Starting phenix.real_space_refine on Fri Feb 14 03:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1x_39739/02_2025/8z1x_39739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1x_39739/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1x_39739/02_2025/8z1x_39739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1x_39739/02_2025/8z1x_39739.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1x_39739/02_2025/8z1x_39739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1x_39739/02_2025/8z1x_39739_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.22, per 1000 atoms: 0.64 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.95 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: 2.73 Time building geometry restraints manager: 3.04 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: 1.490 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.540 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- 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 : 0.019 0.165 9857 Z= 1.261 Angle : 2.018 11.761 13409 Z= 1.350 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (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 TRP 0.139 0.022 TRP A 293 HIS 0.010 0.002 HIS C 12 PHE 0.048 0.010 PHE D 162 TYR 0.107 0.015 TYR B 96 ARG 0.008 0.001 ARG C 62 *********************** 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 : 1.019 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: 0.7464 (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: 0.6644 (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: 0.3045 time to fit residues: 134.8422 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 : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 299 GLN C 12 HIS 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113889 restraints weight = 12691.313| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.39 r_work: 0.3329 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.259 9857 Z= 0.841 Angle : 2.315 50.674 13409 Z= 1.519 Chirality : 0.450 6.298 1554 Planarity : 0.005 0.036 1707 Dihedral : 7.791 76.030 1377 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.13 % Allowed : 8.44 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1230 helix: 1.03 (0.19), residues: 671 sheet: -0.02 (0.54), residues: 95 loop : -0.04 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 293 HIS 0.004 0.001 HIS A 204 PHE 0.016 0.002 PHE D 303 TYR 0.011 0.002 TYR B 192 ARG 0.005 0.001 ARG A 222 *********************** 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 350 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 328 time to evaluate : 1.048 Fit side-chains REVERT: A 30 ILE cc_start: 0.8295 (mt) cc_final: 0.7852 (mp) REVERT: A 70 ILE cc_start: 0.7793 (pt) cc_final: 0.7585 (mm) REVERT: A 143 MET cc_start: 0.7891 (ttm) cc_final: 0.7449 (ttm) REVERT: A 156 VAL cc_start: 0.8152 (m) cc_final: 0.7769 (p) REVERT: A 238 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8329 (ttp-170) REVERT: A 247 ARG cc_start: 0.7296 (ttt180) cc_final: 0.7095 (ttt180) REVERT: A 296 ASP cc_start: 0.7728 (t70) cc_final: 0.7478 (t0) REVERT: A 302 ASP cc_start: 0.8272 (t0) cc_final: 0.7913 (t70) REVERT: B 27 LYS cc_start: 0.8612 (tttm) cc_final: 0.8327 (tttm) REVERT: B 65 LEU cc_start: 0.7963 (tt) cc_final: 0.7603 (tp) REVERT: C 10 SER cc_start: 0.8618 (m) cc_final: 0.8254 (p) REVERT: C 163 MET cc_start: 0.8453 (mmm) cc_final: 0.8060 (mmm) REVERT: C 210 ILE cc_start: 0.8294 (pt) cc_final: 0.7999 (mt) REVERT: C 234 GLU cc_start: 0.7546 (tt0) cc_final: 0.7325 (tt0) REVERT: C 257 LEU cc_start: 0.8371 (mt) cc_final: 0.8151 (mp) REVERT: C 262 GLN cc_start: 0.7816 (mp10) cc_final: 0.7186 (mp10) REVERT: C 265 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 306 MET cc_start: 0.7711 (tpp) cc_final: 0.7472 (tpp) REVERT: D 33 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7909 (mtp-110) REVERT: D 47 ARG cc_start: 0.6960 (ttt-90) cc_final: 0.6680 (ttt-90) REVERT: D 62 SER cc_start: 0.8499 (m) cc_final: 0.8201 (t) REVERT: D 106 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 209 GLN cc_start: 0.8194 (tp40) cc_final: 0.7958 (tp40) REVERT: D 233 MET cc_start: 0.8436 (mtp) cc_final: 0.8213 (mtm) outliers start: 22 outliers final: 15 residues processed: 335 average time/residue: 0.2985 time to fit residues: 127.2771 Evaluate side-chains 322 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 307 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 49 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 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 111 optimal weight: 0.0870 chunk 96 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114470 restraints weight = 12674.315| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.37 r_work: 0.3341 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9857 Z= 0.793 Angle : 2.291 50.548 13409 Z= 1.508 Chirality : 0.454 6.348 1554 Planarity : 0.004 0.042 1707 Dihedral : 6.506 71.867 1377 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.23 % Allowed : 12.51 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1230 helix: 1.40 (0.20), residues: 681 sheet: -0.22 (0.53), residues: 96 loop : 0.05 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 293 HIS 0.003 0.000 HIS A 337 PHE 0.011 0.001 PHE B 26 TYR 0.009 0.001 TYR D 215 ARG 0.004 0.000 ARG C 25 *********************** 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 328 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 1.048 Fit side-chains REVERT: A 29 MET cc_start: 0.7703 (mtm) cc_final: 0.6879 (ptt) REVERT: A 30 ILE cc_start: 0.8296 (mt) cc_final: 0.7764 (mp) REVERT: A 70 ILE cc_start: 0.7757 (pt) cc_final: 0.7529 (mm) REVERT: A 85 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7537 (mmt-90) REVERT: A 141 TYR cc_start: 0.8151 (t80) cc_final: 0.7829 (t80) REVERT: A 143 MET cc_start: 0.7868 (ttm) cc_final: 0.7406 (ttm) REVERT: A 156 VAL cc_start: 0.8162 (m) cc_final: 0.7794 (p) REVERT: A 238 ARG cc_start: 0.8725 (ttp-170) cc_final: 0.8494 (ttp-170) REVERT: A 247 ARG cc_start: 0.7307 (ttt180) cc_final: 0.7096 (ttt180) REVERT: A 302 ASP cc_start: 0.8263 (t0) cc_final: 0.7881 (t70) REVERT: B 27 LYS cc_start: 0.8609 (tttm) cc_final: 0.8396 (tttm) REVERT: B 62 ARG cc_start: 0.7531 (mmp80) cc_final: 0.7187 (mmp80) REVERT: C 10 SER cc_start: 0.8608 (m) cc_final: 0.8254 (p) REVERT: C 26 ILE cc_start: 0.8255 (pt) cc_final: 0.7979 (pt) REVERT: C 163 MET cc_start: 0.8345 (mmm) cc_final: 0.7978 (mmm) REVERT: C 234 GLU cc_start: 0.7552 (tt0) cc_final: 0.7332 (tt0) REVERT: C 259 GLU cc_start: 0.7790 (mp0) cc_final: 0.7321 (mp0) REVERT: C 262 GLN cc_start: 0.7638 (mp10) cc_final: 0.7050 (mp10) REVERT: C 265 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 274 VAL cc_start: 0.8405 (t) cc_final: 0.8142 (m) REVERT: C 306 MET cc_start: 0.7677 (tpp) cc_final: 0.7432 (tpp) REVERT: D 47 ARG cc_start: 0.6961 (ttt-90) cc_final: 0.6618 (ttt-90) REVERT: D 62 SER cc_start: 0.8459 (m) cc_final: 0.8085 (t) REVERT: D 106 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 209 GLN cc_start: 0.8187 (tp40) cc_final: 0.7976 (tp40) REVERT: D 268 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8353 (tt) outliers start: 23 outliers final: 14 residues processed: 313 average time/residue: 0.2919 time to fit residues: 118.3703 Evaluate side-chains 315 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 300 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 34 GLU 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 D residue 214 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 113 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 111 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN D 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114419 restraints weight = 12525.501| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.36 r_work: 0.3339 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 9857 Z= 0.797 Angle : 2.285 50.578 13409 Z= 1.505 Chirality : 0.453 6.319 1554 Planarity : 0.004 0.041 1707 Dihedral : 5.893 66.802 1377 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.62 % Allowed : 13.19 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1230 helix: 1.59 (0.20), residues: 679 sheet: -0.34 (0.53), residues: 96 loop : 0.06 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 293 HIS 0.003 0.001 HIS A 337 PHE 0.013 0.001 PHE A 96 TYR 0.008 0.001 TYR A 236 ARG 0.009 0.000 ARG A 300 *********************** 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 331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.027 Fit side-chains REVERT: A 29 MET cc_start: 0.7692 (mtm) cc_final: 0.6881 (ptt) REVERT: A 30 ILE cc_start: 0.8315 (mt) cc_final: 0.7913 (mp) REVERT: A 70 ILE cc_start: 0.7767 (pt) cc_final: 0.7560 (mm) REVERT: A 141 TYR cc_start: 0.8144 (t80) cc_final: 0.7852 (t80) REVERT: A 143 MET cc_start: 0.7805 (ttm) cc_final: 0.7358 (ttm) REVERT: A 156 VAL cc_start: 0.8154 (m) cc_final: 0.7803 (p) REVERT: A 238 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8495 (ttp-170) REVERT: A 247 ARG cc_start: 0.7322 (ttt180) cc_final: 0.7121 (ttt180) REVERT: A 302 ASP cc_start: 0.8275 (t0) cc_final: 0.7889 (t70) REVERT: A 327 LEU cc_start: 0.8700 (tp) cc_final: 0.8495 (tt) REVERT: B 45 ILE cc_start: 0.8566 (tt) cc_final: 0.8262 (tt) REVERT: B 133 ILE cc_start: 0.8612 (mm) cc_final: 0.8408 (mt) REVERT: C 26 ILE cc_start: 0.8322 (pt) cc_final: 0.8024 (pt) REVERT: C 163 MET cc_start: 0.8145 (mmm) cc_final: 0.7904 (mmm) REVERT: C 234 GLU cc_start: 0.7577 (tt0) cc_final: 0.7358 (tt0) REVERT: C 259 GLU cc_start: 0.7818 (mp0) cc_final: 0.7403 (mp0) REVERT: C 262 GLN cc_start: 0.7587 (mp10) cc_final: 0.7164 (mp10) REVERT: C 265 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 274 VAL cc_start: 0.8441 (t) cc_final: 0.8176 (m) REVERT: C 306 MET cc_start: 0.7743 (tpp) cc_final: 0.7486 (tpp) REVERT: D 47 ARG cc_start: 0.7036 (ttt-90) cc_final: 0.6776 (ttt-90) REVERT: D 106 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7435 (tm-30) REVERT: D 209 GLN cc_start: 0.8204 (tp40) cc_final: 0.7952 (tp40) REVERT: D 268 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8430 (tt) outliers start: 27 outliers final: 16 residues processed: 313 average time/residue: 0.2952 time to fit residues: 119.1146 Evaluate side-chains 316 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 299 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 B residue 185 LEU 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 117 LYS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 216 LEU 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 2 optimal weight: 0.9990 chunk 84 optimal weight: 0.0060 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.0870 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114820 restraints weight = 12620.047| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.41 r_work: 0.3346 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9857 Z= 0.791 Angle : 2.283 50.524 13409 Z= 1.504 Chirality : 0.453 6.315 1554 Planarity : 0.004 0.040 1707 Dihedral : 5.595 61.067 1377 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.42 % Allowed : 13.97 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1230 helix: 1.61 (0.20), residues: 690 sheet: -0.37 (0.50), residues: 106 loop : 0.02 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 293 HIS 0.002 0.000 HIS A 337 PHE 0.017 0.001 PHE A 96 TYR 0.007 0.001 TYR A 236 ARG 0.010 0.000 ARG A 300 *********************** 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 326 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 1.009 Fit side-chains REVERT: A 29 MET cc_start: 0.7651 (mtm) cc_final: 0.6907 (ptt) REVERT: A 30 ILE cc_start: 0.8347 (mt) cc_final: 0.7950 (mp) REVERT: A 70 ILE cc_start: 0.7753 (pt) cc_final: 0.7550 (mm) REVERT: A 141 TYR cc_start: 0.8142 (t80) cc_final: 0.7849 (t80) REVERT: A 143 MET cc_start: 0.7817 (ttm) cc_final: 0.7367 (ttm) REVERT: A 156 VAL cc_start: 0.8156 (m) cc_final: 0.7771 (p) REVERT: A 302 ASP cc_start: 0.8291 (t0) cc_final: 0.7893 (t70) REVERT: A 327 LEU cc_start: 0.8702 (tp) cc_final: 0.8497 (tt) REVERT: B 45 ILE cc_start: 0.8562 (tt) cc_final: 0.8227 (tt) REVERT: C 26 ILE cc_start: 0.8357 (pt) cc_final: 0.8057 (pt) REVERT: C 262 GLN cc_start: 0.7565 (mp10) cc_final: 0.7146 (mp10) REVERT: C 265 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 274 VAL cc_start: 0.8436 (t) cc_final: 0.8186 (m) REVERT: C 306 MET cc_start: 0.7643 (tpp) cc_final: 0.7400 (tpp) REVERT: D 33 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7896 (mtm110) REVERT: D 106 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7500 (tm-30) outliers start: 25 outliers final: 17 residues processed: 309 average time/residue: 0.2968 time to fit residues: 118.0002 Evaluate side-chains 319 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 302 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 145 ILE 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 185 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 C residue 202 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.124165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113270 restraints weight = 12655.193| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.45 r_work: 0.3324 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9857 Z= 0.807 Angle : 2.291 50.635 13409 Z= 1.507 Chirality : 0.453 6.326 1554 Planarity : 0.004 0.045 1707 Dihedral : 5.520 55.596 1377 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.62 % Allowed : 14.45 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1230 helix: 1.63 (0.20), residues: 687 sheet: -0.41 (0.50), residues: 106 loop : -0.03 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 293 HIS 0.003 0.001 HIS D 160 PHE 0.019 0.001 PHE A 96 TYR 0.010 0.001 TYR B 192 ARG 0.011 0.001 ARG D 97 *********************** 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 327 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 1.162 Fit side-chains REVERT: A 9 LEU cc_start: 0.8095 (mt) cc_final: 0.7846 (mt) REVERT: A 29 MET cc_start: 0.7638 (mtm) cc_final: 0.6862 (ptt) REVERT: A 70 ILE cc_start: 0.7840 (pt) cc_final: 0.7592 (mm) REVERT: A 141 TYR cc_start: 0.8155 (t80) cc_final: 0.7886 (t80) REVERT: A 143 MET cc_start: 0.7833 (ttm) cc_final: 0.7360 (ttm) REVERT: A 156 VAL cc_start: 0.8193 (m) cc_final: 0.7786 (p) REVERT: A 247 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7255 (ttt180) REVERT: A 302 ASP cc_start: 0.8322 (t0) cc_final: 0.7942 (t70) REVERT: B 44 PHE cc_start: 0.7982 (t80) cc_final: 0.7778 (t80) REVERT: B 45 ILE cc_start: 0.8538 (tt) cc_final: 0.8223 (tt) REVERT: C 26 ILE cc_start: 0.8402 (pt) cc_final: 0.8086 (pt) REVERT: C 133 ASP cc_start: 0.7629 (m-30) cc_final: 0.7419 (m-30) REVERT: C 234 GLU cc_start: 0.7618 (tt0) cc_final: 0.7362 (tt0) REVERT: C 262 GLN cc_start: 0.7620 (mp10) cc_final: 0.7191 (mp10) REVERT: C 265 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 274 VAL cc_start: 0.8490 (t) cc_final: 0.8240 (m) REVERT: C 306 MET cc_start: 0.7799 (tpp) cc_final: 0.7556 (tpp) REVERT: D 33 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7921 (mtm110) REVERT: D 47 ARG cc_start: 0.7071 (ttt-90) cc_final: 0.6793 (ttt-90) REVERT: D 106 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 233 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (ttm) outliers start: 27 outliers final: 21 residues processed: 309 average time/residue: 0.2768 time to fit residues: 111.2573 Evaluate side-chains 326 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 145 ILE 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 185 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 117 LYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU 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 Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113665 restraints weight = 12742.765| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.45 r_work: 0.3331 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 9857 Z= 0.798 Angle : 2.290 50.567 13409 Z= 1.506 Chirality : 0.453 6.310 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.396 51.930 1377 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.33 % Allowed : 14.94 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1230 helix: 1.72 (0.20), residues: 683 sheet: -0.35 (0.51), residues: 106 loop : -0.10 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.002 0.001 HIS A 337 PHE 0.025 0.001 PHE A 96 TYR 0.008 0.001 TYR B 192 ARG 0.009 0.001 ARG D 97 *********************** 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 319 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 295 time to evaluate : 1.106 Fit side-chains REVERT: A 9 LEU cc_start: 0.8104 (mt) cc_final: 0.7847 (mt) REVERT: A 29 MET cc_start: 0.7650 (mtm) cc_final: 0.6872 (ptt) REVERT: A 70 ILE cc_start: 0.7824 (pt) cc_final: 0.7595 (mm) REVERT: A 141 TYR cc_start: 0.8166 (t80) cc_final: 0.7893 (t80) REVERT: A 143 MET cc_start: 0.7873 (ttm) cc_final: 0.7403 (ttm) REVERT: A 156 VAL cc_start: 0.8169 (m) cc_final: 0.7777 (p) REVERT: A 247 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7284 (ttt180) REVERT: A 302 ASP cc_start: 0.8331 (t0) cc_final: 0.7948 (t70) REVERT: B 44 PHE cc_start: 0.7962 (t80) cc_final: 0.7759 (t80) REVERT: B 45 ILE cc_start: 0.8545 (tt) cc_final: 0.8216 (tt) REVERT: B 170 PHE cc_start: 0.7904 (t80) cc_final: 0.7614 (t80) REVERT: C 26 ILE cc_start: 0.8404 (pt) cc_final: 0.8091 (pt) REVERT: C 234 GLU cc_start: 0.7610 (tt0) cc_final: 0.7354 (tt0) REVERT: C 262 GLN cc_start: 0.7612 (mp10) cc_final: 0.7256 (mp10) REVERT: C 265 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 274 VAL cc_start: 0.8502 (t) cc_final: 0.8256 (m) REVERT: C 306 MET cc_start: 0.7802 (tpp) cc_final: 0.7567 (tpp) REVERT: D 33 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7918 (mtm110) REVERT: D 47 ARG cc_start: 0.7072 (ttt-90) cc_final: 0.6779 (ttt-90) REVERT: D 106 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 115 ARG cc_start: 0.8244 (mmm160) cc_final: 0.8031 (mmm160) REVERT: D 177 MET cc_start: 0.8255 (tpp) cc_final: 0.7772 (mmm) REVERT: D 233 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8065 (ttm) outliers start: 24 outliers final: 20 residues processed: 304 average time/residue: 0.2829 time to fit residues: 111.4277 Evaluate side-chains 314 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 145 ILE 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 185 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 117 LYS 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 Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.0870 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 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 = 0.3576 r_free = 0.3576 target = 0.123904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113016 restraints weight = 12788.993| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.45 r_work: 0.3321 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9857 Z= 0.809 Angle : 2.296 50.643 13409 Z= 1.508 Chirality : 0.452 6.323 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.352 49.730 1377 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.23 % Allowed : 15.91 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1230 helix: 1.63 (0.20), residues: 688 sheet: -0.36 (0.51), residues: 106 loop : -0.12 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.003 0.001 HIS D 160 PHE 0.024 0.001 PHE A 96 TYR 0.010 0.001 TYR B 192 ARG 0.011 0.000 ARG D 97 *********************** 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 330 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 307 time to evaluate : 0.845 Fit side-chains REVERT: A 9 LEU cc_start: 0.8188 (mt) cc_final: 0.7923 (mt) REVERT: A 29 MET cc_start: 0.7660 (mtm) cc_final: 0.6937 (ptt) REVERT: A 70 ILE cc_start: 0.7835 (pt) cc_final: 0.7621 (mm) REVERT: A 141 TYR cc_start: 0.8138 (t80) cc_final: 0.7878 (t80) REVERT: A 143 MET cc_start: 0.7855 (ttm) cc_final: 0.7371 (ttm) REVERT: A 156 VAL cc_start: 0.8198 (m) cc_final: 0.7807 (p) REVERT: A 302 ASP cc_start: 0.8331 (t0) cc_final: 0.7963 (t70) REVERT: B 44 PHE cc_start: 0.7949 (t80) cc_final: 0.7724 (t80) REVERT: B 65 LEU cc_start: 0.8120 (tp) cc_final: 0.7912 (mp) REVERT: B 136 ARG cc_start: 0.7739 (mmp80) cc_final: 0.7330 (mmp80) REVERT: C 26 ILE cc_start: 0.8423 (pt) cc_final: 0.8107 (pt) REVERT: C 133 ASP cc_start: 0.7643 (m-30) cc_final: 0.7399 (m-30) REVERT: C 234 GLU cc_start: 0.7614 (tt0) cc_final: 0.7366 (tt0) REVERT: C 262 GLN cc_start: 0.7635 (mp10) cc_final: 0.7103 (tm-30) REVERT: C 265 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 274 VAL cc_start: 0.8503 (t) cc_final: 0.8270 (m) REVERT: C 306 MET cc_start: 0.7806 (tpp) cc_final: 0.7566 (tpp) REVERT: D 33 ARG cc_start: 0.8192 (ptm160) cc_final: 0.7911 (mtm110) REVERT: D 106 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7629 (tm-30) REVERT: D 233 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8020 (ttm) outliers start: 23 outliers final: 19 residues processed: 316 average time/residue: 0.3167 time to fit residues: 127.5740 Evaluate side-chains 334 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 145 ILE 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 185 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 C residue 216 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113525 restraints weight = 12619.368| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.41 r_work: 0.3334 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 9857 Z= 0.801 Angle : 2.300 50.597 13409 Z= 1.509 Chirality : 0.453 6.315 1554 Planarity : 0.005 0.056 1707 Dihedral : 5.321 48.626 1377 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.13 % Allowed : 16.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1230 helix: 1.67 (0.20), residues: 683 sheet: -0.33 (0.51), residues: 106 loop : -0.19 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.002 0.001 HIS D 160 PHE 0.016 0.001 PHE A 96 TYR 0.009 0.001 TYR B 192 ARG 0.021 0.001 ARG D 97 *********************** 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 334 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 312 time to evaluate : 1.109 Fit side-chains REVERT: A 9 LEU cc_start: 0.8203 (mt) cc_final: 0.7892 (mt) REVERT: A 29 MET cc_start: 0.7639 (mtm) cc_final: 0.6728 (ptt) REVERT: A 141 TYR cc_start: 0.8115 (t80) cc_final: 0.7858 (t80) REVERT: A 143 MET cc_start: 0.7807 (ttm) cc_final: 0.7334 (ttm) REVERT: A 156 VAL cc_start: 0.8210 (m) cc_final: 0.7831 (p) REVERT: A 302 ASP cc_start: 0.8266 (t0) cc_final: 0.7925 (t70) REVERT: B 44 PHE cc_start: 0.7905 (t80) cc_final: 0.7688 (t80) REVERT: B 65 LEU cc_start: 0.8065 (tp) cc_final: 0.7860 (mp) REVERT: B 136 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7290 (mmp80) REVERT: B 170 PHE cc_start: 0.7889 (t80) cc_final: 0.7612 (t80) REVERT: C 26 ILE cc_start: 0.8415 (pt) cc_final: 0.8111 (pt) REVERT: C 133 ASP cc_start: 0.7597 (m-30) cc_final: 0.7376 (m-30) REVERT: C 234 GLU cc_start: 0.7562 (tt0) cc_final: 0.7338 (tt0) REVERT: C 262 GLN cc_start: 0.7570 (mp10) cc_final: 0.7169 (tm-30) REVERT: C 265 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7334 (mt-10) REVERT: C 274 VAL cc_start: 0.8499 (t) cc_final: 0.8273 (m) REVERT: C 306 MET cc_start: 0.7701 (tpp) cc_final: 0.7456 (tpp) REVERT: D 33 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7896 (mtm110) REVERT: D 106 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7604 (tm-30) REVERT: D 177 MET cc_start: 0.8202 (tpp) cc_final: 0.7781 (mmm) REVERT: D 233 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8029 (ttm) outliers start: 22 outliers final: 18 residues processed: 321 average time/residue: 0.3393 time to fit residues: 136.4874 Evaluate side-chains 330 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 311 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 145 ILE 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 185 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 Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.5980 chunk 102 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.125137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114482 restraints weight = 12675.120| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.41 r_work: 0.3346 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9857 Z= 0.795 Angle : 2.300 50.555 13409 Z= 1.509 Chirality : 0.452 6.307 1554 Planarity : 0.005 0.044 1707 Dihedral : 5.184 47.030 1377 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.94 % Allowed : 17.26 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1230 helix: 1.76 (0.20), residues: 682 sheet: -0.26 (0.52), residues: 106 loop : -0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.002 0.000 HIS A 254 PHE 0.037 0.001 PHE A 96 TYR 0.007 0.001 TYR B 192 ARG 0.018 0.001 ARG D 97 ********************** 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 321 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8196 (mt) cc_final: 0.7908 (mt) REVERT: A 141 TYR cc_start: 0.8102 (t80) cc_final: 0.7880 (t80) REVERT: A 143 MET cc_start: 0.7779 (ttm) cc_final: 0.7334 (ttm) REVERT: A 156 VAL cc_start: 0.8145 (m) cc_final: 0.7739 (p) REVERT: A 302 ASP cc_start: 0.8285 (t0) cc_final: 0.7932 (t70) REVERT: B 65 LEU cc_start: 0.8055 (tp) cc_final: 0.7855 (mp) REVERT: B 170 PHE cc_start: 0.7885 (t80) cc_final: 0.7615 (t80) REVERT: C 15 ASP cc_start: 0.7472 (p0) cc_final: 0.7257 (p0) REVERT: C 26 ILE cc_start: 0.8411 (pt) cc_final: 0.8116 (pt) REVERT: C 234 GLU cc_start: 0.7553 (tt0) cc_final: 0.7336 (tt0) REVERT: C 262 GLN cc_start: 0.7554 (mp10) cc_final: 0.7172 (tm-30) REVERT: C 265 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 274 VAL cc_start: 0.8507 (t) cc_final: 0.8269 (m) REVERT: C 306 MET cc_start: 0.7699 (tpp) cc_final: 0.7460 (tpp) REVERT: D 33 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7910 (mtp-110) REVERT: D 106 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7585 (tm-30) REVERT: D 177 MET cc_start: 0.8122 (tpp) cc_final: 0.7693 (mmm) REVERT: D 233 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.8001 (ttm) outliers start: 20 outliers final: 18 residues processed: 308 average time/residue: 0.3061 time to fit residues: 119.8972 Evaluate side-chains 320 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 145 ILE 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 185 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 C residue 210 ILE Chi-restraints excluded: chain C residue 216 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 Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.122899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112069 restraints weight = 12586.233| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.43 r_work: 0.3310 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.250 9857 Z= 0.828 Angle : 2.314 50.763 13409 Z= 1.515 Chirality : 0.453 6.344 1554 Planarity : 0.005 0.053 1707 Dihedral : 5.340 44.586 1377 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.42 % Allowed : 17.56 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1230 helix: 1.51 (0.20), residues: 686 sheet: -0.31 (0.51), residues: 106 loop : -0.31 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 293 HIS 0.005 0.001 HIS C 316 PHE 0.013 0.002 PHE A 96 TYR 0.011 0.001 TYR B 192 ARG 0.020 0.001 ARG D 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5110.59 seconds wall clock time: 91 minutes 2.41 seconds (5462.41 seconds total)