Starting phenix.real_space_refine on Sun Jun 8 23:50:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjg_60144/06_2025/8zjg_60144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjg_60144/06_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_60144/06_2025/8zjg_60144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjg_60144/06_2025/8zjg_60144.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjg_60144/06_2025/8zjg_60144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjg_60144/06_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-5710/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: 6.69, per 1000 atoms: 0.66 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: 2.71 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: 3.12 Time building geometry restraints manager: 3.17 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13665 ( 464) hydrogen bonds : angle 5.99156 ( 1338) SS BOND : bond 0.00416 ( 5) SS BOND : angle 0.78222 ( 10) covalent geometry : bond 0.00529 (10348) covalent geometry : angle 0.81988 (14029) *********************** 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 : 1.052 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: 0.2456 time to fit residues: 57.4277 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 : 1.047 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.167222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119642 restraints weight = 13587.291| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.74 r_work: 0.3401 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1116 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= 0.130 Angle : 0.653 10.175 14039 Z= 0.329 Chirality : 0.045 0.391 1601 Planarity : 0.005 0.062 1749 Dihedral : 6.551 46.697 1634 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 3.71 % Allowed : 21.38 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.25), residues: 1252 helix: 2.26 (0.27), residues: 392 sheet: -0.14 (0.30), residues: 300 loop : -1.10 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 62 HIS 0.009 0.001 HIS L 126 PHE 0.022 0.001 PHE L 17 TYR 0.013 0.001 TYR A 103 ARG 0.007 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 464) hydrogen bonds : angle 4.88122 ( 1338) SS BOND : bond 0.00531 ( 5) SS BOND : angle 1.36377 ( 10) covalent geometry : bond 0.00288 (10348) covalent geometry : angle 0.65179 (14029) *********************** 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 196 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.6829 (mmt) cc_final: 0.6288 (mtt) REVERT: B 254 ASP cc_start: 0.8047 (t0) cc_final: 0.7754 (t0) REVERT: B 266 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7720 (t-170) REVERT: L 37 ASP cc_start: 0.5663 (t0) cc_final: 0.5113 (p0) REVERT: L 45 PHE cc_start: 0.7332 (t80) cc_final: 0.6607 (t80) REVERT: L 83 LYS cc_start: 0.7639 (ttmm) cc_final: 0.7422 (ttmm) outliers start: 41 outliers final: 25 residues processed: 188 average time/residue: 0.2578 time to fit residues: 67.0379 Evaluate side-chains 167 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain B residue 266 HIS 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 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 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: 0.6980 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.160847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112554 restraints weight = 13739.470| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.73 r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10353 Z= 0.195 Angle : 0.682 10.235 14039 Z= 0.347 Chirality : 0.046 0.418 1601 Planarity : 0.005 0.065 1749 Dihedral : 6.436 45.343 1630 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 4.26 % Allowed : 22.19 % 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 (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: 0.25 (0.25), residues: 1252 helix: 2.24 (0.27), residues: 392 sheet: -0.05 (0.31), residues: 293 loop : -1.24 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 62 HIS 0.007 0.001 HIS L 126 PHE 0.020 0.002 PHE B 292 TYR 0.023 0.002 TYR A 103 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 464) hydrogen bonds : angle 4.85430 ( 1338) SS BOND : bond 0.00575 ( 5) SS BOND : angle 1.38179 ( 10) covalent geometry : bond 0.00470 (10348) covalent geometry : angle 0.68085 (14029) *********************** 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 192 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8249 (mtpp) REVERT: A 102 ASP cc_start: 0.8516 (t0) cc_final: 0.8230 (t0) REVERT: A 161 MET cc_start: 0.6887 (mmt) cc_final: 0.6285 (mtt) REVERT: B 254 ASP cc_start: 0.8064 (t0) cc_final: 0.7759 (t0) REVERT: L 44 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6711 (tp) REVERT: L 45 PHE cc_start: 0.7341 (t80) cc_final: 0.7081 (t80) REVERT: L 96 HIS cc_start: 0.8446 (OUTLIER) cc_final: 0.8233 (t-90) outliers start: 47 outliers final: 31 residues processed: 181 average time/residue: 0.2249 time to fit residues: 56.5055 Evaluate side-chains 162 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 B residue 17 GLN 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 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 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 147 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: 0.2980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.164015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115817 restraints weight = 13733.217| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.72 r_work: 0.3356 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1916 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= 0.124 Angle : 0.599 10.264 14039 Z= 0.307 Chirality : 0.044 0.429 1601 Planarity : 0.004 0.058 1749 Dihedral : 5.943 43.122 1630 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.62 % Allowed : 23.37 % 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: 0.38 (0.25), residues: 1252 helix: 2.43 (0.27), residues: 391 sheet: 0.05 (0.31), residues: 303 loop : -1.25 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 62 HIS 0.007 0.001 HIS L 126 PHE 0.013 0.001 PHE B 292 TYR 0.018 0.001 TYR A 103 ARG 0.003 0.000 ARG L 8 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 464) hydrogen bonds : angle 4.58420 ( 1338) SS BOND : bond 0.00508 ( 5) SS BOND : angle 1.28636 ( 10) covalent geometry : bond 0.00283 (10348) covalent geometry : angle 0.59841 (14029) *********************** 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 183 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7891 (ttp-110) cc_final: 0.7439 (ttp-170) REVERT: B 254 ASP cc_start: 0.8067 (t0) cc_final: 0.7739 (t0) REVERT: L 15 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: L 45 PHE cc_start: 0.7000 (t80) cc_final: 0.6679 (t80) REVERT: L 48 LEU cc_start: 0.7389 (tp) cc_final: 0.6974 (mt) outliers start: 40 outliers final: 32 residues processed: 173 average time/residue: 0.2375 time to fit residues: 56.8826 Evaluate side-chains 168 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 176 VAL 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 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 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 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 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 147 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 78 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.157625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108993 restraints weight = 13710.764| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.72 r_work: 0.3254 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10353 Z= 0.237 Angle : 0.696 10.204 14039 Z= 0.359 Chirality : 0.048 0.436 1601 Planarity : 0.005 0.065 1749 Dihedral : 6.373 41.633 1630 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 4.80 % Allowed : 23.37 % 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 (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: 0.06 (0.25), residues: 1252 helix: 2.08 (0.27), residues: 398 sheet: -0.14 (0.31), residues: 302 loop : -1.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 62 HIS 0.006 0.001 HIS L 126 PHE 0.022 0.002 PHE L 134 TYR 0.033 0.002 TYR A 103 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05875 ( 464) hydrogen bonds : angle 4.91774 ( 1338) SS BOND : bond 0.00570 ( 5) SS BOND : angle 1.42554 ( 10) covalent geometry : bond 0.00576 (10348) covalent geometry : angle 0.69475 (14029) *********************** 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 191 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8540 (t70) cc_final: 0.8258 (t0) REVERT: B 254 ASP cc_start: 0.8126 (t0) cc_final: 0.7783 (t0) REVERT: C 25 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 230 TYR cc_start: 0.7336 (p90) cc_final: 0.7114 (p90) REVERT: L 15 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: L 17 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6246 (t80) REVERT: L 45 PHE cc_start: 0.6960 (t80) cc_final: 0.6742 (t80) outliers start: 53 outliers final: 37 residues processed: 185 average time/residue: 0.2342 time to fit residues: 59.8509 Evaluate side-chains 173 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 330 LEU 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 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 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 184 ILE 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 14 LEU Chi-restraints excluded: chain L residue 15 GLU Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 116 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.161595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113403 restraints weight = 13713.878| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.72 r_work: 0.3321 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10353 Z= 0.132 Angle : 0.604 10.113 14039 Z= 0.311 Chirality : 0.044 0.433 1601 Planarity : 0.004 0.052 1749 Dihedral : 5.852 40.445 1630 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.62 % Allowed : 25.09 % 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 (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: 0.26 (0.25), residues: 1252 helix: 2.42 (0.27), residues: 391 sheet: -0.09 (0.31), residues: 306 loop : -1.36 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 62 HIS 0.006 0.001 HIS L 126 PHE 0.034 0.001 PHE S 68 TYR 0.024 0.001 TYR A 103 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 464) hydrogen bonds : angle 4.61478 ( 1338) SS BOND : bond 0.00539 ( 5) SS BOND : angle 1.28451 ( 10) covalent geometry : bond 0.00302 (10348) covalent geometry : angle 0.60291 (14029) *********************** 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 185 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8417 (t70) cc_final: 0.8159 (t0) REVERT: A 195 LEU cc_start: 0.9003 (tp) cc_final: 0.8767 (mp) REVERT: B 46 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7525 (ttp-170) REVERT: B 254 ASP cc_start: 0.8079 (t0) cc_final: 0.7751 (t0) REVERT: C 25 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7180 (tm-30) REVERT: C 230 TYR cc_start: 0.7162 (p90) cc_final: 0.6923 (p90) REVERT: L 15 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: L 17 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6219 (t80) REVERT: L 89 LYS cc_start: 0.6315 (tptp) cc_final: 0.5954 (pttp) outliers start: 40 outliers final: 30 residues processed: 181 average time/residue: 0.2481 time to fit residues: 61.8321 Evaluate side-chains 171 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 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 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain L residue 15 GLU 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: 0.7980 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112368 restraints weight = 13846.477| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.74 r_work: 0.3304 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10353 Z= 0.157 Angle : 0.618 10.066 14039 Z= 0.318 Chirality : 0.045 0.430 1601 Planarity : 0.004 0.057 1749 Dihedral : 5.832 39.997 1630 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 4.17 % Allowed : 25.18 % Favored : 70.65 % 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: 0.24 (0.25), residues: 1252 helix: 2.41 (0.27), residues: 391 sheet: -0.08 (0.31), residues: 305 loop : -1.40 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 62 HIS 0.006 0.001 HIS L 126 PHE 0.030 0.002 PHE S 68 TYR 0.033 0.001 TYR A 103 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 464) hydrogen bonds : angle 4.64797 ( 1338) SS BOND : bond 0.00571 ( 5) SS BOND : angle 1.23537 ( 10) covalent geometry : bond 0.00374 (10348) covalent geometry : angle 0.61692 (14029) *********************** 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 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8402 (t70) cc_final: 0.8170 (t0) REVERT: A 195 LEU cc_start: 0.8992 (tp) cc_final: 0.8766 (mp) REVERT: B 46 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7521 (ttp-170) REVERT: B 243 THR cc_start: 0.8788 (p) cc_final: 0.8583 (p) REVERT: B 254 ASP cc_start: 0.8091 (t0) cc_final: 0.7730 (t0) REVERT: C 25 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7252 (tm-30) REVERT: S 140 MET cc_start: 0.7591 (mtp) cc_final: 0.6814 (mtp) REVERT: S 186 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: L 15 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8414 (tt0) outliers start: 46 outliers final: 36 residues processed: 181 average time/residue: 0.2382 time to fit residues: 59.7582 Evaluate side-chains 175 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 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 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 ARG 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 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 15 GLU 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: 9.9990 chunk 83 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.162784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114815 restraints weight = 13750.991| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.73 r_work: 0.3342 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2495 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= 0.125 Angle : 0.602 13.308 14039 Z= 0.306 Chirality : 0.044 0.425 1601 Planarity : 0.004 0.054 1749 Dihedral : 5.572 40.181 1630 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 4.17 % Allowed : 25.27 % Favored : 70.56 % 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: 0.33 (0.25), residues: 1252 helix: 2.51 (0.27), residues: 391 sheet: -0.03 (0.31), residues: 304 loop : -1.37 (0.26), residues: 557 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 0.022 0.001 PHE S 68 TYR 0.030 0.001 TYR A 103 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 464) hydrogen bonds : angle 4.50591 ( 1338) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.06291 ( 10) covalent geometry : bond 0.00286 (10348) covalent geometry : angle 0.60118 (14029) *********************** 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 186 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LEU cc_start: 0.9002 (tp) cc_final: 0.8792 (mp) REVERT: B 46 ARG cc_start: 0.7984 (ttp-110) cc_final: 0.7559 (ttp-170) REVERT: B 243 THR cc_start: 0.8738 (p) cc_final: 0.8538 (p) REVERT: B 254 ASP cc_start: 0.8075 (t70) cc_final: 0.7716 (t0) REVERT: C 25 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7179 (tm-30) REVERT: S 140 MET cc_start: 0.7507 (mtp) cc_final: 0.6700 (mmm) REVERT: S 186 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: L 15 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: L 124 ASP cc_start: 0.8431 (t0) cc_final: 0.7684 (p0) outliers start: 46 outliers final: 37 residues processed: 179 average time/residue: 0.2452 time to fit residues: 60.7999 Evaluate side-chains 175 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 294 CYS Chi-restraints excluded: chain B residue 318 LEU 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 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 15 GLU 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: 0.9980 chunk 64 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 S 194 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113376 restraints weight = 13706.731| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.72 r_work: 0.3323 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2573 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= 0.145 Angle : 0.619 12.135 14039 Z= 0.315 Chirality : 0.045 0.423 1601 Planarity : 0.004 0.057 1749 Dihedral : 5.618 39.901 1630 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 3.89 % Allowed : 25.72 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.28 (0.25), residues: 1252 helix: 2.50 (0.26), residues: 390 sheet: -0.04 (0.31), residues: 304 loop : -1.42 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 62 HIS 0.005 0.001 HIS L 126 PHE 0.016 0.001 PHE B 292 TYR 0.037 0.001 TYR A 103 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 464) hydrogen bonds : angle 4.54947 ( 1338) SS BOND : bond 0.00473 ( 5) SS BOND : angle 1.02841 ( 10) covalent geometry : bond 0.00344 (10348) covalent geometry : angle 0.61838 (14029) *********************** 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 183 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7563 (ttp-170) REVERT: B 254 ASP cc_start: 0.8089 (t70) cc_final: 0.7730 (t0) REVERT: C 25 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7280 (tm-30) REVERT: S 140 MET cc_start: 0.7529 (mtp) cc_final: 0.6665 (mmm) REVERT: S 186 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: L 15 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: L 124 ASP cc_start: 0.8382 (t0) cc_final: 0.7691 (p0) outliers start: 43 outliers final: 39 residues processed: 178 average time/residue: 0.2382 time to fit residues: 58.2659 Evaluate side-chains 176 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 284 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 65 THR 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 294 CYS Chi-restraints excluded: chain B residue 318 LEU 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 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 15 GLU 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: 0.0980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113818 restraints weight = 13517.533| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.58 r_work: 0.3314 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10353 Z= 0.162 Angle : 0.639 10.532 14039 Z= 0.325 Chirality : 0.045 0.423 1601 Planarity : 0.004 0.065 1749 Dihedral : 5.691 39.780 1630 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 4.26 % Allowed : 25.72 % Favored : 70.02 % 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: 2.45 (0.26), residues: 391 sheet: -0.07 (0.31), residues: 303 loop : -1.47 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 62 HIS 0.005 0.001 HIS L 126 PHE 0.024 0.002 PHE S 68 TYR 0.040 0.002 TYR A 103 ARG 0.012 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 464) hydrogen bonds : angle 4.61790 ( 1338) SS BOND : bond 0.00494 ( 5) SS BOND : angle 1.10093 ( 10) covalent geometry : bond 0.00389 (10348) covalent geometry : angle 0.63807 (14029) ********************** 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 185 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8587 (mmtt) cc_final: 0.7856 (mtpt) REVERT: A 102 ASP cc_start: 0.8318 (t0) cc_final: 0.8049 (t0) REVERT: B 46 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7541 (ttp-170) REVERT: B 254 ASP cc_start: 0.8074 (t70) cc_final: 0.7728 (t0) REVERT: C 25 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7233 (tm-30) REVERT: S 186 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: L 15 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: L 124 ASP cc_start: 0.8385 (t0) cc_final: 0.7681 (p0) outliers start: 47 outliers final: 41 residues processed: 178 average time/residue: 0.2387 time to fit residues: 58.9142 Evaluate side-chains 181 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 284 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 65 THR 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 318 LEU 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 84 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 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN B 225 HIS S 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114323 restraints weight = 13657.544| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.74 r_work: 0.3347 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2666 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= 0.129 Angle : 0.618 10.020 14039 Z= 0.313 Chirality : 0.045 0.420 1601 Planarity : 0.004 0.054 1749 Dihedral : 5.578 39.875 1630 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 3.71 % Allowed : 26.27 % Favored : 70.02 % 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: 0.29 (0.25), residues: 1252 helix: 2.50 (0.26), residues: 392 sheet: -0.02 (0.31), residues: 304 loop : -1.44 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.006 0.001 HIS L 126 PHE 0.019 0.001 PHE S 68 TYR 0.038 0.001 TYR A 103 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 464) hydrogen bonds : angle 4.55698 ( 1338) SS BOND : bond 0.00454 ( 5) SS BOND : angle 1.00989 ( 10) covalent geometry : bond 0.00299 (10348) covalent geometry : angle 0.61751 (14029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5649.55 seconds wall clock time: 98 minutes 36.31 seconds (5916.31 seconds total)