Starting phenix.real_space_refine on Wed Sep 17 16:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1x_39739/09_2025/8z1x_39739.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 3 5.49 5 S 75 5.16 5 C 6183 2.51 5 N 1676 2.21 5 O 1703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9648 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2406 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2129 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 15, 'TRANS': 265} Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2502 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain: "D" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2564 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 301} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6805 SG CYS C 297 22.536 20.322 99.874 1.00120.01 S ATOM 6941 SG CYS C 315 23.663 25.714 103.145 1.00100.37 S ATOM 6749 SG CYS C 290 28.972 22.706 100.536 1.00109.91 S ATOM 6701 SG CYS C 284 24.148 25.100 96.492 1.00 90.21 S ATOM 9508 SG CYS D 323 64.051 57.696 109.686 1.00116.75 S ATOM 9318 SG CYS D 299 59.208 60.866 107.274 1.00124.80 S ATOM 9379 SG CYS D 306 65.063 63.862 107.343 1.00119.39 S ATOM 9272 SG CYS D 293 64.446 59.555 103.050 1.00107.89 S Time building chain proxies: 2.19, per 1000 atoms: 0.23 Number of scatterers: 9648 At special positions: 0 Unit cell: (93.6, 94.64, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 75 16.00 P 3 15.00 O 1703 8.00 N 1676 7.00 C 6183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 372.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C1000 " pdb="FE1 SF4 C1000 " - pdb=" SG CYS C 297 " pdb="FE4 SF4 C1000 " - pdb=" SG CYS C 284 " pdb="FE3 SF4 C1000 " - pdb=" SG CYS C 290 " pdb="FE2 SF4 C1000 " - pdb=" SG CYS C 315 " pdb=" SF4 D 402 " pdb="FE4 SF4 D 402 " - pdb=" SG CYS D 293 " pdb="FE3 SF4 D 402 " - pdb=" SG CYS D 306 " pdb="FE2 SF4 D 402 " - pdb=" SG CYS D 299 " pdb="FE1 SF4 D 402 " - pdb=" SG CYS D 323 " Number of angles added : 24 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 60.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 30 removed outlier: 4.423A pdb=" N ARG A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 63 through 75 removed outlier: 4.028A pdb=" N LEU A 67 " --> pdb=" O TRP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 124 Proline residue: A 94 - end of helix removed outlier: 3.959A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 144 through 157 Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 205 through 232 removed outlier: 4.757A pdb=" N ILE A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 234 through 243 removed outlier: 3.533A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 254 through 285 removed outlier: 3.973A pdb=" N ASN A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 5.403A pdb=" N LEU A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.722A pdb=" N VAL A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 29 through 53 removed outlier: 5.962A pdb=" N ASN B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 127 removed outlier: 3.521A pdb=" N ARG B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 160 through 189 Proline residue: B 174 - end of helix removed outlier: 3.625A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 3.615A pdb=" N THR B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 211 through 240 removed outlier: 5.091A pdb=" N ALA B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.588A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.669A pdb=" N LEU B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.921A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 272 - end of helix Processing helix chain 'C' and resid 45 through 54 removed outlier: 4.099A pdb=" N SER C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.627A pdb=" N ASN C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.732A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.542A pdb=" N SER C 145 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 147 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 185 through 204 Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.669A pdb=" N VAL C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 removed outlier: 3.824A pdb=" N PHE C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 242' Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'D' and resid 90 through 100 removed outlier: 4.304A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 Proline residue: D 125 - end of helix Processing helix chain 'D' and resid 133 through 149 removed outlier: 3.865A pdb=" N GLU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 removed outlier: 4.078A pdb=" N ASP D 156 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 193 through 212 removed outlier: 3.771A pdb=" N GLN D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.597A pdb=" N VAL D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.538A pdb=" N ARG D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.028A pdb=" N THR D 307 " --> pdb=" O GLY D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 Processing sheet with id=AA1, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.362A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 30 removed outlier: 6.362A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 67 " --> pdb=" O ASP C 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.525A pdb=" N VAL C 36 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR C 211 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 38 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 234 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 228 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 45 removed outlier: 6.499A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 41 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE D 16 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE D 43 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN D 14 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.595A pdb=" N GLN D 102 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ASP D 186 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL D 104 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL D 183 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE D 218 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D 185 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR D 50 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N MET D 233 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA D 52 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET D 235 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 54 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 242 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR D 236 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N CYS D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 4158 1.43 - 1.65: 5556 1.65 - 1.88: 119 1.88 - 2.10: 0 2.10 - 2.33: 24 Bond restraints: 9857 Sorted by residual: bond pdb=" CE1 HIS B 175 " pdb=" NE2 HIS B 175 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.80e+01 bond pdb=" CE1 HIS A 337 " pdb=" NE2 HIS A 337 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.70e+01 bond pdb=" CE1 HIS C 222 " pdb=" NE2 HIS C 222 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.63e+01 bond pdb=" ND1 HIS D 227 " pdb=" CE1 HIS D 227 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.50e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 9852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 10495 2.35 - 4.70: 2574 4.70 - 7.06: 258 7.06 - 9.41: 71 9.41 - 11.76: 11 Bond angle restraints: 13409 Sorted by residual: angle pdb=" CA ASN C 136 " pdb=" CB ASN C 136 " pdb=" CG ASN C 136 " ideal model delta sigma weight residual 112.60 120.03 -7.43 1.00e+00 1.00e+00 5.53e+01 angle pdb=" CA ASN C 71 " pdb=" CB ASN C 71 " pdb=" CG ASN C 71 " ideal model delta sigma weight residual 112.60 119.57 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA HIS C 222 " pdb=" CB HIS C 222 " pdb=" CG HIS C 222 " ideal model delta sigma weight residual 113.80 120.75 -6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" CA ASP D 17 " pdb=" CB ASP D 17 " pdb=" CG ASP D 17 " ideal model delta sigma weight residual 112.60 119.53 -6.93 1.00e+00 1.00e+00 4.80e+01 angle pdb=" CA HIS B 175 " pdb=" CB HIS B 175 " pdb=" CG HIS B 175 " ideal model delta sigma weight residual 113.80 120.59 -6.79 1.00e+00 1.00e+00 4.61e+01 ... (remaining 13404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5561 17.81 - 35.61: 298 35.61 - 53.42: 50 53.42 - 71.23: 30 71.23 - 89.03: 11 Dihedral angle restraints: 5950 sinusoidal: 2401 harmonic: 3549 Sorted by residual: dihedral pdb=" CA GLN D 187 " pdb=" C GLN D 187 " pdb=" N PRO D 188 " pdb=" CA PRO D 188 " ideal model delta harmonic sigma weight residual 180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA TYR D 215 " pdb=" C TYR D 215 " pdb=" N VAL D 216 " pdb=" CA VAL D 216 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA THR D 63 " pdb=" C THR D 63 " pdb=" N LEU D 64 " pdb=" CA LEU D 64 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.191: 1546 4.191 - 8.383: 0 8.383 - 12.574: 0 12.574 - 16.766: 0 16.766 - 20.957: 8 Chirality restraints: 1554 Sorted by residual: chirality pdb="FE3 SF4 C1000 " pdb=" S1 SF4 C1000 " pdb=" S2 SF4 C1000 " pdb=" S4 SF4 C1000 " both_signs ideal model delta sigma weight residual False -10.55 10.40 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 D 402 " pdb=" S2 SF4 D 402 " pdb=" S3 SF4 D 402 " pdb=" S4 SF4 D 402 " both_signs ideal model delta sigma weight residual False -10.55 10.38 -20.93 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 C1000 " pdb=" S2 SF4 C1000 " pdb=" S3 SF4 C1000 " pdb=" S4 SF4 C1000 " both_signs ideal model delta sigma weight residual False -10.55 10.26 -20.81 2.00e-01 2.50e+01 1.08e+04 ... (remaining 1551 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " 0.139 2.00e-02 2.50e+03 6.77e-02 1.15e+02 pdb=" CG TRP A 293 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " -0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " -0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 192 " -0.114 2.00e-02 2.50e+03 5.89e-02 8.68e+01 pdb=" CG TRP A 192 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 192 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 192 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 192 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 192 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 192 " 0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 192 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 192 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 192 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 96 " -0.107 2.00e-02 2.50e+03 5.60e-02 6.27e+01 pdb=" CG TYR B 96 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 96 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 96 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR B 96 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 96 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 96 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 96 " -0.068 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 4 2.52 - 3.11: 6682 3.11 - 3.71: 14366 3.71 - 4.30: 20241 4.30 - 4.90: 34541 Nonbonded interactions: 75834 Sorted by model distance: nonbonded pdb=" OH TYR D 22 " pdb=" OE1 GLU D 72 " model vdw 1.925 3.040 nonbonded pdb=" N GLN C 262 " pdb=" OE1 GLN C 262 " model vdw 2.360 3.120 nonbonded pdb=" N SER D 62 " pdb=" O2B ANP D 401 " model vdw 2.470 3.120 nonbonded pdb=" OD2 ASP C 142 " pdb=" OG SER C 145 " model vdw 2.509 3.040 nonbonded pdb=" OH TYR D 316 " pdb=" OD1 ASP D 327 " model vdw 2.553 3.040 ... (remaining 75829 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 : 0.020 0.305 9865 Z= 1.081 Angle : 2.047 16.452 13433 Z= 1.349 Chirality : 1.497 20.957 1554 Planarity : 0.013 0.127 1707 Dihedral : 13.048 89.034 3668 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 3.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.22), residues: 1230 helix: -0.81 (0.17), residues: 688 sheet: 0.13 (0.54), residues: 88 loop : -0.32 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 62 TYR 0.107 0.015 TYR B 96 PHE 0.048 0.010 PHE D 162 TRP 0.139 0.022 TRP A 293 HIS 0.010 0.002 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.01915 ( 9857) covalent geometry : angle 2.01762 (13409) hydrogen bonds : bond 0.17066 ( 532) hydrogen bonds : angle 7.45060 ( 1527) metal coordination : bond 0.15712 ( 8) metal coordination : angle 8.40743 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 14 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7752 (Cg_endo) REVERT: A 30 ILE cc_start: 0.6273 (mt) cc_final: 0.5840 (mp) REVERT: A 74 MET cc_start: 0.7256 (mmt) cc_final: 0.6911 (mmt) REVERT: A 145 ILE cc_start: 0.8007 (mm) cc_final: 0.7687 (tt) REVERT: A 150 MET cc_start: 0.7582 (mtt) cc_final: 0.7275 (mtm) REVERT: A 174 PHE cc_start: 0.8055 (t80) cc_final: 0.7508 (t80) REVERT: A 238 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7160 (ttp80) REVERT: A 247 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6605 (ttt180) REVERT: A 248 MET cc_start: 0.7084 (mmp) cc_final: 0.6644 (mmt) REVERT: A 249 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6926 (mtp-110) REVERT: B 27 LYS cc_start: 0.8036 (tttm) cc_final: 0.7573 (tttm) REVERT: B 68 PRO cc_start: 0.8463 (Cg_exo) cc_final: 0.8234 (Cg_endo) REVERT: B 141 MET cc_start: 0.7673 (ttm) cc_final: 0.7465 (ttm) REVERT: B 170 PHE cc_start: 0.7115 (t80) cc_final: 0.6852 (t80) REVERT: B 210 ASN cc_start: 0.7991 (m-40) cc_final: 0.7658 (m-40) REVERT: C 10 SER cc_start: 0.7948 (m) cc_final: 0.7392 (p) REVERT: C 24 ASP cc_start: 0.7998 (t0) cc_final: 0.7593 (t0) REVERT: C 26 ILE cc_start: 0.7280 (pt) cc_final: 0.6953 (pt) REVERT: C 46 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7550 (mtpt) REVERT: C 62 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6774 (ptp90) REVERT: C 67 LYS cc_start: 0.7235 (ttmm) cc_final: 0.6960 (ttmm) REVERT: C 77 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6757 (mmm160) REVERT: C 101 SER cc_start: 0.7920 (m) cc_final: 0.7673 (t) REVERT: C 114 GLU cc_start: 0.6986 (tt0) cc_final: 0.6643 (tt0) REVERT: C 134 LEU cc_start: 0.7320 (tp) cc_final: 0.7114 (tp) REVERT: C 163 MET cc_start: 0.7873 (mmm) cc_final: 0.7650 (mmm) REVERT: C 171 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7272 (mtm180) REVERT: C 219 GLU cc_start: 0.7295 (tp30) cc_final: 0.6929 (tp30) REVERT: C 234 GLU cc_start: 0.7950 (tt0) cc_final: 0.7615 (tt0) REVERT: C 257 LEU cc_start: 0.7451 (mt) cc_final: 0.7242 (mp) REVERT: D 12 LEU cc_start: 0.8340 (tp) cc_final: 0.8116 (tt) REVERT: D 39 ASP cc_start: 0.7233 (t70) cc_final: 0.6736 (t0) REVERT: D 42 SER cc_start: 0.8170 (p) cc_final: 0.7859 (m) REVERT: D 62 SER cc_start: 0.7459 (m) cc_final: 0.7048 (p) REVERT: D 97 ARG cc_start: 0.7606 (ptt90) cc_final: 0.7019 (ptp-170) REVERT: D 117 LYS cc_start: 0.7524 (mttt) cc_final: 0.7067 (mttm) REVERT: D 144 MET cc_start: 0.7355 (tpp) cc_final: 0.7141 (tpp) REVERT: D 157 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7607 (mtt-85) REVERT: D 181 ASP cc_start: 0.7919 (m-30) cc_final: 0.7676 (m-30) REVERT: D 195 SER cc_start: 0.8270 (t) cc_final: 0.7984 (m) REVERT: D 209 GLN cc_start: 0.7721 (tp40) cc_final: 0.7472 (tp40) REVERT: D 239 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7508 (mtp85) REVERT: D 243 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7504 (ttpp) REVERT: D 300 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7320 (mtm180) REVERT: D 312 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6470 (mm-40) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1355 time to fit residues: 60.2441 Evaluate side-chains 318 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 299 GLN C 71 ASN C 96 GLN C 136 ASN C 137 GLN D 21 HIS D 102 GLN D 251 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114700 restraints weight = 12705.735| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.40 r_work: 0.3338 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 9865 Z= 0.425 Angle : 2.656 50.931 13433 Z= 1.523 Chirality : 0.446 6.267 1554 Planarity : 0.005 0.035 1707 Dihedral : 7.823 75.928 1377 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.13 % Allowed : 8.15 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.24), residues: 1230 helix: 1.11 (0.20), residues: 671 sheet: 0.18 (0.54), residues: 93 loop : 0.02 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 222 TYR 0.011 0.001 TYR A 236 PHE 0.015 0.001 PHE D 303 TRP 0.035 0.002 TRP A 293 HIS 0.003 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.01238 ( 9857) covalent geometry : angle 2.31451 (13409) hydrogen bonds : bond 0.04536 ( 532) hydrogen bonds : angle 5.15219 ( 1527) metal coordination : bond 0.03984 ( 8) metal coordination : angle 30.89458 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 0.368 Fit side-chains REVERT: A 29 MET cc_start: 0.7717 (mtm) cc_final: 0.6803 (ptt) REVERT: A 30 ILE cc_start: 0.8281 (mt) cc_final: 0.7725 (mp) REVERT: A 70 ILE cc_start: 0.7762 (pt) cc_final: 0.7547 (mm) REVERT: A 143 MET cc_start: 0.7824 (ttm) cc_final: 0.7381 (ttm) REVERT: A 156 VAL cc_start: 0.8128 (m) cc_final: 0.7745 (p) REVERT: A 238 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8310 (ttp-170) REVERT: A 296 ASP cc_start: 0.7698 (t70) cc_final: 0.7441 (t0) REVERT: B 27 LYS cc_start: 0.8609 (tttm) cc_final: 0.8343 (tttm) REVERT: B 65 LEU cc_start: 0.7932 (tt) cc_final: 0.7633 (tp) REVERT: C 10 SER cc_start: 0.8609 (m) cc_final: 0.8233 (p) REVERT: C 163 MET cc_start: 0.8470 (mmm) cc_final: 0.8089 (mmm) REVERT: C 234 GLU cc_start: 0.7498 (tt0) cc_final: 0.7292 (tt0) REVERT: C 257 LEU cc_start: 0.8389 (mt) cc_final: 0.8161 (mp) REVERT: C 262 GLN cc_start: 0.7768 (mp10) cc_final: 0.7198 (mp10) REVERT: C 306 MET cc_start: 0.7715 (tpp) cc_final: 0.7479 (tpp) REVERT: D 47 ARG cc_start: 0.6923 (ttt-90) cc_final: 0.6677 (ttt-90) REVERT: D 62 SER cc_start: 0.8505 (m) cc_final: 0.8141 (t) REVERT: D 106 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7510 (tm-30) REVERT: D 209 GLN cc_start: 0.8197 (tp40) cc_final: 0.7977 (tp40) outliers start: 22 outliers final: 15 residues processed: 333 average time/residue: 0.1368 time to fit residues: 58.2902 Evaluate side-chains 317 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 302 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 237 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 62 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN C 137 GLN C 179 GLN C 287 ASN D 136 GLN D 208 GLN D 308 GLN D 312 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115277 restraints weight = 12643.366| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.38 r_work: 0.3352 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9865 Z= 0.410 Angle : 2.629 50.547 13433 Z= 1.509 Chirality : 0.453 6.331 1554 Planarity : 0.004 0.042 1707 Dihedral : 6.361 71.711 1377 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.23 % Allowed : 11.83 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.25), residues: 1230 helix: 1.51 (0.20), residues: 681 sheet: -0.11 (0.54), residues: 96 loop : 0.10 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 95 TYR 0.011 0.001 TYR C 292 PHE 0.012 0.001 PHE B 170 TRP 0.028 0.001 TRP A 293 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01205 ( 9857) covalent geometry : angle 2.28758 (13409) hydrogen bonds : bond 0.03861 ( 532) hydrogen bonds : angle 4.70136 ( 1527) metal coordination : bond 0.02993 ( 8) metal coordination : angle 30.73894 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.7644 (mtm) cc_final: 0.6863 (ptt) REVERT: A 30 ILE cc_start: 0.8288 (mt) cc_final: 0.7786 (mp) REVERT: A 70 ILE cc_start: 0.7725 (pt) cc_final: 0.7498 (mm) REVERT: A 141 TYR cc_start: 0.8124 (t80) cc_final: 0.7781 (t80) REVERT: A 143 MET cc_start: 0.7848 (ttm) cc_final: 0.7396 (ttm) REVERT: A 156 VAL cc_start: 0.8133 (m) cc_final: 0.7770 (p) REVERT: A 238 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8515 (ttp-170) REVERT: A 302 ASP cc_start: 0.8243 (t0) cc_final: 0.7856 (t70) REVERT: B 27 LYS cc_start: 0.8610 (tttm) cc_final: 0.8403 (tttm) REVERT: B 80 LEU cc_start: 0.8144 (mt) cc_final: 0.7943 (mp) REVERT: B 133 ILE cc_start: 0.8643 (mm) cc_final: 0.8424 (mt) REVERT: C 10 SER cc_start: 0.8587 (m) cc_final: 0.8226 (p) REVERT: C 26 ILE cc_start: 0.8245 (pt) cc_final: 0.7964 (pt) REVERT: C 62 ARG cc_start: 0.7808 (ptp90) cc_final: 0.7400 (mtm-85) REVERT: C 163 MET cc_start: 0.8290 (mmm) cc_final: 0.7848 (mmm) REVERT: C 234 GLU cc_start: 0.7526 (tt0) cc_final: 0.7313 (tt0) REVERT: C 259 GLU cc_start: 0.7778 (mp0) cc_final: 0.7335 (mp0) REVERT: C 306 MET cc_start: 0.7690 (tpp) cc_final: 0.7421 (tpp) REVERT: D 47 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6653 (ttt-90) REVERT: D 62 SER cc_start: 0.8402 (m) cc_final: 0.8061 (t) REVERT: D 66 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: D 106 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 209 GLN cc_start: 0.8158 (tp40) cc_final: 0.7948 (tp40) REVERT: D 268 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8359 (tt) outliers start: 23 outliers final: 15 residues processed: 313 average time/residue: 0.1319 time to fit residues: 53.6845 Evaluate side-chains 314 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 298 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN C 12 HIS D 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113759 restraints weight = 12697.239| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.39 r_work: 0.3329 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9865 Z= 0.422 Angle : 2.634 50.640 13433 Z= 1.511 Chirality : 0.453 6.327 1554 Planarity : 0.005 0.040 1707 Dihedral : 5.975 67.666 1377 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.23 % Allowed : 13.19 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.25), residues: 1230 helix: 1.53 (0.20), residues: 681 sheet: -0.26 (0.54), residues: 96 loop : 0.01 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 25 TYR 0.010 0.001 TYR B 192 PHE 0.014 0.001 PHE A 96 TRP 0.026 0.002 TRP A 293 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01231 ( 9857) covalent geometry : angle 2.29364 (13409) hydrogen bonds : bond 0.04049 ( 532) hydrogen bonds : angle 4.64042 ( 1527) metal coordination : bond 0.02814 ( 8) metal coordination : angle 30.73562 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.327 Fit side-chains REVERT: A 9 LEU cc_start: 0.8079 (mt) cc_final: 0.7766 (mt) REVERT: A 29 MET cc_start: 0.7668 (mtm) cc_final: 0.6885 (ptt) REVERT: A 30 ILE cc_start: 0.8337 (mt) cc_final: 0.7908 (mp) REVERT: A 70 ILE cc_start: 0.7794 (pt) cc_final: 0.7574 (mm) REVERT: A 141 TYR cc_start: 0.8139 (t80) cc_final: 0.7837 (t80) REVERT: A 143 MET cc_start: 0.7824 (ttm) cc_final: 0.7378 (ttm) REVERT: A 156 VAL cc_start: 0.8175 (m) cc_final: 0.7804 (p) REVERT: A 238 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.8489 (ttp-170) REVERT: A 302 ASP cc_start: 0.8294 (t0) cc_final: 0.7900 (t70) REVERT: B 62 ARG cc_start: 0.7439 (mmp80) cc_final: 0.7215 (mmt90) REVERT: C 10 SER cc_start: 0.8638 (m) cc_final: 0.8233 (p) REVERT: C 26 ILE cc_start: 0.8352 (pt) cc_final: 0.8038 (pt) REVERT: C 163 MET cc_start: 0.8172 (mmm) cc_final: 0.7922 (mmm) REVERT: C 234 GLU cc_start: 0.7611 (tt0) cc_final: 0.7348 (tt0) REVERT: C 259 GLU cc_start: 0.7826 (mp0) cc_final: 0.7401 (mp0) REVERT: C 274 VAL cc_start: 0.8457 (t) cc_final: 0.8196 (m) REVERT: C 306 MET cc_start: 0.7740 (tpp) cc_final: 0.7470 (tpp) REVERT: D 47 ARG cc_start: 0.7023 (ttt-90) cc_final: 0.6744 (ttt-90) REVERT: D 66 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7538 (mtm180) REVERT: D 106 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7513 (tm-30) REVERT: D 209 GLN cc_start: 0.8209 (tp40) cc_final: 0.7972 (tp40) REVERT: D 268 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8436 (tt) outliers start: 23 outliers final: 16 residues processed: 311 average time/residue: 0.1374 time to fit residues: 55.0862 Evaluate side-chains 318 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 301 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114676 restraints weight = 12622.882| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.37 r_work: 0.3347 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 9865 Z= 0.409 Angle : 2.628 50.530 13433 Z= 1.508 Chirality : 0.453 6.307 1554 Planarity : 0.004 0.042 1707 Dihedral : 5.681 62.425 1377 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.23 % Allowed : 13.87 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1230 helix: 1.74 (0.20), residues: 674 sheet: -0.32 (0.51), residues: 106 loop : 0.03 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 25 TYR 0.008 0.001 TYR A 236 PHE 0.014 0.001 PHE A 96 TRP 0.022 0.001 TRP A 293 HIS 0.002 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01204 ( 9857) covalent geometry : angle 2.28587 (13409) hydrogen bonds : bond 0.03613 ( 532) hydrogen bonds : angle 4.54615 ( 1527) metal coordination : bond 0.02136 ( 8) metal coordination : angle 30.74083 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.374 Fit side-chains REVERT: A 9 LEU cc_start: 0.8156 (mt) cc_final: 0.7818 (mt) REVERT: A 29 MET cc_start: 0.7618 (mtm) cc_final: 0.6899 (ptt) REVERT: A 30 ILE cc_start: 0.8400 (mt) cc_final: 0.8000 (mp) REVERT: A 70 ILE cc_start: 0.7761 (pt) cc_final: 0.7555 (mm) REVERT: A 141 TYR cc_start: 0.8126 (t80) cc_final: 0.7835 (t80) REVERT: A 143 MET cc_start: 0.7871 (ttm) cc_final: 0.7431 (ttm) REVERT: A 156 VAL cc_start: 0.8148 (m) cc_final: 0.7771 (p) REVERT: A 302 ASP cc_start: 0.8286 (t0) cc_final: 0.7921 (t70) REVERT: C 234 GLU cc_start: 0.7506 (tt0) cc_final: 0.7284 (tt0) REVERT: C 274 VAL cc_start: 0.8442 (t) cc_final: 0.8200 (m) REVERT: C 306 MET cc_start: 0.7732 (tpp) cc_final: 0.7478 (tpp) REVERT: D 33 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7839 (mtp-110) REVERT: D 97 ARG cc_start: 0.7839 (ptt-90) cc_final: 0.7509 (ptt-90) REVERT: D 106 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7583 (tm-30) REVERT: D 209 GLN cc_start: 0.8241 (tp40) cc_final: 0.7989 (tp40) outliers start: 23 outliers final: 14 residues processed: 308 average time/residue: 0.1330 time to fit residues: 52.8136 Evaluate side-chains 311 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 297 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112907 restraints weight = 12663.293| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.45 r_work: 0.3317 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 9865 Z= 0.425 Angle : 2.636 50.667 13433 Z= 1.511 Chirality : 0.453 6.328 1554 Planarity : 0.004 0.040 1707 Dihedral : 5.616 57.105 1377 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.33 % Allowed : 14.26 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1230 helix: 1.58 (0.20), residues: 686 sheet: -0.27 (0.51), residues: 106 loop : -0.08 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 336 TYR 0.011 0.001 TYR B 192 PHE 0.012 0.001 PHE B 26 TRP 0.023 0.001 TRP A 293 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.01236 ( 9857) covalent geometry : angle 2.29493 (13409) hydrogen bonds : bond 0.03960 ( 532) hydrogen bonds : angle 4.59161 ( 1527) metal coordination : bond 0.02534 ( 8) metal coordination : angle 30.76751 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 0.364 Fit side-chains REVERT: A 9 LEU cc_start: 0.8168 (mt) cc_final: 0.7824 (mt) REVERT: A 29 MET cc_start: 0.7626 (mtm) cc_final: 0.6859 (ptt) REVERT: A 70 ILE cc_start: 0.7846 (pt) cc_final: 0.7605 (mm) REVERT: A 85 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7610 (mmt-90) REVERT: A 141 TYR cc_start: 0.8151 (t80) cc_final: 0.7867 (t80) REVERT: A 143 MET cc_start: 0.7891 (ttm) cc_final: 0.7426 (ttm) REVERT: A 156 VAL cc_start: 0.8186 (m) cc_final: 0.7791 (p) REVERT: A 247 ARG cc_start: 0.7632 (ttt180) cc_final: 0.7406 (tmt170) REVERT: A 302 ASP cc_start: 0.8309 (t0) cc_final: 0.7948 (t70) REVERT: C 26 ILE cc_start: 0.8431 (pt) cc_final: 0.8099 (pt) REVERT: C 234 GLU cc_start: 0.7616 (tt0) cc_final: 0.7382 (tt0) REVERT: C 274 VAL cc_start: 0.8502 (t) cc_final: 0.8246 (m) REVERT: C 306 MET cc_start: 0.7830 (tpp) cc_final: 0.7562 (tpp) REVERT: D 33 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7801 (mtp-110) REVERT: D 47 ARG cc_start: 0.7070 (ttt-90) cc_final: 0.6807 (ttt-90) REVERT: D 97 ARG cc_start: 0.7899 (ptt-90) cc_final: 0.7698 (ptt-90) REVERT: D 106 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7542 (tm-30) outliers start: 24 outliers final: 18 residues processed: 315 average time/residue: 0.1324 time to fit residues: 53.5737 Evaluate side-chains 319 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 0.0040 chunk 116 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 104 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 337 HIS C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114677 restraints weight = 12624.750| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.44 r_work: 0.3345 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9865 Z= 0.406 Angle : 2.631 50.492 13433 Z= 1.508 Chirality : 0.453 6.305 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.402 53.202 1377 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.23 % Allowed : 15.13 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1230 helix: 1.77 (0.20), residues: 683 sheet: -0.20 (0.53), residues: 108 loop : -0.05 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 300 TYR 0.007 0.001 TYR A 236 PHE 0.008 0.001 PHE B 26 TRP 0.020 0.001 TRP A 293 HIS 0.002 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.01200 ( 9857) covalent geometry : angle 2.28909 (13409) hydrogen bonds : bond 0.03447 ( 532) hydrogen bonds : angle 4.48071 ( 1527) metal coordination : bond 0.01789 ( 8) metal coordination : angle 30.77207 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 302 time to evaluate : 0.288 Fit side-chains REVERT: A 9 LEU cc_start: 0.8143 (mt) cc_final: 0.7800 (mt) REVERT: A 70 ILE cc_start: 0.7804 (pt) cc_final: 0.7580 (mm) REVERT: A 141 TYR cc_start: 0.8125 (t80) cc_final: 0.7849 (t80) REVERT: A 143 MET cc_start: 0.7886 (ttm) cc_final: 0.7424 (ttm) REVERT: A 156 VAL cc_start: 0.8138 (m) cc_final: 0.7729 (p) REVERT: A 247 ARG cc_start: 0.7590 (ttt180) cc_final: 0.7385 (tmt170) REVERT: A 302 ASP cc_start: 0.8309 (t0) cc_final: 0.7937 (t70) REVERT: A 327 LEU cc_start: 0.8638 (tt) cc_final: 0.8337 (tp) REVERT: A 330 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8281 (t) REVERT: A 336 ARG cc_start: 0.6929 (ttm110) cc_final: 0.6703 (ttm110) REVERT: C 26 ILE cc_start: 0.8420 (pt) cc_final: 0.8104 (pt) REVERT: C 234 GLU cc_start: 0.7583 (tt0) cc_final: 0.7354 (tt0) REVERT: C 274 VAL cc_start: 0.8488 (t) cc_final: 0.8237 (m) REVERT: C 306 MET cc_start: 0.7807 (tpp) cc_final: 0.7561 (tpp) REVERT: D 47 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6809 (ttt-90) REVERT: D 106 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 177 MET cc_start: 0.8181 (tpp) cc_final: 0.7776 (mmm) outliers start: 23 outliers final: 17 residues processed: 310 average time/residue: 0.1312 time to fit residues: 52.1519 Evaluate side-chains 314 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112796 restraints weight = 12593.336| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.44 r_work: 0.3320 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 9865 Z= 0.429 Angle : 2.644 50.703 13433 Z= 1.514 Chirality : 0.452 6.323 1554 Planarity : 0.004 0.038 1707 Dihedral : 5.428 50.370 1377 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.23 % Allowed : 16.20 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.25), residues: 1230 helix: 1.57 (0.20), residues: 686 sheet: -0.21 (0.52), residues: 106 loop : -0.14 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 97 TYR 0.011 0.001 TYR B 192 PHE 0.012 0.001 PHE B 26 TRP 0.021 0.001 TRP A 293 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.01244 ( 9857) covalent geometry : angle 2.30275 (13409) hydrogen bonds : bond 0.04025 ( 532) hydrogen bonds : angle 4.57979 ( 1527) metal coordination : bond 0.02510 ( 8) metal coordination : angle 30.82881 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8195 (mt) cc_final: 0.7831 (mt) REVERT: A 29 MET cc_start: 0.7729 (mtm) cc_final: 0.7051 (ptt) REVERT: A 70 ILE cc_start: 0.7819 (pt) cc_final: 0.7614 (mm) REVERT: A 141 TYR cc_start: 0.8142 (t80) cc_final: 0.7885 (t80) REVERT: A 143 MET cc_start: 0.7852 (ttm) cc_final: 0.7385 (ttm) REVERT: A 156 VAL cc_start: 0.8214 (m) cc_final: 0.7823 (p) REVERT: A 302 ASP cc_start: 0.8306 (t0) cc_final: 0.7973 (t70) REVERT: B 136 ARG cc_start: 0.7723 (mmp80) cc_final: 0.7327 (mmp80) REVERT: C 26 ILE cc_start: 0.8433 (pt) cc_final: 0.8118 (pt) REVERT: C 234 GLU cc_start: 0.7604 (tt0) cc_final: 0.7367 (tt0) REVERT: C 274 VAL cc_start: 0.8509 (t) cc_final: 0.8265 (m) REVERT: C 306 MET cc_start: 0.7849 (tpp) cc_final: 0.7604 (tpp) REVERT: D 47 ARG cc_start: 0.7108 (ttt-90) cc_final: 0.6823 (ttt-90) REVERT: D 97 ARG cc_start: 0.7895 (ptt-90) cc_final: 0.7645 (ptp-170) REVERT: D 106 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7612 (tm-30) REVERT: D 115 ARG cc_start: 0.8260 (mmm160) cc_final: 0.8048 (mmm160) outliers start: 23 outliers final: 20 residues processed: 326 average time/residue: 0.1415 time to fit residues: 57.7949 Evaluate side-chains 336 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 307 GLN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112723 restraints weight = 12573.120| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.42 r_work: 0.3317 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 9865 Z= 0.427 Angle : 2.646 50.691 13433 Z= 1.514 Chirality : 0.452 6.322 1554 Planarity : 0.005 0.039 1707 Dihedral : 5.408 48.315 1377 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.04 % Allowed : 16.88 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.25), residues: 1230 helix: 1.50 (0.20), residues: 686 sheet: -0.31 (0.51), residues: 106 loop : -0.20 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 222 TYR 0.010 0.001 TYR B 192 PHE 0.012 0.001 PHE B 26 TRP 0.021 0.001 TRP A 293 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.01241 ( 9857) covalent geometry : angle 2.30508 (13409) hydrogen bonds : bond 0.03974 ( 532) hydrogen bonds : angle 4.57676 ( 1527) metal coordination : bond 0.02387 ( 8) metal coordination : angle 30.83679 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8250 (mt) cc_final: 0.7897 (mt) REVERT: A 29 MET cc_start: 0.7773 (mtm) cc_final: 0.7055 (ptt) REVERT: A 70 ILE cc_start: 0.7834 (pt) cc_final: 0.7630 (mm) REVERT: A 141 TYR cc_start: 0.8102 (t80) cc_final: 0.7858 (t80) REVERT: A 143 MET cc_start: 0.7870 (ttm) cc_final: 0.7385 (ttm) REVERT: A 156 VAL cc_start: 0.8193 (m) cc_final: 0.7819 (p) REVERT: A 302 ASP cc_start: 0.8296 (t0) cc_final: 0.7951 (t70) REVERT: B 65 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7718 (mp) REVERT: B 170 PHE cc_start: 0.7911 (t80) cc_final: 0.7628 (t80) REVERT: C 26 ILE cc_start: 0.8432 (pt) cc_final: 0.8113 (pt) REVERT: C 234 GLU cc_start: 0.7606 (tt0) cc_final: 0.7360 (tt0) REVERT: C 274 VAL cc_start: 0.8515 (t) cc_final: 0.8278 (m) REVERT: C 306 MET cc_start: 0.7827 (tpp) cc_final: 0.7556 (tpp) REVERT: D 106 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7620 (tm-30) REVERT: D 177 MET cc_start: 0.8285 (tpp) cc_final: 0.7833 (mmm) outliers start: 21 outliers final: 20 residues processed: 317 average time/residue: 0.1251 time to fit residues: 50.9479 Evaluate side-chains 329 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112914 restraints weight = 12677.524| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.42 r_work: 0.3322 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9865 Z= 0.418 Angle : 2.645 50.626 13433 Z= 1.513 Chirality : 0.453 6.316 1554 Planarity : 0.005 0.040 1707 Dihedral : 5.340 47.178 1377 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.84 % Allowed : 17.56 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1230 helix: 1.52 (0.20), residues: 686 sheet: -0.25 (0.52), residues: 106 loop : -0.22 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 222 TYR 0.009 0.001 TYR B 192 PHE 0.010 0.001 PHE B 26 TRP 0.020 0.001 TRP A 293 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.01223 ( 9857) covalent geometry : angle 2.30322 (13409) hydrogen bonds : bond 0.03850 ( 532) hydrogen bonds : angle 4.55839 ( 1527) metal coordination : bond 0.02232 ( 8) metal coordination : angle 30.83864 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8241 (mt) cc_final: 0.7884 (mt) REVERT: A 29 MET cc_start: 0.7759 (mtm) cc_final: 0.7062 (ptt) REVERT: A 70 ILE cc_start: 0.7830 (pt) cc_final: 0.7628 (mm) REVERT: A 141 TYR cc_start: 0.8075 (t80) cc_final: 0.7828 (t80) REVERT: A 143 MET cc_start: 0.7854 (ttm) cc_final: 0.7393 (ttm) REVERT: A 156 VAL cc_start: 0.8203 (m) cc_final: 0.7816 (p) REVERT: A 257 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8432 (tpt90) REVERT: A 302 ASP cc_start: 0.8290 (t0) cc_final: 0.7939 (t70) REVERT: B 170 PHE cc_start: 0.7922 (t80) cc_final: 0.7635 (t80) REVERT: C 26 ILE cc_start: 0.8422 (pt) cc_final: 0.8110 (pt) REVERT: C 234 GLU cc_start: 0.7602 (tt0) cc_final: 0.7347 (tt0) REVERT: C 274 VAL cc_start: 0.8525 (t) cc_final: 0.8284 (m) REVERT: C 306 MET cc_start: 0.7839 (tpp) cc_final: 0.7579 (tpp) REVERT: D 47 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6838 (ttt-90) REVERT: D 106 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 177 MET cc_start: 0.8293 (tpp) cc_final: 0.7787 (mmm) outliers start: 19 outliers final: 18 residues processed: 314 average time/residue: 0.1391 time to fit residues: 55.8381 Evaluate side-chains 323 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 305 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 11 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.0060 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114185 restraints weight = 12508.260| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.37 r_work: 0.3341 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 9865 Z= 0.411 Angle : 2.646 50.543 13433 Z= 1.514 Chirality : 0.453 6.312 1554 Planarity : 0.005 0.039 1707 Dihedral : 5.236 45.993 1377 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.84 % Allowed : 17.26 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1230 helix: 1.62 (0.20), residues: 683 sheet: -0.23 (0.52), residues: 106 loop : -0.24 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 97 TYR 0.007 0.001 TYR A 236 PHE 0.008 0.001 PHE B 26 TRP 0.019 0.001 TRP A 293 HIS 0.002 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.01209 ( 9857) covalent geometry : angle 2.30503 (13409) hydrogen bonds : bond 0.03621 ( 532) hydrogen bonds : angle 4.52865 ( 1527) metal coordination : bond 0.02000 ( 8) metal coordination : angle 30.80680 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.82 seconds wall clock time: 43 minutes 12.62 seconds (2592.62 seconds total)