Starting phenix.real_space_refine on Fri Feb 14 10:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjg_60144/02_2025/8zjg_60144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjg_60144/02_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_60144/02_2025/8zjg_60144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjg_60144/02_2025/8zjg_60144.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjg_60144/02_2025/8zjg_60144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjg_60144/02_2025/8zjg_60144.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.45, per 1000 atoms: 0.64 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.24 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: 3.22 Time building geometry restraints manager: 3.03 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: 2.980 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 10348 Z= 0.361 Angle : 0.820 13.197 14029 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (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 TRP 0.026 0.002 TRP L 62 HIS 0.007 0.001 HIS L 126 PHE 0.031 0.001 PHE L 17 TYR 0.021 0.001 TYR A 103 ARG 0.023 0.001 ARG L 47 *********************** 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 : 1.091 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: 0.2494 time to fit residues: 57.9994 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 : 1.221 ------------------------------------------------------------------------------- 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 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119069 restraints weight = 13593.223| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.75 r_work: 0.3393 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10348 Z= 0.189 Angle : 0.655 10.162 14029 Z= 0.330 Chirality : 0.045 0.385 1601 Planarity : 0.005 0.062 1749 Dihedral : 6.632 46.936 1634 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.35 % Allowed : 21.92 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1252 helix: 2.23 (0.27), residues: 392 sheet: -0.15 (0.30), residues: 300 loop : -1.09 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 62 HIS 0.008 0.001 HIS L 126 PHE 0.020 0.001 PHE L 17 TYR 0.013 0.001 TYR A 103 ARG 0.007 0.000 ARG L 8 *********************** 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 191 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.6855 (mmt) cc_final: 0.6308 (mtt) REVERT: B 198 LEU cc_start: 0.8285 (pp) cc_final: 0.8069 (pp) REVERT: B 254 ASP cc_start: 0.8052 (t0) cc_final: 0.7773 (t0) REVERT: L 37 ASP cc_start: 0.5630 (t0) cc_final: 0.5102 (p0) REVERT: L 45 PHE cc_start: 0.7276 (t80) cc_final: 0.6509 (t80) REVERT: L 83 LYS cc_start: 0.7657 (ttmm) cc_final: 0.7389 (ttmm) outliers start: 37 outliers final: 23 residues processed: 185 average time/residue: 0.2504 time to fit residues: 63.2407 Evaluate side-chains 164 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 175 LEU 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 160 SER Chi-restraints excluded: chain B residue 161 SER 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.157173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108850 restraints weight = 13838.949| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.72 r_work: 0.3260 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10348 Z= 0.436 Angle : 0.761 10.215 14029 Z= 0.390 Chirality : 0.049 0.410 1601 Planarity : 0.005 0.066 1749 Dihedral : 6.914 45.438 1630 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.55 % Favored : 93.37 % Rotamer: Outliers : 5.25 % Allowed : 22.10 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1252 helix: 1.91 (0.26), residues: 398 sheet: -0.11 (0.31), residues: 290 loop : -1.39 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.007 0.001 HIS L 126 PHE 0.025 0.002 PHE B 292 TYR 0.026 0.002 TYR A 103 ARG 0.007 0.001 ARG B 314 *********************** 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 199 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8536 (mtmm) cc_final: 0.8304 (mtpp) REVERT: A 102 ASP cc_start: 0.8621 (t0) cc_final: 0.8342 (t0) REVERT: A 161 MET cc_start: 0.6958 (mmt) cc_final: 0.6369 (mtt) REVERT: B 254 ASP cc_start: 0.8122 (t0) cc_final: 0.7805 (t0) REVERT: C 230 TYR cc_start: 0.7418 (p90) cc_final: 0.7145 (p90) REVERT: S 140 MET cc_start: 0.8155 (mtm) cc_final: 0.7781 (mtp) REVERT: L 44 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6730 (tp) REVERT: L 45 PHE cc_start: 0.7354 (t80) cc_final: 0.7142 (t80) REVERT: L 89 LYS cc_start: 0.6628 (tptp) cc_final: 0.6358 (pttt) REVERT: L 96 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8246 (t-90) outliers start: 58 outliers final: 39 residues processed: 189 average time/residue: 0.2412 time to fit residues: 62.9204 Evaluate side-chains 173 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 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 279 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL 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 165 THR 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 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 184 ILE 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 G residue 30 VAL 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 Chi-restraints excluded: chain L residue 14 LEU 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 115 optimal weight: 0.0070 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN S 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115029 restraints weight = 13575.609| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.72 r_work: 0.3338 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10348 Z= 0.178 Angle : 0.605 10.266 14029 Z= 0.310 Chirality : 0.044 0.426 1601 Planarity : 0.004 0.055 1749 Dihedral : 6.070 42.919 1630 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 2.81 % Allowed : 25.00 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1252 helix: 2.27 (0.27), residues: 396 sheet: -0.01 (0.31), residues: 297 loop : -1.34 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.007 0.001 HIS L 126 PHE 0.013 0.001 PHE B 292 TYR 0.017 0.001 TYR A 103 ARG 0.003 0.000 ARG L 8 *********************** 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 175 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7437 (ttp-170) REVERT: B 254 ASP cc_start: 0.8042 (t0) cc_final: 0.7711 (t0) REVERT: C 25 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7140 (tm-30) REVERT: L 45 PHE cc_start: 0.6897 (t80) cc_final: 0.6603 (t80) REVERT: L 48 LEU cc_start: 0.7429 (tp) cc_final: 0.7009 (mt) REVERT: L 89 LYS cc_start: 0.6415 (tptp) cc_final: 0.6115 (pttt) REVERT: L 96 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.8221 (t-90) outliers start: 31 outliers final: 21 residues processed: 168 average time/residue: 0.2677 time to fit residues: 60.2982 Evaluate side-chains 160 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 302 THR 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 294 CYS 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 38 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 224 VAL 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 103 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 84 optimal weight: 0.0170 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116908 restraints weight = 13635.965| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.73 r_work: 0.3366 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10348 Z= 0.152 Angle : 0.566 10.135 14029 Z= 0.291 Chirality : 0.043 0.430 1601 Planarity : 0.004 0.060 1749 Dihedral : 5.595 41.049 1630 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 3.71 % Allowed : 24.64 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1252 helix: 2.43 (0.27), residues: 396 sheet: 0.05 (0.31), residues: 298 loop : -1.32 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.007 0.001 HIS L 126 PHE 0.029 0.001 PHE S 68 TYR 0.025 0.001 TYR A 103 ARG 0.003 0.000 ARG B 49 *********************** 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 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7525 (ttp-170) REVERT: B 254 ASP cc_start: 0.8054 (t0) cc_final: 0.7703 (t0) REVERT: B 258 ASP cc_start: 0.7456 (t0) cc_final: 0.7238 (t0) REVERT: C 25 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7158 (tm-30) REVERT: S 140 MET cc_start: 0.7697 (mtp) cc_final: 0.7040 (mtp) REVERT: L 17 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5986 (t80) REVERT: L 45 PHE cc_start: 0.6940 (t80) cc_final: 0.6679 (t80) outliers start: 41 outliers final: 27 residues processed: 178 average time/residue: 0.2538 time to fit residues: 61.4866 Evaluate side-chains 171 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 218 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 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 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 201 VAL 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 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 17 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114113 restraints weight = 13682.808| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.73 r_work: 0.3332 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10348 Z= 0.212 Angle : 0.596 10.100 14029 Z= 0.305 Chirality : 0.044 0.428 1601 Planarity : 0.004 0.060 1749 Dihedral : 5.646 40.269 1630 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 4.08 % Allowed : 24.91 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1252 helix: 2.49 (0.27), residues: 391 sheet: 0.01 (0.31), residues: 300 loop : -1.30 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.006 0.001 HIS L 126 PHE 0.024 0.001 PHE S 68 TYR 0.029 0.001 TYR A 103 ARG 0.004 0.000 ARG B 129 *********************** 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 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7536 (ttp-170) REVERT: B 254 ASP cc_start: 0.8075 (t70) cc_final: 0.7721 (t0) REVERT: C 25 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7150 (tm-30) REVERT: L 17 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6004 (t80) REVERT: L 45 PHE cc_start: 0.6968 (t80) cc_final: 0.6725 (t80) outliers start: 45 outliers final: 34 residues processed: 182 average time/residue: 0.2437 time to fit residues: 60.8052 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 : 1.130 ------------------------------------------------------------------------------- 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 176 VAL 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 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 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 C residue 22 ASN Chi-restraints excluded: chain C residue 201 VAL 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 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 17 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS C 331 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114034 restraints weight = 13818.136| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.73 r_work: 0.3330 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10348 Z= 0.214 Angle : 0.596 10.015 14029 Z= 0.307 Chirality : 0.044 0.427 1601 Planarity : 0.004 0.060 1749 Dihedral : 5.544 40.204 1628 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 4.17 % Allowed : 24.82 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1252 helix: 2.54 (0.26), residues: 390 sheet: 0.05 (0.31), residues: 298 loop : -1.35 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 203 HIS 0.006 0.001 HIS L 126 PHE 0.023 0.001 PHE S 68 TYR 0.032 0.001 TYR A 103 ARG 0.007 0.000 ARG B 129 *********************** 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 185 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8344 (t0) cc_final: 0.8092 (t0) REVERT: B 254 ASP cc_start: 0.8070 (t70) cc_final: 0.7707 (t0) REVERT: C 25 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7159 (tm-30) REVERT: S 140 MET cc_start: 0.7660 (mtp) cc_final: 0.6846 (mtp) REVERT: S 186 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: L 17 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6031 (t80) REVERT: L 45 PHE cc_start: 0.6959 (t80) cc_final: 0.6752 (t80) outliers start: 46 outliers final: 37 residues processed: 181 average time/residue: 0.2441 time to fit residues: 60.5929 Evaluate side-chains 176 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 176 VAL 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 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 201 VAL 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 116 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 17 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111903 restraints weight = 13574.034| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.58 r_work: 0.3288 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10348 Z= 0.322 Angle : 0.660 9.965 14029 Z= 0.340 Chirality : 0.046 0.429 1601 Planarity : 0.004 0.060 1749 Dihedral : 5.872 40.194 1628 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 4.44 % Allowed : 24.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1252 helix: 2.39 (0.26), residues: 391 sheet: -0.11 (0.31), residues: 305 loop : -1.42 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 47 HIS 0.006 0.001 HIS A 217 PHE 0.018 0.002 PHE S 68 TYR 0.040 0.002 TYR A 103 ARG 0.011 0.001 ARG B 129 *********************** 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: 49 poor density : 142 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8637 (mmtt) cc_final: 0.7912 (mtpt) REVERT: A 102 ASP cc_start: 0.8341 (t0) cc_final: 0.8080 (t0) REVERT: B 46 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7529 (ttp-170) REVERT: B 243 THR cc_start: 0.8817 (p) cc_final: 0.8613 (p) REVERT: B 254 ASP cc_start: 0.8086 (t70) cc_final: 0.7730 (t0) REVERT: C 25 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7135 (tm-30) REVERT: S 186 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: L 17 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.6048 (t80) REVERT: L 45 PHE cc_start: 0.7000 (t80) cc_final: 0.6799 (t80) REVERT: L 124 ASP cc_start: 0.8343 (t0) cc_final: 0.7545 (p0) outliers start: 49 outliers final: 39 residues processed: 184 average time/residue: 0.2425 time to fit residues: 60.9435 Evaluate side-chains 177 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 176 VAL 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 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 31 SER 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 21 ARG Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 245 GLU 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 116 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 17 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112385 restraints weight = 13708.680| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.72 r_work: 0.3312 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10348 Z= 0.236 Angle : 0.627 9.901 14029 Z= 0.322 Chirality : 0.045 0.426 1601 Planarity : 0.004 0.055 1749 Dihedral : 5.697 39.802 1628 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 3.89 % Allowed : 26.18 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1252 helix: 2.32 (0.26), residues: 397 sheet: -0.08 (0.31), residues: 303 loop : -1.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.007 0.001 HIS L 126 PHE 0.020 0.001 PHE S 68 TYR 0.038 0.001 TYR A 103 ARG 0.005 0.000 ARG B 46 *********************** 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: 43 poor density : 145 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8526 (mmtt) cc_final: 0.7795 (mtpt) REVERT: A 102 ASP cc_start: 0.8242 (t0) cc_final: 0.8001 (t0) REVERT: B 46 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7581 (ttp-170) REVERT: B 243 THR cc_start: 0.8798 (p) cc_final: 0.8589 (p) REVERT: B 254 ASP cc_start: 0.8072 (t70) cc_final: 0.7716 (t0) REVERT: C 25 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7167 (tm-30) REVERT: S 140 MET cc_start: 0.7560 (mtp) cc_final: 0.6713 (mmm) REVERT: S 186 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: L 17 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.6059 (t80) REVERT: L 124 ASP cc_start: 0.8361 (t0) cc_final: 0.7622 (p0) outliers start: 43 outliers final: 37 residues processed: 183 average time/residue: 0.2542 time to fit residues: 63.7763 Evaluate side-chains 179 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 31 SER 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 201 VAL Chi-restraints excluded: chain C residue 245 GLU 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 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 17 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 0.0020 chunk 32 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112050 restraints weight = 13769.944| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.72 r_work: 0.3307 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10348 Z= 0.249 Angle : 0.647 13.684 14029 Z= 0.329 Chirality : 0.046 0.425 1601 Planarity : 0.004 0.078 1749 Dihedral : 5.688 39.743 1628 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 3.89 % Allowed : 26.18 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1252 helix: 2.42 (0.26), residues: 391 sheet: -0.08 (0.31), residues: 298 loop : -1.42 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.006 0.001 HIS L 126 PHE 0.018 0.001 PHE S 68 TYR 0.042 0.002 TYR A 103 ARG 0.014 0.000 ARG B 129 ********************** 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 182 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7798 (mtpt) REVERT: A 102 ASP cc_start: 0.8239 (t0) cc_final: 0.8006 (t0) REVERT: A 214 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.6380 (t80) REVERT: B 46 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7569 (ttp-170) REVERT: B 243 THR cc_start: 0.8802 (p) cc_final: 0.8601 (p) REVERT: B 254 ASP cc_start: 0.8085 (t70) cc_final: 0.7733 (t0) REVERT: C 25 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7167 (tm-30) REVERT: S 140 MET cc_start: 0.7526 (mtp) cc_final: 0.6672 (mmm) REVERT: S 186 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: L 17 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.6025 (t80) REVERT: L 124 ASP cc_start: 0.8325 (t0) cc_final: 0.7578 (p0) outliers start: 43 outliers final: 38 residues processed: 179 average time/residue: 0.2434 time to fit residues: 59.8872 Evaluate side-chains 177 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 214 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 31 SER 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 201 VAL Chi-restraints excluded: chain C residue 245 GLU 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 116 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112522 restraints weight = 13691.510| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.72 r_work: 0.3314 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10348 Z= 0.237 Angle : 0.639 11.998 14029 Z= 0.326 Chirality : 0.045 0.423 1601 Planarity : 0.004 0.053 1749 Dihedral : 5.616 39.764 1628 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 3.89 % Allowed : 26.27 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1252 helix: 2.32 (0.26), residues: 397 sheet: -0.02 (0.32), residues: 291 loop : -1.47 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.006 0.001 HIS L 126 PHE 0.016 0.001 PHE S 68 TYR 0.039 0.001 TYR A 103 ARG 0.004 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5219.44 seconds wall clock time: 93 minutes 36.75 seconds (5616.75 seconds total)