Starting phenix.real_space_refine on Sun Jun 8 15:51:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1x_39739/06_2025/8z1x_39739_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1x_39739/06_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_39739/06_2025/8z1x_39739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1x_39739/06_2025/8z1x_39739.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1x_39739/06_2025/8z1x_39739_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1x_39739/06_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-5710/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: 6.72, per 1000 atoms: 0.70 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: 2.67 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: 1.17 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: 2.74 Time building geometry restraints manager: 3.13 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: 2.030 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.770 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.305 9865 Z= 1.081 Angle : 2.047 16.452 13433 Z= 1.349 Chirality : 1.497 20.957 1554 Planarity : 0.013 0.127 1707 Dihedral : 13.048 89.034 3668 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 3.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.17066 ( 532) hydrogen bonds : angle 7.45060 ( 1527) metal coordination : bond 0.15712 ( 8) metal coordination : angle 8.40743 ( 24) covalent geometry : bond 0.01915 ( 9857) covalent geometry : angle 2.01762 (13409) *********************** 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 : 1.053 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: 0.3056 time to fit residues: 135.4946 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 : 1.181 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113873 restraints weight = 12691.082| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.40 r_work: 0.3328 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 9865 Z= 0.439 Angle : 2.654 50.674 13433 Z= 1.522 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 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 532) hydrogen bonds : angle 5.16104 ( 1527) metal coordination : bond 0.01855 ( 8) metal coordination : angle 30.79728 ( 24) covalent geometry : bond 0.01279 ( 9857) covalent geometry : angle 2.31505 (13409) *********************** 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 : 1.072 Fit side-chains REVERT: A 30 ILE cc_start: 0.8296 (mt) cc_final: 0.7852 (mp) REVERT: A 70 ILE cc_start: 0.7792 (pt) cc_final: 0.7584 (mm) REVERT: A 143 MET cc_start: 0.7892 (ttm) cc_final: 0.7450 (ttm) REVERT: A 156 VAL cc_start: 0.8152 (m) cc_final: 0.7769 (p) REVERT: A 238 ARG cc_start: 0.8644 (ttp-170) cc_final: 0.8326 (ttp-170) REVERT: A 247 ARG cc_start: 0.7314 (ttt180) cc_final: 0.7112 (ttt180) REVERT: A 296 ASP cc_start: 0.7728 (t70) cc_final: 0.7478 (t0) REVERT: A 302 ASP cc_start: 0.8274 (t0) cc_final: 0.7914 (t70) REVERT: B 27 LYS cc_start: 0.8624 (tttm) cc_final: 0.8345 (tttm) REVERT: B 65 LEU cc_start: 0.7966 (tt) cc_final: 0.7605 (tp) REVERT: C 10 SER cc_start: 0.8618 (m) cc_final: 0.8254 (p) REVERT: C 163 MET cc_start: 0.8459 (mmm) cc_final: 0.8070 (mmm) REVERT: C 210 ILE cc_start: 0.8295 (pt) cc_final: 0.7998 (mt) REVERT: C 234 GLU cc_start: 0.7547 (tt0) cc_final: 0.7328 (tt0) REVERT: C 257 LEU cc_start: 0.8377 (mt) cc_final: 0.8157 (mp) REVERT: C 262 GLN cc_start: 0.7805 (mp10) cc_final: 0.7187 (mp10) REVERT: C 265 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 306 MET cc_start: 0.7716 (tpp) cc_final: 0.7479 (tpp) REVERT: D 47 ARG cc_start: 0.6953 (ttt-90) cc_final: 0.6674 (ttt-90) REVERT: D 62 SER cc_start: 0.8498 (m) cc_final: 0.8200 (t) REVERT: D 106 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 209 GLN cc_start: 0.8195 (tp40) cc_final: 0.7959 (tp40) REVERT: D 233 MET cc_start: 0.8432 (mtp) cc_final: 0.8211 (mtm) outliers start: 22 outliers final: 15 residues processed: 335 average time/residue: 0.3002 time to fit residues: 128.0483 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 : 1.066 ------------------------------------------------------------------------------- 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: 0.0270 chunk 96 optimal weight: 0.1980 chunk 101 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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 D 319 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115297 restraints weight = 12753.701| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.41 r_work: 0.3349 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 9865 Z= 0.409 Angle : 2.628 50.477 13433 Z= 1.509 Chirality : 0.454 6.340 1554 Planarity : 0.004 0.041 1707 Dihedral : 6.398 71.642 1377 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.23 % Allowed : 12.22 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1230 helix: 1.51 (0.20), residues: 677 sheet: -0.18 (0.54), residues: 96 loop : 0.03 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 293 HIS 0.003 0.000 HIS A 337 PHE 0.011 0.001 PHE B 170 TYR 0.009 0.001 TYR D 215 ARG 0.005 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 532) hydrogen bonds : angle 4.72426 ( 1527) metal coordination : bond 0.02929 ( 8) metal coordination : angle 30.72115 ( 24) covalent geometry : bond 0.01201 ( 9857) covalent geometry : angle 2.28693 (13409) *********************** 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 331 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 1.225 Fit side-chains REVERT: A 29 MET cc_start: 0.7698 (mtm) cc_final: 0.6867 (ptt) REVERT: A 30 ILE cc_start: 0.8277 (mt) cc_final: 0.7754 (mp) REVERT: A 70 ILE cc_start: 0.7746 (pt) cc_final: 0.7514 (mm) REVERT: A 85 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7460 (mmt-90) REVERT: A 141 TYR cc_start: 0.8163 (t80) cc_final: 0.7816 (t80) REVERT: A 143 MET cc_start: 0.7869 (ttm) cc_final: 0.7408 (ttm) REVERT: A 156 VAL cc_start: 0.8125 (m) cc_final: 0.7756 (p) REVERT: A 238 ARG cc_start: 0.8731 (ttp-170) cc_final: 0.8507 (ttp-170) REVERT: A 247 ARG cc_start: 0.7299 (ttt180) cc_final: 0.7091 (ttt180) REVERT: A 302 ASP cc_start: 0.8258 (t0) cc_final: 0.7867 (t70) REVERT: B 27 LYS cc_start: 0.8609 (tttm) cc_final: 0.8383 (tttm) REVERT: B 133 ILE cc_start: 0.8634 (mm) cc_final: 0.8416 (mt) REVERT: C 10 SER cc_start: 0.8602 (m) cc_final: 0.8236 (p) REVERT: C 26 ILE cc_start: 0.8242 (pt) cc_final: 0.7976 (pt) REVERT: C 62 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7427 (mtm-85) REVERT: C 163 MET cc_start: 0.8335 (mmm) cc_final: 0.7889 (mmm) REVERT: C 234 GLU cc_start: 0.7563 (tt0) cc_final: 0.7333 (tt0) REVERT: C 259 GLU cc_start: 0.7815 (mp0) cc_final: 0.7344 (mp0) REVERT: C 262 GLN cc_start: 0.7621 (mp10) cc_final: 0.7037 (mp10) REVERT: C 265 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 274 VAL cc_start: 0.8396 (t) cc_final: 0.8127 (m) REVERT: C 306 MET cc_start: 0.7723 (tpp) cc_final: 0.7465 (tpp) REVERT: D 47 ARG cc_start: 0.6983 (ttt-90) cc_final: 0.6653 (ttt-90) REVERT: D 62 SER cc_start: 0.8456 (m) cc_final: 0.8061 (t) REVERT: D 106 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D 209 GLN cc_start: 0.8175 (tp40) cc_final: 0.7944 (tp40) REVERT: D 268 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8322 (tt) outliers start: 23 outliers final: 14 residues processed: 316 average time/residue: 0.3016 time to fit residues: 124.3239 Evaluate side-chains 313 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 298 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 34 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 223 SER Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN D 208 GLN D 308 GLN D 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112679 restraints weight = 12619.435| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.43 r_work: 0.3312 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.249 9865 Z= 0.432 Angle : 2.638 50.719 13433 Z= 1.513 Chirality : 0.453 6.334 1554 Planarity : 0.005 0.039 1707 Dihedral : 5.995 66.581 1377 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.42 % Allowed : 13.58 % Favored : 84.00 % 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: 1.05 (0.24), residues: 1230 helix: 1.44 (0.20), residues: 680 sheet: -0.44 (0.52), residues: 96 loop : -0.07 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 293 HIS 0.004 0.001 HIS D 160 PHE 0.016 0.002 PHE A 96 TYR 0.011 0.001 TYR B 192 ARG 0.010 0.001 ARG C 25 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 532) hydrogen bonds : angle 4.69022 ( 1527) metal coordination : bond 0.03037 ( 8) metal coordination : angle 30.75398 ( 24) covalent geometry : bond 0.01249 ( 9857) covalent geometry : angle 2.29795 (13409) *********************** 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 335 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 310 time to evaluate : 1.176 Fit side-chains REVERT: A 9 LEU cc_start: 0.8136 (mt) cc_final: 0.7821 (mt) REVERT: A 29 MET cc_start: 0.7703 (mtm) cc_final: 0.6862 (ptt) REVERT: A 30 ILE cc_start: 0.8349 (mt) cc_final: 0.7900 (mp) REVERT: A 70 ILE cc_start: 0.7813 (pt) cc_final: 0.7613 (mm) REVERT: A 85 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7669 (mmt-90) REVERT: A 141 TYR cc_start: 0.8160 (t80) cc_final: 0.7874 (t80) REVERT: A 143 MET cc_start: 0.7879 (ttm) cc_final: 0.7414 (ttm) REVERT: A 156 VAL cc_start: 0.8201 (m) cc_final: 0.7840 (p) REVERT: A 238 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8497 (ttp-170) REVERT: A 247 ARG cc_start: 0.7441 (ttt180) cc_final: 0.7214 (ttt180) REVERT: A 302 ASP cc_start: 0.8312 (t0) cc_final: 0.7932 (t70) REVERT: B 133 ILE cc_start: 0.8620 (mm) cc_final: 0.8412 (mt) REVERT: C 10 SER cc_start: 0.8661 (m) cc_final: 0.8416 (p) REVERT: C 26 ILE cc_start: 0.8369 (pt) cc_final: 0.8058 (pt) REVERT: C 163 MET cc_start: 0.8184 (mmm) cc_final: 0.7971 (mmm) REVERT: C 219 GLU cc_start: 0.7804 (tp30) cc_final: 0.7602 (tp30) REVERT: C 234 GLU cc_start: 0.7655 (tt0) cc_final: 0.7409 (tt0) REVERT: C 259 GLU cc_start: 0.7845 (mp0) cc_final: 0.7397 (mp0) REVERT: C 262 GLN cc_start: 0.7644 (mp10) cc_final: 0.7110 (mp10) REVERT: C 265 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 274 VAL cc_start: 0.8478 (t) cc_final: 0.8208 (m) REVERT: C 306 MET cc_start: 0.7783 (tpp) cc_final: 0.7518 (tpp) REVERT: D 106 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 209 GLN cc_start: 0.8212 (tp40) cc_final: 0.7984 (tp40) REVERT: D 268 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 25 outliers final: 18 residues processed: 319 average time/residue: 0.2892 time to fit residues: 119.2338 Evaluate side-chains 323 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL 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 91 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 153 GLU 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: 0.0470 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 63 optimal weight: 0.0070 chunk 82 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 29 optimal weight: 2.9990 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115499 restraints weight = 12602.329| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.43 r_work: 0.3354 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9865 Z= 0.405 Angle : 2.626 50.488 13433 Z= 1.507 Chirality : 0.452 6.311 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.597 60.743 1377 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.23 % Allowed : 14.45 % Favored : 83.32 % 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: 1.30 (0.25), residues: 1230 helix: 1.71 (0.20), residues: 682 sheet: -0.39 (0.50), residues: 106 loop : -0.06 (0.31), residues: 442 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 0.013 0.001 PHE A 96 TYR 0.007 0.001 TYR C 228 ARG 0.009 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 532) hydrogen bonds : angle 4.49937 ( 1527) metal coordination : bond 0.01763 ( 8) metal coordination : angle 30.76003 ( 24) covalent geometry : bond 0.01196 ( 9857) covalent geometry : angle 2.28350 (13409) *********************** 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 321 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 1.033 Fit side-chains REVERT: A 9 LEU cc_start: 0.8105 (mt) cc_final: 0.7770 (mt) REVERT: A 29 MET cc_start: 0.7668 (mtm) cc_final: 0.6890 (ptt) REVERT: A 30 ILE cc_start: 0.8319 (mt) cc_final: 0.7899 (mp) REVERT: A 70 ILE cc_start: 0.7776 (pt) cc_final: 0.7550 (mm) REVERT: A 141 TYR cc_start: 0.8181 (t80) cc_final: 0.7870 (t80) REVERT: A 143 MET cc_start: 0.7842 (ttm) cc_final: 0.7377 (ttm) REVERT: A 156 VAL cc_start: 0.8122 (m) cc_final: 0.7727 (p) REVERT: A 302 ASP cc_start: 0.8337 (t0) cc_final: 0.7947 (t70) REVERT: B 45 ILE cc_start: 0.8532 (tt) cc_final: 0.8196 (tt) REVERT: B 133 ILE cc_start: 0.8566 (mm) cc_final: 0.8360 (mt) REVERT: C 10 SER cc_start: 0.8633 (m) cc_final: 0.8432 (p) REVERT: C 26 ILE cc_start: 0.8355 (pt) cc_final: 0.8042 (pt) REVERT: C 219 GLU cc_start: 0.7734 (tp30) cc_final: 0.7515 (tp30) REVERT: C 234 GLU cc_start: 0.7612 (tt0) cc_final: 0.7376 (tt0) REVERT: C 262 GLN cc_start: 0.7592 (mp10) cc_final: 0.7143 (mp10) REVERT: C 265 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 274 VAL cc_start: 0.8458 (t) cc_final: 0.8199 (m) REVERT: C 306 MET cc_start: 0.7728 (tpp) cc_final: 0.7477 (tpp) REVERT: D 33 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7806 (mtp-110) REVERT: D 97 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7549 (ptt-90) REVERT: D 106 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 209 GLN cc_start: 0.8215 (tp40) cc_final: 0.7961 (tp40) outliers start: 23 outliers final: 17 residues processed: 305 average time/residue: 0.2857 time to fit residues: 112.0670 Evaluate side-chains 305 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 288 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 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 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 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: 2.9990 chunk 101 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112797 restraints weight = 12601.703| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.43 r_work: 0.3316 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 9865 Z= 0.430 Angle : 2.636 50.685 13433 Z= 1.511 Chirality : 0.452 6.326 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.569 55.713 1377 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.42 % Allowed : 14.74 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1230 helix: 1.60 (0.20), residues: 686 sheet: -0.40 (0.50), residues: 106 loop : -0.11 (0.31), residues: 438 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 0.013 0.001 PHE B 26 TYR 0.011 0.001 TYR B 192 ARG 0.010 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 532) hydrogen bonds : angle 4.56854 ( 1527) metal coordination : bond 0.02664 ( 8) metal coordination : angle 30.78875 ( 24) covalent geometry : bond 0.01245 ( 9857) covalent geometry : angle 2.29470 (13409) *********************** 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 330 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 1.132 Fit side-chains REVERT: A 9 LEU cc_start: 0.8189 (mt) cc_final: 0.7839 (mt) REVERT: A 29 MET cc_start: 0.7713 (mtm) cc_final: 0.6958 (ptt) REVERT: A 70 ILE cc_start: 0.7833 (pt) cc_final: 0.7621 (mm) REVERT: A 141 TYR cc_start: 0.8145 (t80) cc_final: 0.7866 (t80) REVERT: A 143 MET cc_start: 0.7853 (ttm) cc_final: 0.7389 (ttt) REVERT: A 156 VAL cc_start: 0.8216 (m) cc_final: 0.7845 (p) REVERT: A 247 ARG cc_start: 0.7477 (ttt180) cc_final: 0.7264 (ttt180) REVERT: A 300 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8182 (mtm-85) REVERT: A 302 ASP cc_start: 0.8340 (t0) cc_final: 0.7966 (t70) REVERT: B 44 PHE cc_start: 0.7976 (t80) cc_final: 0.7768 (t80) REVERT: B 45 ILE cc_start: 0.8536 (tt) cc_final: 0.8210 (tt) REVERT: C 10 SER cc_start: 0.8655 (m) cc_final: 0.8419 (p) REVERT: C 26 ILE cc_start: 0.8426 (pt) cc_final: 0.8106 (pt) REVERT: C 133 ASP cc_start: 0.7630 (m-30) cc_final: 0.7392 (m-30) REVERT: C 219 GLU cc_start: 0.7806 (tp30) cc_final: 0.7590 (tp30) REVERT: C 234 GLU cc_start: 0.7641 (tt0) cc_final: 0.7399 (tt0) REVERT: C 262 GLN cc_start: 0.7653 (mp10) cc_final: 0.7259 (mp10) REVERT: C 265 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 274 VAL cc_start: 0.8498 (t) cc_final: 0.8245 (m) REVERT: C 306 MET cc_start: 0.7813 (tpp) cc_final: 0.7558 (tpp) REVERT: D 33 ARG cc_start: 0.8115 (mtp-110) cc_final: 0.7792 (mtp-110) REVERT: D 47 ARG cc_start: 0.7048 (ttt-90) cc_final: 0.6773 (ttt-90) REVERT: D 97 ARG cc_start: 0.7892 (ptt-90) cc_final: 0.7680 (ptt-90) REVERT: D 106 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 209 GLN cc_start: 0.8213 (tp40) cc_final: 0.7948 (tp40) REVERT: D 233 MET cc_start: 0.8329 (mtp) cc_final: 0.8067 (ttm) outliers start: 25 outliers final: 18 residues processed: 313 average time/residue: 0.2883 time to fit residues: 117.0364 Evaluate side-chains 315 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 A residue 330 VAL 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 184 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.0470 chunk 6 optimal weight: 0.4980 chunk 114 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114352 restraints weight = 12690.428| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.41 r_work: 0.3342 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9865 Z= 0.406 Angle : 2.629 50.484 13433 Z= 1.507 Chirality : 0.453 6.307 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.389 52.305 1377 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.13 % Allowed : 15.23 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.25), residues: 1230 helix: 1.77 (0.20), residues: 683 sheet: -0.23 (0.52), residues: 106 loop : -0.10 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.003 0.000 HIS A 337 PHE 0.008 0.001 PHE B 26 TYR 0.007 0.001 TYR A 236 ARG 0.010 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 532) hydrogen bonds : angle 4.48582 ( 1527) metal coordination : bond 0.01859 ( 8) metal coordination : angle 30.75305 ( 24) covalent geometry : bond 0.01198 ( 9857) covalent geometry : angle 2.28681 (13409) *********************** 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: 22 poor density : 297 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8189 (mt) cc_final: 0.7832 (mt) REVERT: A 29 MET cc_start: 0.7632 (mtm) cc_final: 0.6900 (ptt) REVERT: A 70 ILE cc_start: 0.7798 (pt) cc_final: 0.7578 (mm) REVERT: A 141 TYR cc_start: 0.8118 (t80) cc_final: 0.7856 (t80) REVERT: A 143 MET cc_start: 0.7806 (ttm) cc_final: 0.7354 (ttm) REVERT: A 156 VAL cc_start: 0.8164 (m) cc_final: 0.7770 (p) REVERT: A 302 ASP cc_start: 0.8307 (t0) cc_final: 0.7927 (t70) REVERT: A 330 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 45 ILE cc_start: 0.8539 (tt) cc_final: 0.8212 (tt) REVERT: C 10 SER cc_start: 0.8609 (m) cc_final: 0.8398 (p) REVERT: C 26 ILE cc_start: 0.8411 (pt) cc_final: 0.8103 (pt) REVERT: C 234 GLU cc_start: 0.7538 (tt0) cc_final: 0.7328 (tt0) REVERT: C 262 GLN cc_start: 0.7603 (mp10) cc_final: 0.7245 (mp10) REVERT: C 265 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 274 VAL cc_start: 0.8480 (t) cc_final: 0.8245 (m) REVERT: C 306 MET cc_start: 0.7768 (tpp) cc_final: 0.7520 (tpp) REVERT: D 33 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7733 (mtp-110) REVERT: D 47 ARG cc_start: 0.7035 (ttt-90) cc_final: 0.6797 (ttt-90) REVERT: D 106 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 209 GLN cc_start: 0.8232 (tp40) cc_final: 0.7967 (tp40) outliers start: 22 outliers final: 17 residues processed: 304 average time/residue: 0.2710 time to fit residues: 107.1336 Evaluate side-chains 312 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 294 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 A residue 330 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.124801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113931 restraints weight = 12754.516| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.45 r_work: 0.3334 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 9865 Z= 0.410 Angle : 2.632 50.567 13433 Z= 1.509 Chirality : 0.453 6.309 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.278 50.139 1377 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.94 % Allowed : 16.10 % Favored : 81.96 % 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: 1.36 (0.25), residues: 1230 helix: 1.78 (0.20), residues: 683 sheet: -0.25 (0.52), residues: 106 loop : -0.11 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.002 0.000 HIS D 160 PHE 0.009 0.001 PHE B 26 TYR 0.008 0.001 TYR B 192 ARG 0.011 0.001 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 532) hydrogen bonds : angle 4.47114 ( 1527) metal coordination : bond 0.02016 ( 8) metal coordination : angle 30.75266 ( 24) covalent geometry : bond 0.01207 ( 9857) covalent geometry : angle 2.29099 (13409) *********************** 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 325 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 305 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8171 (mt) cc_final: 0.7818 (mt) REVERT: A 70 ILE cc_start: 0.7819 (pt) cc_final: 0.7602 (mm) REVERT: A 141 TYR cc_start: 0.8156 (t80) cc_final: 0.7913 (t80) REVERT: A 143 MET cc_start: 0.7808 (ttm) cc_final: 0.7339 (ttm) REVERT: A 156 VAL cc_start: 0.8167 (m) cc_final: 0.7768 (p) REVERT: A 302 ASP cc_start: 0.8345 (t0) cc_final: 0.7958 (t70) REVERT: A 327 LEU cc_start: 0.8644 (tt) cc_final: 0.8289 (tp) REVERT: A 330 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (t) REVERT: B 45 ILE cc_start: 0.8504 (tt) cc_final: 0.8179 (tt) REVERT: B 136 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7326 (mmp80) REVERT: B 170 PHE cc_start: 0.7907 (t80) cc_final: 0.7624 (t80) REVERT: C 10 SER cc_start: 0.8638 (m) cc_final: 0.8409 (p) REVERT: C 26 ILE cc_start: 0.8424 (pt) cc_final: 0.8114 (pt) REVERT: C 234 GLU cc_start: 0.7598 (tt0) cc_final: 0.7351 (tt0) REVERT: C 262 GLN cc_start: 0.7622 (mp10) cc_final: 0.7122 (tm-30) REVERT: C 265 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7378 (mt-10) REVERT: C 274 VAL cc_start: 0.8502 (t) cc_final: 0.8264 (m) REVERT: C 306 MET cc_start: 0.7855 (tpp) cc_final: 0.7593 (tpp) REVERT: D 97 ARG cc_start: 0.7858 (ptt-90) cc_final: 0.7627 (ptp-170) REVERT: D 106 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7523 (tm-30) REVERT: D 209 GLN cc_start: 0.8233 (tp40) cc_final: 0.7959 (tp40) REVERT: D 233 MET cc_start: 0.8199 (mtm) cc_final: 0.7975 (mtp) outliers start: 20 outliers final: 18 residues processed: 313 average time/residue: 0.3033 time to fit residues: 120.9258 Evaluate side-chains 332 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 313 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 A residue 330 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain 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 279 LEU 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: 0.4980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.124183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113312 restraints weight = 12603.860| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.43 r_work: 0.3325 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 9865 Z= 0.416 Angle : 2.639 50.623 13433 Z= 1.511 Chirality : 0.452 6.316 1554 Planarity : 0.004 0.039 1707 Dihedral : 5.255 47.920 1377 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.42 % Allowed : 16.78 % 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: 1.29 (0.25), residues: 1230 helix: 1.73 (0.20), residues: 683 sheet: -0.24 (0.51), residues: 106 loop : -0.17 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.003 0.001 HIS A 28 PHE 0.010 0.001 PHE B 26 TYR 0.009 0.001 TYR B 192 ARG 0.007 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 532) hydrogen bonds : angle 4.51698 ( 1527) metal coordination : bond 0.02198 ( 8) metal coordination : angle 30.78413 ( 24) covalent geometry : bond 0.01219 ( 9857) covalent geometry : angle 2.29843 (13409) *********************** 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 341 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 316 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8245 (mt) cc_final: 0.7888 (mt) REVERT: A 29 MET cc_start: 0.7726 (mtm) cc_final: 0.7060 (ptt) REVERT: A 70 ILE cc_start: 0.7815 (pt) cc_final: 0.7609 (mm) REVERT: A 141 TYR cc_start: 0.8126 (t80) cc_final: 0.7871 (t80) REVERT: A 143 MET cc_start: 0.7843 (ttm) cc_final: 0.7378 (ttm) REVERT: A 156 VAL cc_start: 0.8202 (m) cc_final: 0.7847 (p) REVERT: A 302 ASP cc_start: 0.8305 (t0) cc_final: 0.7964 (t70) REVERT: B 44 PHE cc_start: 0.7961 (t80) cc_final: 0.7746 (t80) REVERT: B 45 ILE cc_start: 0.8512 (tt) cc_final: 0.8181 (tt) REVERT: B 136 ARG cc_start: 0.7739 (mmp80) cc_final: 0.7339 (mmp80) REVERT: B 170 PHE cc_start: 0.7917 (t80) cc_final: 0.7642 (t80) REVERT: B 190 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8030 (mmm-85) REVERT: C 10 SER cc_start: 0.8644 (m) cc_final: 0.8404 (p) REVERT: C 26 ILE cc_start: 0.8428 (pt) cc_final: 0.8120 (pt) REVERT: C 133 ASP cc_start: 0.7621 (m-30) cc_final: 0.7381 (m-30) REVERT: C 163 MET cc_start: 0.7983 (mmm) cc_final: 0.7768 (mtm) REVERT: C 234 GLU cc_start: 0.7594 (tt0) cc_final: 0.7359 (tt0) REVERT: C 262 GLN cc_start: 0.7615 (mp10) cc_final: 0.7105 (tm-30) REVERT: C 265 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 274 VAL cc_start: 0.8509 (t) cc_final: 0.8267 (m) REVERT: C 306 MET cc_start: 0.7839 (tpp) cc_final: 0.7586 (tpp) REVERT: D 97 ARG cc_start: 0.7888 (ptt-90) cc_final: 0.7672 (ptp-170) REVERT: D 106 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7641 (tm-30) REVERT: D 209 GLN cc_start: 0.8226 (tp40) cc_final: 0.7947 (tp40) REVERT: D 233 MET cc_start: 0.8245 (mtm) cc_final: 0.8033 (mtp) outliers start: 25 outliers final: 22 residues processed: 326 average time/residue: 0.5349 time to fit residues: 224.8981 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 : 5.620 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 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 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 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.3980 chunk 102 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.124166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113361 restraints weight = 12696.947| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.44 r_work: 0.3326 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 9865 Z= 0.416 Angle : 2.641 50.640 13433 Z= 1.512 Chirality : 0.453 6.326 1554 Planarity : 0.004 0.049 1707 Dihedral : 5.234 46.292 1377 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1.25 (0.25), residues: 1230 helix: 1.68 (0.20), residues: 684 sheet: -0.25 (0.51), residues: 106 loop : -0.16 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.003 0.001 HIS A 159 PHE 0.010 0.001 PHE B 26 TYR 0.009 0.001 TYR B 192 ARG 0.011 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 532) hydrogen bonds : angle 4.51108 ( 1527) metal coordination : bond 0.02244 ( 8) metal coordination : angle 30.77973 ( 24) covalent geometry : bond 0.01219 ( 9857) covalent geometry : angle 2.30015 (13409) ********************** 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 334 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8251 (mt) cc_final: 0.7895 (mt) REVERT: A 29 MET cc_start: 0.7769 (mtm) cc_final: 0.7056 (ptt) REVERT: A 141 TYR cc_start: 0.8122 (t80) cc_final: 0.7894 (t80) REVERT: A 143 MET cc_start: 0.7870 (ttm) cc_final: 0.7396 (ttm) REVERT: A 154 MET cc_start: 0.8273 (ptp) cc_final: 0.8071 (ptt) REVERT: A 156 VAL cc_start: 0.8140 (m) cc_final: 0.7750 (p) REVERT: A 302 ASP cc_start: 0.8313 (t0) cc_final: 0.7964 (t70) REVERT: B 44 PHE cc_start: 0.7952 (t80) cc_final: 0.7738 (t80) REVERT: B 45 ILE cc_start: 0.8512 (tt) cc_final: 0.8182 (tt) REVERT: B 136 ARG cc_start: 0.7720 (mmp80) cc_final: 0.7308 (mmp80) REVERT: B 170 PHE cc_start: 0.7919 (t80) cc_final: 0.7643 (t80) REVERT: C 10 SER cc_start: 0.8642 (m) cc_final: 0.8394 (p) REVERT: C 26 ILE cc_start: 0.8432 (pt) cc_final: 0.8125 (pt) REVERT: C 133 ASP cc_start: 0.7624 (m-30) cc_final: 0.7381 (m-30) REVERT: C 163 MET cc_start: 0.7990 (mmm) cc_final: 0.7775 (mtm) REVERT: C 234 GLU cc_start: 0.7602 (tt0) cc_final: 0.7359 (tt0) REVERT: C 262 GLN cc_start: 0.7607 (mp10) cc_final: 0.7116 (tm-30) REVERT: C 265 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7291 (mt-10) REVERT: C 274 VAL cc_start: 0.8520 (t) cc_final: 0.8277 (m) REVERT: C 306 MET cc_start: 0.7853 (tpp) cc_final: 0.7601 (tpp) REVERT: D 106 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 177 MET cc_start: 0.8269 (tpp) cc_final: 0.7474 (tpp) REVERT: D 209 GLN cc_start: 0.8222 (tp40) cc_final: 0.7936 (tp40) outliers start: 20 outliers final: 20 residues processed: 324 average time/residue: 0.3247 time to fit residues: 132.7556 Evaluate side-chains 330 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 281 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain 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 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112664 restraints weight = 12587.894| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.43 r_work: 0.3317 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.012 0.248 9865 Z= 0.428 Angle : 2.648 50.702 13433 Z= 1.515 Chirality : 0.452 6.328 1554 Planarity : 0.005 0.047 1707 Dihedral : 5.332 44.834 1377 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.04 % Allowed : 17.46 % Favored : 80.50 % 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: 1.12 (0.25), residues: 1230 helix: 1.53 (0.20), residues: 688 sheet: -0.26 (0.51), residues: 106 loop : -0.15 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 293 HIS 0.003 0.001 HIS C 316 PHE 0.011 0.001 PHE B 26 TYR 0.011 0.001 TYR B 192 ARG 0.011 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 532) hydrogen bonds : angle 4.57362 ( 1527) metal coordination : bond 0.02435 ( 8) metal coordination : angle 30.81330 ( 24) covalent geometry : bond 0.01242 ( 9857) covalent geometry : angle 2.30729 (13409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5751.62 seconds wall clock time: 100 minutes 52.48 seconds (6052.48 seconds total)