Starting phenix.real_space_refine on Mon May 12 17:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317.map" model { file = "/net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jil_36317/05_2025/8jil_36317_neut.cif" } resolution = 3.5 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= 0.011 sd= 0.078 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 69 5.16 5 C 5765 2.51 5 N 1535 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9028 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1796 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2364 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'CLR': 1, 'NIO': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.45, per 1000 atoms: 0.60 Number of scatterers: 9028 At special positions: 0 Unit cell: (109.48, 135.24, 104.88, 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 69 16.00 O 1659 8.00 N 1535 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 2.10 Conformation dependent library (CDL) restraints added in 984.1 milliseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 34.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.614A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.518A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.525A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 241 through 254 removed outlier: 3.726A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 6.118A pdb=" N TRP D 258 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.945A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 309 removed outlier: 3.691A pdb=" N ALA D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 351 removed outlier: 3.816A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'A' and resid 25 through 55 removed outlier: 3.749A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 4.211A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 79 removed outlier: 3.948A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.782A pdb=" N LEU A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 4.251A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.622A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.231A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.144A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 187 through 215 removed outlier: 4.223A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.390A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.740A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Proline residue: A 246 - end of helix removed outlier: 3.528A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.550A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.555A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.860A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.857A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.685A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.563A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.634A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.496A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 190 removed outlier: 3.561A pdb=" N PHE D 189 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS D 35 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE D 222 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 37 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS D 224 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 39 " --> pdb=" O CYS D 224 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA D 226 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 7.235A pdb=" N GLY S 16 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER S 85 " --> pdb=" O GLY S 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.080A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.642A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB4, first strand: chain 'A' and resid 11 through 13 364 hydrogen bonds defined for protein. 1017 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: 2.31 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2903 1.34 - 1.47: 2302 1.47 - 1.60: 3920 1.60 - 1.72: 0 1.72 - 1.85: 100 Bond restraints: 9225 Sorted by residual: bond pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.38e-02 5.25e+03 1.70e+01 bond pdb=" N CYS A 183 " pdb=" CA CYS A 183 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.39e-02 5.18e+03 9.61e+00 bond pdb=" N PHE A 186 " pdb=" CA PHE A 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.25e+00 bond pdb=" N ILE A 77 " pdb=" CA ILE A 77 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.18e-02 7.18e+03 7.87e+00 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.82e+00 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12292 2.83 - 5.67: 172 5.67 - 8.50: 17 8.50 - 11.34: 3 11.34 - 14.17: 1 Bond angle restraints: 12485 Sorted by residual: angle pdb=" CB MET S 230 " pdb=" CG MET S 230 " pdb=" SD MET S 230 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N SER A 178 " pdb=" CA SER A 178 " pdb=" C SER A 178 " ideal model delta sigma weight residual 108.96 114.78 -5.82 1.49e+00 4.50e-01 1.53e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 114.31 109.31 5.00 1.29e+00 6.01e-01 1.50e+01 angle pdb=" CA MET C 21 " pdb=" CB MET C 21 " pdb=" CG MET C 21 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" C CYS A 183 " pdb=" CA CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sigma weight residual 112.43 105.21 7.22 1.91e+00 2.74e-01 1.43e+01 ... (remaining 12480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 4887 16.33 - 32.67: 506 32.67 - 49.00: 100 49.00 - 65.34: 10 65.34 - 81.67: 8 Dihedral angle restraints: 5511 sinusoidal: 2208 harmonic: 3303 Sorted by residual: dihedral pdb=" CA PHE S 239 " pdb=" C PHE S 239 " pdb=" N GLY S 240 " pdb=" CA GLY S 240 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D 8 " pdb=" C GLU D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 837 0.037 - 0.075: 371 0.075 - 0.112: 146 0.112 - 0.150: 39 0.150 - 0.187: 10 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1400 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 182 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE A 182 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 182 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 183 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 49 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO S 75 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.033 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1058 2.75 - 3.29: 8595 3.29 - 3.82: 14216 3.82 - 4.36: 17102 4.36 - 4.90: 30046 Nonbonded interactions: 71017 Sorted by model distance: nonbonded pdb=" O ALA C 56 " pdb=" NH1 ARG C 62 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE C 61 " model vdw 2.216 3.120 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.241 3.040 nonbonded pdb=" NH2 ARG B 22 " pdb=" O THR B 221 " model vdw 2.254 3.120 nonbonded pdb=" OG SER S 30 " pdb=" OD1 ASP S 74 " model vdw 2.279 3.040 ... (remaining 71012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.530 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.061 9229 Z= 0.274 Angle : 0.879 14.172 12493 Z= 0.503 Chirality : 0.050 0.187 1403 Planarity : 0.005 0.069 1574 Dihedral : 13.683 81.670 3365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.24), residues: 1127 helix: -0.21 (0.29), residues: 325 sheet: -0.34 (0.30), residues: 273 loop : -2.35 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 169 HIS 0.010 0.002 HIS A 189 PHE 0.023 0.002 PHE A 105 TYR 0.022 0.002 TYR S 50 ARG 0.005 0.001 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.16112 ( 364) hydrogen bonds : angle 6.81685 ( 1017) SS BOND : bond 0.01057 ( 4) SS BOND : angle 2.80672 ( 8) covalent geometry : bond 0.00554 ( 9225) covalent geometry : angle 0.87625 (12485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.001 Fit side-chains REVERT: A 167 MET cc_start: 0.5256 (tpt) cc_final: 0.5011 (tpp) REVERT: A 217 GLN cc_start: 0.7802 (pp30) cc_final: 0.7594 (pp30) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2782 time to fit residues: 42.8451 Evaluate side-chains 98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN C 18 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.145246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123596 restraints weight = 15390.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123033 restraints weight = 19607.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124543 restraints weight = 16536.349| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9229 Z= 0.151 Angle : 0.672 10.521 12493 Z= 0.342 Chirality : 0.045 0.146 1403 Planarity : 0.005 0.059 1574 Dihedral : 6.036 51.981 1300 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.61 % Allowed : 6.92 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1127 helix: 0.31 (0.29), residues: 335 sheet: -0.22 (0.30), residues: 281 loop : -2.26 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 169 HIS 0.008 0.002 HIS A 184 PHE 0.018 0.002 PHE A 67 TYR 0.014 0.002 TYR B 105 ARG 0.003 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 364) hydrogen bonds : angle 5.37125 ( 1017) SS BOND : bond 0.00768 ( 4) SS BOND : angle 1.50732 ( 8) covalent geometry : bond 0.00336 ( 9225) covalent geometry : angle 0.67095 (12485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.7258 (mtm180) outliers start: 6 outliers final: 1 residues processed: 108 average time/residue: 0.2507 time to fit residues: 36.1171 Evaluate side-chains 98 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 0 optimal weight: 40.0000 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN D 188 HIS A 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.147513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.124456 restraints weight = 15318.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124643 restraints weight = 17317.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125617 restraints weight = 15436.567| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9229 Z= 0.122 Angle : 0.615 10.246 12493 Z= 0.314 Chirality : 0.043 0.177 1403 Planarity : 0.004 0.054 1574 Dihedral : 5.716 49.057 1300 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.22 % Allowed : 9.77 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1127 helix: 0.66 (0.29), residues: 341 sheet: -0.14 (0.30), residues: 282 loop : -2.12 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.014 0.001 PHE A 105 TYR 0.010 0.001 TYR B 105 ARG 0.005 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 364) hydrogen bonds : angle 4.98870 ( 1017) SS BOND : bond 0.00706 ( 4) SS BOND : angle 2.60964 ( 8) covalent geometry : bond 0.00271 ( 9225) covalent geometry : angle 0.61146 (12485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.5082 (pp) outliers start: 12 outliers final: 5 residues processed: 114 average time/residue: 0.2465 time to fit residues: 37.5900 Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.146297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123828 restraints weight = 15332.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122551 restraints weight = 18693.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124250 restraints weight = 15784.692| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9229 Z= 0.126 Angle : 0.608 10.202 12493 Z= 0.308 Chirality : 0.043 0.202 1403 Planarity : 0.004 0.051 1574 Dihedral : 5.614 48.265 1300 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.42 % Allowed : 11.29 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.24), residues: 1127 helix: 0.80 (0.30), residues: 340 sheet: -0.01 (0.30), residues: 280 loop : -2.03 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.015 0.001 PHE A 105 TYR 0.012 0.001 TYR B 105 ARG 0.006 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 364) hydrogen bonds : angle 4.83776 ( 1017) SS BOND : bond 0.00880 ( 4) SS BOND : angle 2.44974 ( 8) covalent geometry : bond 0.00289 ( 9225) covalent geometry : angle 0.60553 (12485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: B 332 TRP cc_start: 0.8208 (m-10) cc_final: 0.7964 (m-10) REVERT: D 227 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.4959 (pp) REVERT: A 103 MET cc_start: 0.5827 (ttt) cc_final: 0.5437 (ttt) REVERT: A 167 MET cc_start: 0.4979 (tpp) cc_final: 0.4765 (tpt) outliers start: 14 outliers final: 6 residues processed: 117 average time/residue: 0.2285 time to fit residues: 36.6122 Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 66 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.147080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124145 restraints weight = 15313.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.123805 restraints weight = 19838.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125600 restraints weight = 16393.528| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9229 Z= 0.128 Angle : 0.593 9.482 12493 Z= 0.305 Chirality : 0.043 0.165 1403 Planarity : 0.004 0.051 1574 Dihedral : 5.519 48.344 1300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.03 % Allowed : 11.60 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.89 (0.24), residues: 1127 helix: 0.91 (0.30), residues: 339 sheet: 0.00 (0.30), residues: 274 loop : -2.02 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.015 0.001 PHE A 105 TYR 0.014 0.001 TYR B 105 ARG 0.006 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 364) hydrogen bonds : angle 4.73945 ( 1017) SS BOND : bond 0.00724 ( 4) SS BOND : angle 1.87142 ( 8) covalent geometry : bond 0.00295 ( 9225) covalent geometry : angle 0.59136 (12485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: S 233 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.5501 (tp) REVERT: S 239 PHE cc_start: 0.4065 (OUTLIER) cc_final: 0.3843 (m-80) REVERT: A 103 MET cc_start: 0.5799 (ttt) cc_final: 0.5516 (ttt) outliers start: 20 outliers final: 14 residues processed: 121 average time/residue: 0.2302 time to fit residues: 38.1212 Evaluate side-chains 116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 239 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 3 optimal weight: 30.0000 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125470 restraints weight = 15148.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125226 restraints weight = 17563.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126465 restraints weight = 15769.981| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9229 Z= 0.117 Angle : 0.581 11.076 12493 Z= 0.295 Chirality : 0.043 0.150 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.384 47.057 1300 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.83 % Allowed : 13.73 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.76 (0.25), residues: 1127 helix: 1.09 (0.30), residues: 336 sheet: 0.10 (0.30), residues: 270 loop : -1.98 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.014 0.001 PHE S 203 TYR 0.011 0.001 TYR B 105 ARG 0.007 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 364) hydrogen bonds : angle 4.65102 ( 1017) SS BOND : bond 0.00646 ( 4) SS BOND : angle 1.54201 ( 8) covalent geometry : bond 0.00264 ( 9225) covalent geometry : angle 0.57960 (12485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.964 Fit side-chains REVERT: S 118 THR cc_start: 0.8109 (m) cc_final: 0.7779 (p) REVERT: S 233 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5413 (tp) REVERT: A 103 MET cc_start: 0.5801 (ttt) cc_final: 0.5404 (ttt) outliers start: 18 outliers final: 13 residues processed: 114 average time/residue: 0.2240 time to fit residues: 35.1696 Evaluate side-chains 113 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126120 restraints weight = 15413.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125800 restraints weight = 21113.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126363 restraints weight = 18875.819| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9229 Z= 0.171 Angle : 0.635 10.440 12493 Z= 0.323 Chirality : 0.045 0.161 1403 Planarity : 0.004 0.049 1574 Dihedral : 5.653 51.752 1300 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.03 % Allowed : 14.04 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.86 (0.24), residues: 1127 helix: 0.90 (0.30), residues: 338 sheet: 0.03 (0.29), residues: 286 loop : -2.01 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.026 0.002 PHE S 29 TYR 0.015 0.002 TYR B 105 ARG 0.012 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 364) hydrogen bonds : angle 4.79545 ( 1017) SS BOND : bond 0.00739 ( 4) SS BOND : angle 1.70426 ( 8) covalent geometry : bond 0.00406 ( 9225) covalent geometry : angle 0.63378 (12485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: S 233 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5411 (tp) REVERT: A 103 MET cc_start: 0.5621 (ttt) cc_final: 0.5420 (ttt) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.2280 time to fit residues: 34.9506 Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.146141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126354 restraints weight = 15494.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125353 restraints weight = 22908.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126446 restraints weight = 20109.539| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9229 Z= 0.132 Angle : 0.593 10.334 12493 Z= 0.303 Chirality : 0.043 0.147 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.511 51.309 1300 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 14.85 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.79 (0.24), residues: 1127 helix: 0.95 (0.30), residues: 339 sheet: 0.10 (0.29), residues: 287 loop : -2.00 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.008 0.001 HIS A 133 PHE 0.022 0.002 PHE S 29 TYR 0.011 0.001 TYR B 105 ARG 0.004 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 364) hydrogen bonds : angle 4.73742 ( 1017) SS BOND : bond 0.00675 ( 4) SS BOND : angle 1.56485 ( 8) covalent geometry : bond 0.00305 ( 9225) covalent geometry : angle 0.59165 (12485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 0.2316 time to fit residues: 34.3308 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.147714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128015 restraints weight = 15290.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127441 restraints weight = 21347.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128412 restraints weight = 18430.128| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9229 Z= 0.118 Angle : 0.582 11.588 12493 Z= 0.298 Chirality : 0.043 0.138 1403 Planarity : 0.004 0.051 1574 Dihedral : 5.379 49.293 1300 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.83 % Allowed : 14.45 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.67 (0.25), residues: 1127 helix: 1.09 (0.30), residues: 336 sheet: 0.14 (0.30), residues: 282 loop : -1.91 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS A 133 PHE 0.021 0.001 PHE S 29 TYR 0.010 0.001 TYR S 50 ARG 0.009 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 364) hydrogen bonds : angle 4.65234 ( 1017) SS BOND : bond 0.00620 ( 4) SS BOND : angle 1.52748 ( 8) covalent geometry : bond 0.00267 ( 9225) covalent geometry : angle 0.58092 (12485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7358 (mt) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.2353 time to fit residues: 37.3510 Evaluate side-chains 115 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128780 restraints weight = 15354.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128196 restraints weight = 20966.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128801 restraints weight = 18748.418| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9229 Z= 0.116 Angle : 0.581 11.558 12493 Z= 0.298 Chirality : 0.043 0.171 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.285 40.972 1300 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.73 % Allowed : 15.06 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.61 (0.25), residues: 1127 helix: 1.14 (0.30), residues: 336 sheet: 0.18 (0.30), residues: 282 loop : -1.87 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.021 0.001 PHE S 29 TYR 0.010 0.001 TYR S 50 ARG 0.008 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 364) hydrogen bonds : angle 4.58658 ( 1017) SS BOND : bond 0.00603 ( 4) SS BOND : angle 1.48597 ( 8) covalent geometry : bond 0.00260 ( 9225) covalent geometry : angle 0.57978 (12485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.961 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 118 average time/residue: 0.2467 time to fit residues: 39.0152 Evaluate side-chains 116 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.148055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.125412 restraints weight = 15202.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125187 restraints weight = 18408.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126315 restraints weight = 15914.372| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9229 Z= 0.123 Angle : 0.590 11.435 12493 Z= 0.303 Chirality : 0.043 0.205 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.305 39.905 1300 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.73 % Allowed : 15.16 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1127 helix: 1.14 (0.30), residues: 336 sheet: 0.21 (0.30), residues: 282 loop : -1.81 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.021 0.001 PHE S 29 TYR 0.011 0.001 TYR S 50 ARG 0.008 0.000 ARG A 222 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 364) hydrogen bonds : angle 4.58204 ( 1017) SS BOND : bond 0.00627 ( 4) SS BOND : angle 1.67465 ( 8) covalent geometry : bond 0.00283 ( 9225) covalent geometry : angle 0.58867 (12485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.60 seconds wall clock time: 49 minutes 19.01 seconds (2959.01 seconds total)