Starting phenix.real_space_refine on Wed Sep 17 17:25:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjg_60144/09_2025/8zjg_60144.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.074 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 75 5.16 5 C 6485 2.51 5 N 1705 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10123 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2540 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1799 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 856 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain breaks: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.37, per 1000 atoms: 0.23 Number of scatterers: 10123 At special positions: 0 Unit cell: (101.15, 121.55, 152.15, 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 75 16.00 O 1858 8.00 N 1705 7.00 C 6485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS L 78 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 115 " 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: 0.71 Conformation dependent library (CDL) restraints added in 387.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.7% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 removed outlier: 3.689A pdb=" N THR A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 101 removed outlier: 4.014A pdb=" N VAL A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.726A pdb=" N MET A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 143 removed outlier: 3.837A pdb=" N CYS A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 152 through 172 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 212 through 250 removed outlier: 5.862A pdb=" N VAL A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 256 through 283 removed outlier: 3.652A pdb=" N THR A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.830A pdb=" N SER A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.565A pdb=" N TYR A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 339 removed outlier: 3.657A pdb=" N LYS A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.501A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 6 through 30 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.984A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.670A pdb=" N GLU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 4.026A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.548A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.563A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.125A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.773A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'L' and resid 118 through 120 No H-bonds generated for 'chain 'L' and resid 118 through 120' Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.324A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.986A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.676A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.282A 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: 6.828A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.532A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.519A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.143A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.143A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.847A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.025A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AB6, first strand: chain 'L' and resid 35 through 40 removed outlier: 6.282A pdb=" N ILE L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY L 92 " --> pdb=" O LYS L 83 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1629 1.31 - 1.44: 2825 1.44 - 1.56: 5782 1.56 - 1.69: 4 1.69 - 1.82: 108 Bond restraints: 10348 Sorted by residual: bond pdb=" CA SER A 309 " pdb=" C SER A 309 " ideal model delta sigma weight residual 1.524 1.434 0.089 1.31e-02 5.83e+03 4.66e+01 bond pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 1.525 1.446 0.079 1.27e-02 6.20e+03 3.86e+01 bond pdb=" CA ALA A 167 " pdb=" C ALA A 167 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.30e-02 5.92e+03 3.15e+01 bond pdb=" CA ALA A 167 " pdb=" CB ALA A 167 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.09e+01 bond pdb=" CA ILE A 306 " pdb=" C ILE A 306 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.27e-02 6.20e+03 2.80e+01 ... (remaining 10343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 13760 2.64 - 5.28: 225 5.28 - 7.92: 33 7.92 - 10.56: 10 10.56 - 13.20: 1 Bond angle restraints: 14029 Sorted by residual: angle pdb=" N CYS A 310 " pdb=" CA CYS A 310 " pdb=" C CYS A 310 " ideal model delta sigma weight residual 114.09 100.89 13.20 1.55e+00 4.16e-01 7.25e+01 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 110.42 117.69 -7.27 9.60e-01 1.09e+00 5.74e+01 angle pdb=" N VAL A 317 " pdb=" CA VAL A 317 " pdb=" C VAL A 317 " ideal model delta sigma weight residual 112.29 119.05 -6.76 9.40e-01 1.13e+00 5.17e+01 angle pdb=" N LEU A 304 " pdb=" CA LEU A 304 " pdb=" C LEU A 304 " ideal model delta sigma weight residual 111.07 104.03 7.04 1.07e+00 8.73e-01 4.33e+01 angle pdb=" N PHE A 318 " pdb=" CA PHE A 318 " pdb=" C PHE A 318 " ideal model delta sigma weight residual 111.87 102.79 9.08 1.41e+00 5.03e-01 4.15e+01 ... (remaining 14024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5524 17.96 - 35.92: 647 35.92 - 53.88: 153 53.88 - 71.84: 20 71.84 - 89.81: 6 Dihedral angle restraints: 6350 sinusoidal: 2654 harmonic: 3696 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 189 " pdb=" CB CYS A 189 " ideal model delta sinusoidal sigma weight residual -86.00 -139.56 53.56 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CA GLN A 208 " pdb=" C GLN A 208 " pdb=" N MET A 209 " pdb=" CA MET A 209 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA MET A 209 " pdb=" C MET A 209 " pdb=" N ASP A 210 " pdb=" CA ASP A 210 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1412 0.074 - 0.149: 173 0.149 - 0.223: 14 0.223 - 0.298: 1 0.298 - 0.372: 1 Chirality restraints: 1601 Sorted by residual: chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C20 CLR A 402 " pdb=" C17 CLR A 402 " pdb=" C21 CLR A 402 " pdb=" C22 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.59 2.35 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA CYS A 160 " pdb=" N CYS A 160 " pdb=" C CYS A 160 " pdb=" CB CYS A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1598 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 157 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C TYR A 157 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" N MET A 158 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO A 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 130 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO L 131 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 131 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 131 " -0.039 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 573 2.72 - 3.27: 10010 3.27 - 3.81: 15963 3.81 - 4.36: 19344 4.36 - 4.90: 34055 Nonbonded interactions: 79945 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.180 3.040 nonbonded pdb=" NH2 ARG A 40 " pdb=" O ALA A 100 " model vdw 2.194 3.120 nonbonded pdb=" NH1 ARG L 7 " pdb=" OE1 GLN L 11 " model vdw 2.211 3.120 nonbonded pdb=" OG SER C 326 " pdb=" OD1 ASP C 328 " model vdw 2.234 3.040 nonbonded pdb=" O HIS S 232 " pdb=" ND1 HIS S 232 " model vdw 2.266 3.120 ... (remaining 79940 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: 2.050 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10353 Z= 0.347 Angle : 0.820 13.197 14039 Z= 0.458 Chirality : 0.048 0.372 1601 Planarity : 0.006 0.073 1749 Dihedral : 15.707 89.806 3941 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 1.00 % Allowed : 26.00 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.25), residues: 1252 helix: 1.79 (0.27), residues: 390 sheet: -0.29 (0.30), residues: 306 loop : -1.07 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG L 47 TYR 0.021 0.001 TYR A 103 PHE 0.031 0.001 PHE L 17 TRP 0.026 0.002 TRP L 62 HIS 0.007 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00529 (10348) covalent geometry : angle 0.81988 (14029) SS BOND : bond 0.00416 ( 5) SS BOND : angle 0.78222 ( 10) hydrogen bonds : bond 0.13665 ( 464) hydrogen bonds : angle 5.99156 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7041 (mmt) cc_final: 0.6598 (mtt) REVERT: B 311 HIS cc_start: 0.6747 (m-70) cc_final: 0.6544 (m-70) REVERT: C 29 LYS cc_start: 0.8048 (tttm) cc_final: 0.7511 (ttmm) REVERT: S 18 ARG cc_start: 0.7327 (tpt90) cc_final: 0.7063 (mtt-85) REVERT: S 218 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8135 (mmm-85) REVERT: L 15 GLU cc_start: 0.7338 (tt0) cc_final: 0.7131 (tt0) outliers start: 11 outliers final: 4 residues processed: 170 average time/residue: 0.1113 time to fit residues: 26.0133 Evaluate side-chains 158 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 331 ASN C 347 ASN ** L 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113137 restraints weight = 13805.003| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.73 r_work: 0.3317 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10353 Z= 0.199 Angle : 0.718 10.143 14039 Z= 0.364 Chirality : 0.047 0.386 1601 Planarity : 0.005 0.063 1749 Dihedral : 6.918 47.658 1634 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 4.89 % Allowed : 21.20 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.25), residues: 1252 helix: 2.09 (0.27), residues: 391 sheet: -0.23 (0.30), residues: 300 loop : -1.20 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 8 TYR 0.018 0.002 TYR A 103 PHE 0.021 0.002 PHE B 292 TRP 0.019 0.002 TRP B 332 HIS 0.009 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00471 (10348) covalent geometry : angle 0.71742 (14029) SS BOND : bond 0.00624 ( 5) SS BOND : angle 1.51143 ( 10) hydrogen bonds : bond 0.05418 ( 464) hydrogen bonds : angle 5.07123 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8120 (mtpp) REVERT: A 161 MET cc_start: 0.6941 (mmt) cc_final: 0.6411 (mtt) REVERT: B 254 ASP cc_start: 0.8087 (t0) cc_final: 0.7756 (t0) REVERT: C 29 LYS cc_start: 0.8206 (tttm) cc_final: 0.7644 (ttmm) REVERT: C 230 TYR cc_start: 0.7197 (p90) cc_final: 0.6957 (p90) REVERT: L 37 ASP cc_start: 0.5687 (t0) cc_final: 0.4650 (p0) REVERT: L 45 PHE cc_start: 0.7361 (t80) cc_final: 0.6654 (t80) REVERT: L 130 PHE cc_start: 0.8615 (m-80) cc_final: 0.8322 (m-80) outliers start: 54 outliers final: 33 residues processed: 194 average time/residue: 0.1072 time to fit residues: 28.7003 Evaluate side-chains 173 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 91 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.163245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115011 restraints weight = 13693.728| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.74 r_work: 0.3347 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10353 Z= 0.137 Angle : 0.625 10.233 14039 Z= 0.317 Chirality : 0.045 0.414 1601 Planarity : 0.004 0.059 1749 Dihedral : 6.280 44.915 1630 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 3.26 % Allowed : 23.19 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.25), residues: 1252 helix: 2.32 (0.27), residues: 391 sheet: -0.06 (0.31), residues: 295 loop : -1.24 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 8 TYR 0.016 0.001 TYR A 103 PHE 0.017 0.001 PHE B 292 TRP 0.017 0.001 TRP L 62 HIS 0.007 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00316 (10348) covalent geometry : angle 0.62420 (14029) SS BOND : bond 0.00607 ( 5) SS BOND : angle 1.40116 ( 10) hydrogen bonds : bond 0.04605 ( 464) hydrogen bonds : angle 4.74826 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.6810 (mmt) cc_final: 0.6226 (mtt) REVERT: B 254 ASP cc_start: 0.8056 (t0) cc_final: 0.7731 (t0) REVERT: C 25 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7064 (tm-30) REVERT: S 140 MET cc_start: 0.7699 (mtp) cc_final: 0.7003 (mtp) REVERT: L 44 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6593 (tp) REVERT: L 45 PHE cc_start: 0.7295 (t80) cc_final: 0.7061 (t80) REVERT: L 96 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.8216 (t-90) outliers start: 36 outliers final: 28 residues processed: 173 average time/residue: 0.1142 time to fit residues: 26.8476 Evaluate side-chains 164 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 96 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114090 restraints weight = 13687.210| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.73 r_work: 0.3333 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10353 Z= 0.145 Angle : 0.610 10.232 14039 Z= 0.312 Chirality : 0.045 0.427 1601 Planarity : 0.004 0.061 1749 Dihedral : 6.028 43.470 1630 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 4.53 % Allowed : 22.37 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.25), residues: 1252 helix: 2.37 (0.27), residues: 391 sheet: -0.02 (0.31), residues: 300 loop : -1.26 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.024 0.001 TYR A 103 PHE 0.023 0.001 PHE S 68 TRP 0.011 0.001 TRP L 62 HIS 0.007 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00341 (10348) covalent geometry : angle 0.60968 (14029) SS BOND : bond 0.00515 ( 5) SS BOND : angle 1.19673 ( 10) hydrogen bonds : bond 0.04592 ( 464) hydrogen bonds : angle 4.67133 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7470 (ttp-170) REVERT: B 254 ASP cc_start: 0.8077 (t0) cc_final: 0.7748 (t0) REVERT: L 15 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: L 17 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.6028 (t80) REVERT: L 96 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (t-90) outliers start: 50 outliers final: 35 residues processed: 176 average time/residue: 0.1054 time to fit residues: 25.5603 Evaluate side-chains 169 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 96 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 108 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.164762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116535 restraints weight = 13625.013| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.73 r_work: 0.3362 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10353 Z= 0.114 Angle : 0.577 10.167 14039 Z= 0.294 Chirality : 0.044 0.432 1601 Planarity : 0.004 0.059 1749 Dihedral : 5.648 41.677 1630 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 3.99 % Allowed : 24.18 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1252 helix: 2.50 (0.27), residues: 391 sheet: 0.07 (0.31), residues: 300 loop : -1.23 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.024 0.001 TYR A 103 PHE 0.015 0.001 PHE L 45 TRP 0.012 0.001 TRP L 62 HIS 0.006 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00255 (10348) covalent geometry : angle 0.57615 (14029) SS BOND : bond 0.00454 ( 5) SS BOND : angle 0.98810 ( 10) hydrogen bonds : bond 0.03941 ( 464) hydrogen bonds : angle 4.51106 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7498 (ttp-170) REVERT: B 254 ASP cc_start: 0.8070 (t0) cc_final: 0.7711 (t0) REVERT: L 15 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: L 17 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.6043 (t80) REVERT: L 89 LYS cc_start: 0.6030 (tptp) cc_final: 0.5725 (pttt) outliers start: 44 outliers final: 33 residues processed: 181 average time/residue: 0.1073 time to fit residues: 26.8010 Evaluate side-chains 174 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 115 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.114640 restraints weight = 13752.994| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.86 r_work: 0.3315 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10353 Z= 0.122 Angle : 0.578 10.104 14039 Z= 0.295 Chirality : 0.044 0.428 1601 Planarity : 0.004 0.062 1749 Dihedral : 5.534 40.742 1630 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 4.44 % Allowed : 24.09 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1252 helix: 2.55 (0.27), residues: 391 sheet: 0.11 (0.31), residues: 301 loop : -1.23 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.027 0.001 TYR A 103 PHE 0.023 0.001 PHE S 68 TRP 0.012 0.001 TRP L 62 HIS 0.006 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00279 (10348) covalent geometry : angle 0.57726 (14029) SS BOND : bond 0.00503 ( 5) SS BOND : angle 1.10062 ( 10) hydrogen bonds : bond 0.04035 ( 464) hydrogen bonds : angle 4.47881 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8303 (t70) cc_final: 0.8036 (t0) REVERT: B 46 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7515 (ttp-170) REVERT: B 198 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (pp) REVERT: B 254 ASP cc_start: 0.8091 (t0) cc_final: 0.7702 (t0) REVERT: L 15 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: L 17 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6134 (t80) REVERT: L 45 PHE cc_start: 0.6822 (t80) cc_final: 0.6484 (t80) outliers start: 49 outliers final: 39 residues processed: 181 average time/residue: 0.1045 time to fit residues: 26.3254 Evaluate side-chains 182 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115510 restraints weight = 13539.440| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.77 r_work: 0.3335 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10353 Z= 0.116 Angle : 0.569 10.023 14039 Z= 0.292 Chirality : 0.044 0.424 1601 Planarity : 0.004 0.061 1749 Dihedral : 5.443 40.571 1630 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 4.71 % Allowed : 24.18 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1252 helix: 2.63 (0.27), residues: 391 sheet: 0.09 (0.31), residues: 308 loop : -1.21 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.029 0.001 TYR A 103 PHE 0.010 0.001 PHE B 241 TRP 0.012 0.001 TRP L 62 HIS 0.005 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00265 (10348) covalent geometry : angle 0.56806 (14029) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.04172 ( 10) hydrogen bonds : bond 0.03977 ( 464) hydrogen bonds : angle 4.42310 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8211 (t70) cc_final: 0.7936 (t0) REVERT: B 198 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8311 (pp) REVERT: B 254 ASP cc_start: 0.8076 (t70) cc_final: 0.7687 (t0) REVERT: S 140 MET cc_start: 0.7748 (mtp) cc_final: 0.6940 (mtp) REVERT: L 15 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: L 45 PHE cc_start: 0.6879 (t80) cc_final: 0.6561 (t80) outliers start: 52 outliers final: 43 residues processed: 184 average time/residue: 0.1081 time to fit residues: 27.2680 Evaluate side-chains 183 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115128 restraints weight = 13557.999| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.78 r_work: 0.3339 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10353 Z= 0.123 Angle : 0.578 9.955 14039 Z= 0.295 Chirality : 0.044 0.421 1601 Planarity : 0.004 0.062 1749 Dihedral : 5.428 40.315 1630 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 4.35 % Allowed : 24.37 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1252 helix: 2.62 (0.27), residues: 391 sheet: 0.15 (0.31), residues: 302 loop : -1.23 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.032 0.001 TYR A 103 PHE 0.019 0.001 PHE S 68 TRP 0.012 0.001 TRP L 62 HIS 0.005 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00286 (10348) covalent geometry : angle 0.57750 (14029) SS BOND : bond 0.00464 ( 5) SS BOND : angle 1.07140 ( 10) hydrogen bonds : bond 0.04078 ( 464) hydrogen bonds : angle 4.43271 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7719 (mtpt) REVERT: A 102 ASP cc_start: 0.8179 (t70) cc_final: 0.7931 (t0) REVERT: B 46 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7532 (ttp-170) REVERT: B 254 ASP cc_start: 0.8092 (t70) cc_final: 0.7699 (t0) REVERT: S 140 MET cc_start: 0.7738 (mtp) cc_final: 0.6988 (mtp) REVERT: S 186 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: L 15 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: L 45 PHE cc_start: 0.6961 (t80) cc_final: 0.6631 (t80) outliers start: 48 outliers final: 41 residues processed: 182 average time/residue: 0.1088 time to fit residues: 27.2461 Evaluate side-chains 183 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 114 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113477 restraints weight = 13614.074| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.76 r_work: 0.3309 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10353 Z= 0.147 Angle : 0.605 9.869 14039 Z= 0.311 Chirality : 0.045 0.421 1601 Planarity : 0.004 0.061 1749 Dihedral : 5.547 39.786 1630 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 4.26 % Allowed : 24.37 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1252 helix: 2.56 (0.27), residues: 391 sheet: 0.11 (0.31), residues: 301 loop : -1.30 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 129 TYR 0.036 0.001 TYR A 103 PHE 0.019 0.001 PHE B 292 TRP 0.012 0.001 TRP L 62 HIS 0.003 0.001 HIS C 213 Details of bonding type rmsd covalent geometry : bond 0.00351 (10348) covalent geometry : angle 0.60390 (14029) SS BOND : bond 0.00449 ( 5) SS BOND : angle 1.56316 ( 10) hydrogen bonds : bond 0.04471 ( 464) hydrogen bonds : angle 4.49862 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7679 (mtpt) REVERT: A 214 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6458 (t80) REVERT: B 46 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7545 (ttp-170) REVERT: B 198 LEU cc_start: 0.8475 (pp) cc_final: 0.8255 (pp) REVERT: B 254 ASP cc_start: 0.8076 (t70) cc_final: 0.7705 (t0) REVERT: C 309 ASP cc_start: 0.8109 (p0) cc_final: 0.7807 (t0) REVERT: S 186 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: L 15 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: L 45 PHE cc_start: 0.7102 (t80) cc_final: 0.6802 (t80) REVERT: L 124 ASP cc_start: 0.8311 (t0) cc_final: 0.7687 (p0) outliers start: 47 outliers final: 39 residues processed: 180 average time/residue: 0.1059 time to fit residues: 26.5799 Evaluate side-chains 180 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115874 restraints weight = 13480.934| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.77 r_work: 0.3350 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10353 Z= 0.116 Angle : 0.582 9.796 14039 Z= 0.299 Chirality : 0.044 0.417 1601 Planarity : 0.004 0.059 1749 Dihedral : 5.401 40.144 1630 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.89 % Allowed : 25.36 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1252 helix: 2.65 (0.27), residues: 391 sheet: 0.16 (0.31), residues: 300 loop : -1.31 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.036 0.001 TYR A 103 PHE 0.029 0.001 PHE S 68 TRP 0.011 0.001 TRP L 62 HIS 0.006 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00264 (10348) covalent geometry : angle 0.58103 (14029) SS BOND : bond 0.00482 ( 5) SS BOND : angle 1.37998 ( 10) hydrogen bonds : bond 0.03916 ( 464) hydrogen bonds : angle 4.41789 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7651 (mtpt) REVERT: B 46 ARG cc_start: 0.8006 (ttp-110) cc_final: 0.7563 (ttp-170) REVERT: B 198 LEU cc_start: 0.8465 (pp) cc_final: 0.8229 (pp) REVERT: B 254 ASP cc_start: 0.8079 (t70) cc_final: 0.7704 (t0) REVERT: C 25 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7021 (mt-10) REVERT: C 309 ASP cc_start: 0.8049 (p0) cc_final: 0.7786 (t0) REVERT: S 140 MET cc_start: 0.7552 (mtp) cc_final: 0.6934 (mmm) REVERT: S 186 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: L 15 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: L 45 PHE cc_start: 0.7020 (t80) cc_final: 0.6705 (t80) REVERT: L 124 ASP cc_start: 0.8257 (t0) cc_final: 0.7650 (p0) outliers start: 43 outliers final: 39 residues processed: 182 average time/residue: 0.1083 time to fit residues: 27.3595 Evaluate side-chains 183 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113302 restraints weight = 13605.704| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.82 r_work: 0.3311 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10353 Z= 0.146 Angle : 0.616 13.456 14039 Z= 0.313 Chirality : 0.045 0.417 1601 Planarity : 0.004 0.076 1749 Dihedral : 5.467 39.794 1630 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 3.89 % Allowed : 25.00 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1252 helix: 2.58 (0.27), residues: 390 sheet: 0.15 (0.31), residues: 299 loop : -1.31 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 129 TYR 0.035 0.001 TYR A 103 PHE 0.031 0.001 PHE S 68 TRP 0.011 0.001 TRP L 62 HIS 0.005 0.001 HIS L 126 Details of bonding type rmsd covalent geometry : bond 0.00347 (10348) covalent geometry : angle 0.61557 (14029) SS BOND : bond 0.00522 ( 5) SS BOND : angle 1.40583 ( 10) hydrogen bonds : bond 0.04358 ( 464) hydrogen bonds : angle 4.47408 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.16 seconds wall clock time: 46 minutes 26.12 seconds (2786.12 seconds total)