedral : 4.357 24.485 1220 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.93 % Allowed : 23.25 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1120 helix: 1.72 (0.27), residues: 366 sheet: -0.08 (0.29), residues: 301 loop : -0.71 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 161 PHE 0.048 0.002 PHE R 255 TYR 0.011 0.001 TYR H 103 ARG 0.005 0.000 ARG R 101 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 421) hydrogen bonds : angle 4.59543 ( 1197) covalent geometry : bond 0.00338 ( 9035) covalent geometry : angle 0.61178 (12241) ********************** 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 151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7044 (mpt180) REVERT: B 234 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 259 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6482 (mm-40) REVERT: B 303 ASP cc_start: 0.6484 (p0) cc_final: 0.6282 (p0) REVERT: H 18 ARG cc_start: 0.4435 (ptm160) cc_final: 0.4160 (ttp-110) REVERT: H 83 MET cc_start: 0.6532 (mtm) cc_final: 0.6217 (mtm) REVERT: H 144 THR cc_start: 0.6119 (OUTLIER) cc_final: 0.5912 (t) REVERT: R 12 GLU cc_start: 0.6817 (mt-10) cc_final: 0.5978 (mp0) REVERT: R 195 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5890 (mp) REVERT: R 264 GLN cc_start: 0.5181 (OUTLIER) cc_final: 0.4624 (mp10) outliers start: 37 outliers final: 29 residues processed: 140 average time/residue: 0.2144 time to fit residues: 42.9517 Evaluate side-chains 142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 21 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 125 ASN B 220 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** 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 = 0.4389 r_free = 0.4389 target = 0.198113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161454 restraints weight = 10545.926| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.24 r_work: 0.3681 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9035 Z= 0.170 Angle : 0.652 13.776 12241 Z= 0.333 Chirality : 0.045 0.213 1387 Planarity : 0.004 0.049 1545 Dihedral : 4.791 35.011 1220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.98 % Rotamer: Outliers : 4.03 % Allowed : 23.14 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1120 helix: 1.57 (0.27), residues: 365 sheet: -0.18 (0.28), residues: 290 loop : -0.86 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.007 0.001 HIS R 161 PHE 0.048 0.002 PHE R 255 TYR 0.013 0.002 TYR A 320 ARG 0.005 0.001 ARG R 101 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 421) hydrogen bonds : angle 4.77200 ( 1197) covalent geometry : bond 0.00392 ( 9035) covalent geometry : angle 0.65198 (12241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5079.48 seconds wall clock time: 88 minutes 43.23 seconds (5323.23 seconds total)