Starting phenix.real_space_refine on Thu Jul 2 18:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1w_39738/07_2026/8z1w_39738_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 74 5.16 5 C 6166 2.51 5 N 1670 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9619 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2380 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain breaks: 1 Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2138 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain: "C" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2481 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2573 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 302} 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: {'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6727 SG CYS C 290 24.604 65.625 26.542 1.00124.46 S ATOM 6679 SG CYS C 284 20.560 62.927 30.932 1.00110.50 S ATOM 6919 SG CYS C 315 20.073 61.844 24.398 1.00110.98 S ATOM 6783 SG CYS C 297 18.221 67.426 27.345 1.00132.73 S ATOM 9243 SG CYS D 293 65.088 33.791 24.910 1.00115.68 S ATOM 9350 SG CYS D 306 66.180 29.596 20.550 1.00144.52 S ATOM 9479 SG CYS D 323 64.156 35.579 18.464 1.00126.42 S ATOM 9289 SG CYS D 299 59.798 31.551 20.995 1.00133.53 S Time building chain proxies: 1.96, per 1000 atoms: 0.20 Number of scatterers: 9619 At special positions: 0 Unit cell: (95.12, 93.48, 126.28, 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 74 16.00 P 3 15.00 O 1698 8.00 N 1670 7.00 C 6166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 340.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 401 " pdb="FE1 SF4 C 401 " - pdb=" SG CYS C 290 " pdb="FE3 SF4 C 401 " - pdb=" SG CYS C 315 " pdb="FE2 SF4 C 401 " - pdb=" SG CYS C 284 " pdb="FE4 SF4 C 401 " - pdb=" SG CYS C 297 " pdb=" SF4 D 401 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 306 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 293 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 323 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 299 " Number of angles added : 24 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 61.0% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 30 removed outlier: 3.847A pdb=" N LEU A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 87 through 124 Proline residue: A 94 - end of helix removed outlier: 3.660A 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 192 removed outlier: 4.048A pdb=" N ALA A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.761A pdb=" N ASP A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 233 removed outlier: 4.921A 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: 3.583A 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: 4.087A pdb=" N ASN A 258 " --> pdb=" O HIS A 254 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.609A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.566A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 65 removed outlier: 4.063A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 127 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 160 through 189 removed outlier: 3.694A pdb=" N LEU B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 3.549A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 211 through 240 removed outlier: 4.764A pdb=" N ALA B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Proline residue: B 218 - end of helix removed outlier: 3.568A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.518A 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 295 removed outlier: 3.974A 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 55 removed outlier: 3.824A pdb=" N SER C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.907A 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 144 through 148 removed outlier: 3.729A 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 168 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 185 through 203 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 257 through 261 removed outlier: 4.071A pdb=" N ALA C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 93 through 98 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 Processing helix chain 'D' and resid 151 through 157 removed outlier: 4.219A 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 removed outlier: 3.527A pdb=" N MET D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 212 Processing helix chain 'D' and resid 221 through 229 removed outlier: 3.639A pdb=" N HIS D 227 " --> pdb=" O SER D 223 " (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 Processing helix chain 'D' and resid 303 through 308 removed outlier: 4.341A 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: 6.404A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.619A 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: 6.404A pdb=" N VAL C 11 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 24 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 9 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 26 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP C 7 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR C 28 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN C 5 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.594A pdb=" N VAL C 35 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE C 225 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY C 37 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N MET C 227 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 39 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 234 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 228 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 5.100A 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: 6.540A pdb=" N LYS D 20 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP D 39 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU D 18 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 41 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 16 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE D 43 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN D 14 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 18 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY D 76 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.644A pdb=" N GLN D 102 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP D 186 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL D 104 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 242 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR D 236 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N CYS D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4126 1.43 - 1.64: 5562 1.64 - 1.86: 115 1.86 - 2.07: 1 2.07 - 2.29: 24 Bond restraints: 9828 Sorted by residual: bond pdb=" CE1 HIS C 212 " pdb=" NE2 HIS C 212 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.69e+01 bond pdb=" CD2 HIS C 212 " pdb=" NE2 HIS C 212 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.10e-02 8.26e+03 6.48e+01 bond pdb=" CZ ARG A 336 " pdb=" NH2 ARG A 336 " ideal model delta sigma weight residual 1.330 1.228 0.102 1.30e-02 5.92e+03 6.10e+01 bond pdb=" CZ ARG D 197 " pdb=" NH2 ARG D 197 " ideal model delta sigma weight residual 1.330 1.229 0.101 1.30e-02 5.92e+03 6.04e+01 bond pdb=" CZ ARG A 334 " pdb=" NH2 ARG A 334 " ideal model delta sigma weight residual 1.330 1.229 0.101 1.30e-02 5.92e+03 6.02e+01 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 10708 2.44 - 4.87: 2403 4.87 - 7.31: 213 7.31 - 9.74: 36 9.74 - 12.18: 11 Bond angle restraints: 13371 Sorted by residual: angle pdb=" N ILE A 115 " pdb=" CA ILE A 115 " pdb=" CB ILE A 115 " ideal model delta sigma weight residual 110.45 117.00 -6.55 7.80e-01 1.64e+00 7.06e+01 angle pdb=" N PRO B 246 " pdb=" CA PRO B 246 " pdb=" C PRO B 246 " ideal model delta sigma weight residual 110.70 119.90 -9.20 1.22e+00 6.72e-01 5.69e+01 angle pdb=" CA ASP D 39 " pdb=" CB ASP D 39 " pdb=" CG ASP D 39 " ideal model delta sigma weight residual 112.60 119.54 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" CA ASN A 321 " pdb=" CB ASN A 321 " pdb=" CG ASN A 321 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" CA PHE B 157 " pdb=" CB PHE B 157 " pdb=" CG PHE B 157 " ideal model delta sigma weight residual 113.80 120.61 -6.81 1.00e+00 1.00e+00 4.64e+01 ... (remaining 13366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 5833 31.96 - 63.93: 88 63.93 - 95.89: 12 95.89 - 127.85: 2 127.85 - 159.82: 1 Dihedral angle restraints: 5936 sinusoidal: 2398 harmonic: 3538 Sorted by residual: dihedral pdb=" C ASP D 181 " pdb=" N ASP D 181 " pdb=" CA ASP D 181 " pdb=" CB ASP D 181 " ideal model delta harmonic sigma weight residual -122.60 -135.27 12.67 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N ASP D 181 " pdb=" C ASP D 181 " pdb=" CA ASP D 181 " pdb=" CB ASP D 181 " ideal model delta harmonic sigma weight residual 122.80 134.77 -11.97 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" C ILE A 115 " pdb=" N ILE A 115 " pdb=" CA ILE A 115 " pdb=" CB ILE A 115 " ideal model delta harmonic sigma weight residual -122.00 -133.74 11.74 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1288 0.143 - 0.285: 146 0.285 - 0.428: 31 0.428 - 0.570: 55 0.570 - 0.713: 29 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CG LEU B 278 " pdb=" CB LEU B 278 " pdb=" CD1 LEU B 278 " pdb=" CD2 LEU B 278 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CG LEU C 270 " pdb=" CB LEU C 270 " pdb=" CD1 LEU C 270 " pdb=" CD2 LEU C 270 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CB VAL D 194 " pdb=" CA VAL D 194 " pdb=" CG1 VAL D 194 " pdb=" CG2 VAL D 194 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 1546 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 293 " -0.142 2.00e-02 2.50e+03 7.53e-02 1.42e+02 pdb=" CG TRP A 293 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 293 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 293 " 0.056 2.00e-02 2.50e+03 pdb=" NE1 TRP A 293 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP A 293 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 293 " 0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 293 " -0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 293 " 0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 293 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 71 " -0.114 2.00e-02 2.50e+03 5.91e-02 8.72e+01 pdb=" CG TRP B 71 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 71 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 71 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP B 71 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP B 71 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 71 " 0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 71 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 71 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 71 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " -0.099 2.00e-02 2.50e+03 4.87e-02 5.94e+01 pdb=" CG TRP B 251 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " -0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " -0.040 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 4512 3.01 - 3.48: 9885 3.48 - 3.95: 15531 3.95 - 4.43: 16944 4.43 - 4.90: 29472 Nonbonded interactions: 76344 Sorted by model distance: nonbonded pdb=" OG SER C 155 " pdb=" OE2 GLU D 282 " model vdw 2.537 3.040 nonbonded pdb=" O PRO A 262 " pdb=" OG1 THR A 265 " model vdw 2.540 3.040 nonbonded pdb=" OE2 GLU D 123 " pdb=" OH TYR D 155 " model vdw 2.544 3.040 nonbonded pdb=" OD2 ASP C 15 " pdb=" OG SER C 17 " model vdw 2.563 3.040 nonbonded pdb=" OG1 THR D 245 " pdb=" OD1 ASP D 247 " model vdw 2.565 3.040 ... (remaining 76339 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: 4.920 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.172 9836 Z= 1.030 Angle : 1.993 15.450 13395 Z= 1.339 Chirality : 0.167 0.713 1549 Planarity : 0.014 0.131 1703 Dihedral : 12.910 159.818 3662 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 3.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1227 helix: -0.29 (0.18), residues: 674 sheet: 0.14 (0.57), residues: 78 loop : -0.18 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 62 TYR 0.090 0.015 TYR B 96 PHE 0.052 0.011 PHE C 70 TRP 0.142 0.022 TRP A 293 HIS 0.015 0.003 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.01828 / 1.03 ( 9828) covalent geometry : angle 1.98030 / 1.34 (13371) hydrogen bonds : bond 0.16931 / 11.69 ( 545) hydrogen bonds : angle 6.70539 / 4.93 ( 1563) metal coordination : bond 0.11906 / 6.35 ( 8) metal coordination : angle 5.69532 / 4.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 24 PHE cc_start: 0.6113 (t80) cc_final: 0.5722 (t80) REVERT: A 29 MET cc_start: 0.7246 (mmt) cc_final: 0.6586 (mpp) REVERT: A 74 MET cc_start: 0.6998 (mmm) cc_final: 0.6566 (mmm) REVERT: A 86 ILE cc_start: 0.7221 (mt) cc_final: 0.6876 (mp) REVERT: A 145 ILE cc_start: 0.7772 (mt) cc_final: 0.7572 (mm) REVERT: A 184 PHE cc_start: 0.5568 (m-80) cc_final: 0.4676 (m-80) REVERT: A 200 ASP cc_start: 0.6836 (t70) cc_final: 0.6391 (t0) REVERT: A 248 MET cc_start: 0.6631 (tpp) cc_final: 0.6411 (tpp) REVERT: A 260 MET cc_start: 0.6608 (mmt) cc_final: 0.6338 (mmt) REVERT: B 27 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7168 (mtpt) REVERT: B 131 ASP cc_start: 0.7100 (t70) cc_final: 0.6622 (t70) REVERT: B 181 ARG cc_start: 0.6943 (tmt170) cc_final: 0.6663 (tpt90) REVERT: B 204 MET cc_start: 0.7084 (mmt) cc_final: 0.6482 (mmt) REVERT: C 5 ASN cc_start: 0.7537 (t0) cc_final: 0.7327 (t0) REVERT: C 25 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6728 (mtm110) REVERT: C 67 LYS cc_start: 0.6864 (tttt) cc_final: 0.6459 (tttt) REVERT: C 117 LYS cc_start: 0.7037 (tttt) cc_final: 0.6780 (tttt) REVERT: C 128 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6880 (mtp85) REVERT: C 194 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6862 (mt-10) REVERT: C 198 GLU cc_start: 0.6691 (tt0) cc_final: 0.6435 (tt0) REVERT: C 202 LYS cc_start: 0.7588 (ttpp) cc_final: 0.7289 (ttpp) REVERT: C 227 MET cc_start: 0.8161 (mmm) cc_final: 0.7901 (mmm) REVERT: D 46 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6935 (mm-30) REVERT: D 73 MET cc_start: 0.7855 (mmm) cc_final: 0.7333 (mmm) REVERT: D 82 GLN cc_start: 0.7832 (mt0) cc_final: 0.7503 (mt0) REVERT: D 100 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6884 (mmtm) REVERT: D 134 LYS cc_start: 0.6846 (tttt) cc_final: 0.6641 (tttt) REVERT: D 156 ASP cc_start: 0.7420 (m-30) cc_final: 0.7145 (m-30) REVERT: D 177 MET cc_start: 0.7711 (mmm) cc_final: 0.7294 (mmm) REVERT: D 197 ARG cc_start: 0.7080 (ttm170) cc_final: 0.6761 (mtp-110) REVERT: D 221 ASP cc_start: 0.6606 (t0) cc_final: 0.6116 (t0) REVERT: D 231 GLU cc_start: 0.7474 (tt0) cc_final: 0.7066 (tt0) REVERT: D 243 LYS cc_start: 0.7885 (tttm) cc_final: 0.7516 (ttmm) outliers start: 1 outliers final: 1 residues processed: 295 average time/residue: 0.6579 time to fit residues: 204.5710 Evaluate side-chains 270 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 GLN C 12 HIS C 73 GLN D 106 GLN D 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108100 restraints weight = 12455.857| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.00 r_work: 0.3227 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9836 Z= 0.174 Angle : 0.655 10.628 13395 Z= 0.320 Chirality : 0.045 0.166 1549 Planarity : 0.005 0.042 1703 Dihedral : 9.435 161.167 1380 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.04 % Allowed : 6.52 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1227 helix: 1.37 (0.20), residues: 681 sheet: 0.02 (0.53), residues: 97 loop : -0.21 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 85 TYR 0.014 0.002 TYR B 192 PHE 0.016 0.002 PHE D 303 TRP 0.030 0.002 TRP A 293 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 9828) covalent geometry : angle 0.61784 / 0.32 (13371) hydrogen bonds : bond 0.04902 / 3.37 ( 545) hydrogen bonds : angle 4.76415 / 3.49 ( 1563) metal coordination : bond 0.00717 / 0.31 ( 8) metal coordination : angle 5.14573 / 3.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 24 PHE cc_start: 0.7986 (t80) cc_final: 0.7614 (t80) REVERT: A 74 MET cc_start: 0.7184 (mmm) cc_final: 0.6776 (mmm) REVERT: A 86 ILE cc_start: 0.8568 (mt) cc_final: 0.8280 (mp) REVERT: A 155 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7526 (tp) REVERT: A 200 ASP cc_start: 0.7907 (t70) cc_final: 0.7607 (t0) REVERT: A 235 ASP cc_start: 0.7679 (m-30) cc_final: 0.7475 (m-30) REVERT: A 248 MET cc_start: 0.7930 (tpp) cc_final: 0.7714 (tpp) REVERT: B 27 LYS cc_start: 0.8539 (mtpt) cc_final: 0.8279 (mtpt) REVERT: B 131 ASP cc_start: 0.8004 (t70) cc_final: 0.7676 (t0) REVERT: B 204 MET cc_start: 0.8139 (mmt) cc_final: 0.7696 (mmt) REVERT: B 216 LEU cc_start: 0.7877 (tp) cc_final: 0.7614 (tt) REVERT: C 74 ASP cc_start: 0.7568 (t0) cc_final: 0.7174 (t70) REVERT: C 130 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7671 (tmt170) REVERT: C 194 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7352 (mt-10) REVERT: C 198 GLU cc_start: 0.7665 (tt0) cc_final: 0.7422 (tt0) REVERT: C 216 LEU cc_start: 0.7776 (tp) cc_final: 0.7562 (tt) REVERT: D 86 LEU cc_start: 0.8195 (mt) cc_final: 0.7983 (mp) REVERT: D 115 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7778 (tpp80) REVERT: D 151 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7258 (mtmt) REVERT: D 177 MET cc_start: 0.8411 (mmm) cc_final: 0.8137 (mmm) REVERT: D 211 LEU cc_start: 0.7687 (mt) cc_final: 0.7484 (mp) REVERT: D 221 ASP cc_start: 0.7012 (t0) cc_final: 0.6388 (t0) REVERT: D 273 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7630 (mtm-85) outliers start: 21 outliers final: 10 residues processed: 278 average time/residue: 0.6797 time to fit residues: 199.8536 Evaluate side-chains 265 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 0.0000 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN C 179 GLN D 102 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110711 restraints weight = 12436.134| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.57 r_work: 0.3293 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9836 Z= 0.176 Angle : 0.616 10.505 13395 Z= 0.295 Chirality : 0.043 0.167 1549 Planarity : 0.004 0.039 1703 Dihedral : 8.921 158.802 1380 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.14 % Allowed : 10.12 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1227 helix: 1.66 (0.20), residues: 683 sheet: 0.06 (0.54), residues: 88 loop : -0.40 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.013 0.001 TYR B 192 PHE 0.015 0.002 PHE D 303 TRP 0.024 0.002 TRP A 293 HIS 0.004 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 ( 9828) covalent geometry : angle 0.57937 / 0.29 (13371) hydrogen bonds : bond 0.04583 / 3.16 ( 545) hydrogen bonds : angle 4.53222 / 3.32 ( 1563) metal coordination : bond 0.00611 / 0.26 ( 8) metal coordination : angle 4.96359 / 3.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7092 (mmm) cc_final: 0.6708 (mmm) REVERT: A 248 MET cc_start: 0.7810 (tpp) cc_final: 0.7603 (tpp) REVERT: A 325 ASP cc_start: 0.7008 (m-30) cc_final: 0.6784 (m-30) REVERT: B 27 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8299 (mtpt) REVERT: B 131 ASP cc_start: 0.7828 (t70) cc_final: 0.7586 (t0) REVERT: B 204 MET cc_start: 0.8027 (mmt) cc_final: 0.7588 (mmt) REVERT: B 216 LEU cc_start: 0.7907 (tp) cc_final: 0.7655 (tt) REVERT: B 294 LEU cc_start: 0.7778 (mm) cc_final: 0.7561 (mp) REVERT: C 24 ASP cc_start: 0.7958 (t0) cc_final: 0.7730 (t70) REVERT: C 74 ASP cc_start: 0.7506 (t0) cc_final: 0.7166 (t70) REVERT: C 194 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 198 GLU cc_start: 0.7490 (tt0) cc_final: 0.7230 (tt0) REVERT: C 216 LEU cc_start: 0.7753 (tp) cc_final: 0.7552 (tt) REVERT: D 86 LEU cc_start: 0.8223 (mt) cc_final: 0.8008 (mp) REVERT: D 106 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: D 151 LYS cc_start: 0.7415 (mtmt) cc_final: 0.7186 (mtmt) REVERT: D 177 MET cc_start: 0.8411 (mmm) cc_final: 0.8138 (mmm) REVERT: D 221 ASP cc_start: 0.6930 (t0) cc_final: 0.6356 (t0) outliers start: 22 outliers final: 12 residues processed: 275 average time/residue: 0.6746 time to fit residues: 196.7576 Evaluate side-chains 273 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.0000 chunk 82 optimal weight: 0.6980 overall best weight: 0.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN D 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114020 restraints weight = 12576.295| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.42 r_work: 0.3354 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9836 Z= 0.105 Angle : 0.555 8.780 13395 Z= 0.259 Chirality : 0.040 0.143 1549 Planarity : 0.004 0.039 1703 Dihedral : 8.664 159.611 1380 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.43 % Allowed : 11.28 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1227 helix: 1.97 (0.20), residues: 686 sheet: 0.00 (0.55), residues: 88 loop : -0.38 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 115 TYR 0.009 0.001 TYR A 236 PHE 0.024 0.001 PHE A 109 TRP 0.019 0.001 TRP A 293 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 9828) covalent geometry : angle 0.51641 / 0.26 (13371) hydrogen bonds : bond 0.03765 / 2.59 ( 545) hydrogen bonds : angle 4.33170 / 3.18 ( 1563) metal coordination : bond 0.00278 / 0.13 ( 8) metal coordination : angle 4.83106 / 3.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.357 Fit side-chains REVERT: A 24 PHE cc_start: 0.8439 (t80) cc_final: 0.8087 (t80) REVERT: A 74 MET cc_start: 0.6974 (mmm) cc_final: 0.6675 (mmm) REVERT: A 325 ASP cc_start: 0.7247 (m-30) cc_final: 0.7043 (m-30) REVERT: B 204 MET cc_start: 0.7957 (mmt) cc_final: 0.7648 (mmt) REVERT: C 74 ASP cc_start: 0.7341 (t0) cc_final: 0.7139 (t0) REVERT: C 198 GLU cc_start: 0.7611 (tt0) cc_final: 0.7374 (tt0) REVERT: D 115 ARG cc_start: 0.7723 (tpp80) cc_final: 0.7146 (tpp80) REVERT: D 177 MET cc_start: 0.8448 (mmm) cc_final: 0.7848 (mmm) REVERT: D 221 ASP cc_start: 0.6869 (t0) cc_final: 0.6510 (t0) REVERT: D 327 ASP cc_start: 0.7843 (t0) cc_final: 0.7634 (t0) outliers start: 25 outliers final: 13 residues processed: 282 average time/residue: 0.6594 time to fit residues: 197.4034 Evaluate side-chains 279 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 266 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 47 optimal weight: 0.0070 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 137 GLN C 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113518 restraints weight = 12520.049| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.43 r_work: 0.3343 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9836 Z= 0.130 Angle : 0.592 11.353 13395 Z= 0.268 Chirality : 0.041 0.148 1549 Planarity : 0.004 0.040 1703 Dihedral : 8.600 159.283 1380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.63 % Allowed : 12.65 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1227 helix: 2.09 (0.20), residues: 679 sheet: 0.14 (0.56), residues: 87 loop : -0.36 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 300 TYR 0.016 0.001 TYR D 155 PHE 0.019 0.001 PHE A 109 TRP 0.018 0.001 TRP A 293 HIS 0.004 0.001 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 9828) covalent geometry : angle 0.55546 / 0.27 (13371) hydrogen bonds : bond 0.03896 / 2.69 ( 545) hydrogen bonds : angle 4.28642 / 3.15 ( 1563) metal coordination : bond 0.00386 / 0.16 ( 8) metal coordination : angle 4.85172 / 3.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.372 Fit side-chains REVERT: A 24 PHE cc_start: 0.8407 (t80) cc_final: 0.8056 (t80) REVERT: A 74 MET cc_start: 0.6961 (mmm) cc_final: 0.6668 (mmm) REVERT: A 325 ASP cc_start: 0.7298 (m-30) cc_final: 0.7094 (m-30) REVERT: B 204 MET cc_start: 0.7946 (mmt) cc_final: 0.7640 (mmt) REVERT: C 198 GLU cc_start: 0.7536 (tt0) cc_final: 0.7321 (tt0) REVERT: C 201 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: D 73 MET cc_start: 0.7999 (mmm) cc_final: 0.7509 (mmm) REVERT: D 177 MET cc_start: 0.8460 (mmm) cc_final: 0.7837 (mmm) REVERT: D 221 ASP cc_start: 0.6853 (t0) cc_final: 0.6502 (t0) REVERT: D 327 ASP cc_start: 0.7860 (t0) cc_final: 0.7639 (t0) outliers start: 27 outliers final: 17 residues processed: 274 average time/residue: 0.6959 time to fit residues: 201.9353 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN C 73 GLN C 137 GLN C 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110894 restraints weight = 12452.129| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.60 r_work: 0.3303 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9836 Z= 0.218 Angle : 0.630 9.888 13395 Z= 0.292 Chirality : 0.044 0.161 1549 Planarity : 0.004 0.041 1703 Dihedral : 8.642 157.580 1380 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 14.30 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1227 helix: 1.98 (0.20), residues: 672 sheet: 0.09 (0.56), residues: 87 loop : -0.30 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 146 TYR 0.018 0.002 TYR D 155 PHE 0.019 0.002 PHE A 109 TRP 0.019 0.002 TRP A 293 HIS 0.004 0.001 HIS D 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.22 ( 9828) covalent geometry : angle 0.59426 / 0.29 (13371) hydrogen bonds : bond 0.04464 / 3.08 ( 545) hydrogen bonds : angle 4.37809 / 3.22 ( 1563) metal coordination : bond 0.00722 / 0.30 ( 8) metal coordination : angle 4.95668 / 3.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.370 Fit side-chains REVERT: A 24 PHE cc_start: 0.7992 (t80) cc_final: 0.7628 (t80) REVERT: A 29 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7392 (mpp) REVERT: A 74 MET cc_start: 0.7079 (mmm) cc_final: 0.6717 (mmm) REVERT: A 77 ASP cc_start: 0.7478 (t0) cc_final: 0.7034 (t0) REVERT: A 247 ARG cc_start: 0.7270 (tpm170) cc_final: 0.7040 (tpm170) REVERT: A 325 ASP cc_start: 0.7229 (m-30) cc_final: 0.7002 (m-30) REVERT: B 204 MET cc_start: 0.7953 (mmt) cc_final: 0.7486 (mmt) REVERT: C 198 GLU cc_start: 0.7493 (tt0) cc_final: 0.7255 (tt0) REVERT: D 176 LEU cc_start: 0.8793 (mt) cc_final: 0.8561 (mp) REVERT: D 221 ASP cc_start: 0.6920 (t0) cc_final: 0.6372 (t0) REVERT: D 239 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.8147 (mtp180) REVERT: D 327 ASP cc_start: 0.7988 (t0) cc_final: 0.7713 (t0) outliers start: 25 outliers final: 13 residues processed: 278 average time/residue: 0.6981 time to fit residues: 205.6463 Evaluate side-chains 281 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112164 restraints weight = 12363.358| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.59 r_work: 0.3336 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9836 Z= 0.141 Angle : 0.595 9.124 13395 Z= 0.273 Chirality : 0.041 0.150 1549 Planarity : 0.004 0.041 1703 Dihedral : 8.568 157.234 1380 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.43 % Allowed : 15.56 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1227 helix: 2.12 (0.20), residues: 674 sheet: 0.09 (0.57), residues: 87 loop : -0.31 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 62 TYR 0.016 0.001 TYR D 155 PHE 0.018 0.001 PHE A 109 TRP 0.018 0.001 TRP A 293 HIS 0.002 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 9828) covalent geometry : angle 0.55838 / 0.27 (13371) hydrogen bonds : bond 0.03994 / 2.75 ( 545) hydrogen bonds : angle 4.28988 / 3.16 ( 1563) metal coordination : bond 0.00430 / 0.19 ( 8) metal coordination : angle 4.86941 / 3.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 0.369 Fit side-chains REVERT: A 20 THR cc_start: 0.8133 (m) cc_final: 0.7720 (p) REVERT: A 24 PHE cc_start: 0.8047 (t80) cc_final: 0.7672 (t80) REVERT: A 74 MET cc_start: 0.7091 (mmm) cc_final: 0.6752 (mmm) REVERT: A 77 ASP cc_start: 0.7504 (t0) cc_final: 0.7094 (t0) REVERT: A 247 ARG cc_start: 0.7253 (tpm170) cc_final: 0.7042 (tpm170) REVERT: A 325 ASP cc_start: 0.7263 (m-30) cc_final: 0.7043 (m-30) REVERT: B 204 MET cc_start: 0.7902 (mmt) cc_final: 0.7444 (mmt) REVERT: C 198 GLU cc_start: 0.7456 (tt0) cc_final: 0.7253 (tt0) REVERT: C 201 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: D 176 LEU cc_start: 0.8777 (mt) cc_final: 0.8570 (mp) REVERT: D 221 ASP cc_start: 0.6875 (t0) cc_final: 0.6361 (t0) REVERT: D 239 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8130 (mtp180) REVERT: D 327 ASP cc_start: 0.7964 (t0) cc_final: 0.7682 (t0) outliers start: 25 outliers final: 20 residues processed: 276 average time/residue: 0.6874 time to fit residues: 201.0213 Evaluate side-chains 287 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 266 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 47 optimal weight: 0.0370 chunk 88 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 GLN D 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112973 restraints weight = 12337.877| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.59 r_work: 0.3328 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9836 Z= 0.113 Angle : 0.585 9.152 13395 Z= 0.266 Chirality : 0.040 0.144 1549 Planarity : 0.004 0.042 1703 Dihedral : 8.518 157.599 1380 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 16.25 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1227 helix: 2.29 (0.20), residues: 667 sheet: 0.10 (0.57), residues: 87 loop : -0.23 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 62 TYR 0.015 0.001 TYR D 155 PHE 0.017 0.001 PHE A 109 TRP 0.016 0.001 TRP A 293 HIS 0.002 0.000 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 9828) covalent geometry : angle 0.54671 / 0.27 (13371) hydrogen bonds : bond 0.03777 / 2.60 ( 545) hydrogen bonds : angle 4.23282 / 3.11 ( 1563) metal coordination : bond 0.00316 / 0.14 ( 8) metal coordination : angle 4.93727 / 3.42 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.338 Fit side-chains REVERT: A 20 THR cc_start: 0.8091 (m) cc_final: 0.7669 (p) REVERT: A 24 PHE cc_start: 0.8017 (t80) cc_final: 0.7678 (t80) REVERT: A 74 MET cc_start: 0.7080 (mmm) cc_final: 0.6741 (mmm) REVERT: A 77 ASP cc_start: 0.7511 (t0) cc_final: 0.7101 (t0) REVERT: A 247 ARG cc_start: 0.7273 (tpm170) cc_final: 0.7049 (tpm170) REVERT: A 325 ASP cc_start: 0.7276 (m-30) cc_final: 0.7056 (m-30) REVERT: B 142 LEU cc_start: 0.8869 (mt) cc_final: 0.8661 (mt) REVERT: B 204 MET cc_start: 0.7931 (mmt) cc_final: 0.7468 (mmt) REVERT: C 198 GLU cc_start: 0.7534 (tt0) cc_final: 0.7311 (tt0) REVERT: C 201 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: C 216 LEU cc_start: 0.7721 (tp) cc_final: 0.7501 (tt) REVERT: C 306 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8008 (tpp) REVERT: D 206 ASP cc_start: 0.7163 (m-30) cc_final: 0.6690 (m-30) REVERT: D 221 ASP cc_start: 0.6806 (t0) cc_final: 0.6300 (t0) REVERT: D 239 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.8136 (mtp180) REVERT: D 327 ASP cc_start: 0.7962 (t0) cc_final: 0.7691 (t0) outliers start: 25 outliers final: 15 residues processed: 280 average time/residue: 0.6468 time to fit residues: 192.1051 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 57 optimal weight: 0.0070 chunk 116 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112198 restraints weight = 12227.714| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.58 r_work: 0.3310 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9836 Z= 0.155 Angle : 0.604 9.441 13395 Z= 0.278 Chirality : 0.042 0.149 1549 Planarity : 0.004 0.043 1703 Dihedral : 8.520 156.964 1380 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.33 % Allowed : 16.44 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1227 helix: 2.23 (0.20), residues: 667 sheet: 0.02 (0.57), residues: 87 loop : -0.24 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 62 TYR 0.016 0.001 TYR D 155 PHE 0.029 0.002 PHE A 109 TRP 0.016 0.001 TRP A 293 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 9828) covalent geometry : angle 0.56728 / 0.28 (13371) hydrogen bonds : bond 0.04031 / 2.78 ( 545) hydrogen bonds : angle 4.27187 / 3.14 ( 1563) metal coordination : bond 0.00507 / 0.21 ( 8) metal coordination : angle 4.96535 / 3.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.376 Fit side-chains REVERT: A 20 THR cc_start: 0.8059 (m) cc_final: 0.7641 (p) REVERT: A 74 MET cc_start: 0.7112 (mmm) cc_final: 0.6770 (mmm) REVERT: A 77 ASP cc_start: 0.7535 (t0) cc_final: 0.7131 (t0) REVERT: A 247 ARG cc_start: 0.7288 (tpm170) cc_final: 0.7038 (tpm170) REVERT: B 142 LEU cc_start: 0.8833 (mt) cc_final: 0.8612 (mt) REVERT: B 204 MET cc_start: 0.7930 (mmt) cc_final: 0.7443 (mmt) REVERT: C 198 GLU cc_start: 0.7461 (tt0) cc_final: 0.7245 (tt0) REVERT: C 201 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7363 (mt0) REVERT: C 216 LEU cc_start: 0.7600 (tp) cc_final: 0.7385 (tt) REVERT: D 206 ASP cc_start: 0.7180 (m-30) cc_final: 0.6683 (m-30) REVERT: D 221 ASP cc_start: 0.6868 (t0) cc_final: 0.6340 (t0) REVERT: D 239 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8146 (mtp180) REVERT: D 327 ASP cc_start: 0.7970 (t0) cc_final: 0.7696 (t0) outliers start: 24 outliers final: 19 residues processed: 272 average time/residue: 0.6008 time to fit residues: 173.5457 Evaluate side-chains 280 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 95 optimal weight: 0.0050 chunk 72 optimal weight: 0.0020 chunk 101 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113428 restraints weight = 12260.925| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.58 r_work: 0.3354 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9836 Z= 0.111 Angle : 0.592 10.095 13395 Z= 0.271 Chirality : 0.040 0.143 1549 Planarity : 0.004 0.041 1703 Dihedral : 8.492 157.395 1380 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.95 % Allowed : 16.93 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.25), residues: 1227 helix: 2.32 (0.20), residues: 667 sheet: -0.00 (0.57), residues: 88 loop : -0.17 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 62 TYR 0.014 0.001 TYR D 155 PHE 0.027 0.001 PHE A 109 TRP 0.016 0.001 TRP A 293 HIS 0.002 0.000 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9828) covalent geometry : angle 0.55354 / 0.27 (13371) hydrogen bonds : bond 0.03735 / 2.56 ( 545) hydrogen bonds : angle 4.22706 / 3.10 ( 1563) metal coordination : bond 0.00302 / 0.14 ( 8) metal coordination : angle 5.00927 / 3.48 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.362 Fit side-chains REVERT: A 20 THR cc_start: 0.8135 (m) cc_final: 0.7728 (p) REVERT: A 24 PHE cc_start: 0.8094 (t80) cc_final: 0.7744 (t80) REVERT: A 74 MET cc_start: 0.7121 (mmm) cc_final: 0.6791 (mmm) REVERT: A 77 ASP cc_start: 0.7541 (t0) cc_final: 0.7148 (t0) REVERT: A 325 ASP cc_start: 0.7377 (m-30) cc_final: 0.7142 (m-30) REVERT: B 142 LEU cc_start: 0.8928 (mt) cc_final: 0.8714 (mt) REVERT: B 204 MET cc_start: 0.7941 (mmt) cc_final: 0.7501 (mmt) REVERT: C 198 GLU cc_start: 0.7509 (tt0) cc_final: 0.7292 (tt0) REVERT: C 201 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: C 216 LEU cc_start: 0.7668 (tp) cc_final: 0.7466 (tt) REVERT: D 206 ASP cc_start: 0.7189 (m-30) cc_final: 0.6701 (m-30) REVERT: D 221 ASP cc_start: 0.6859 (t0) cc_final: 0.6362 (t0) REVERT: D 239 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.8155 (mtp180) REVERT: D 327 ASP cc_start: 0.7956 (t0) cc_final: 0.7694 (t0) outliers start: 20 outliers final: 17 residues processed: 279 average time/residue: 0.5850 time to fit residues: 173.4581 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112281 restraints weight = 12215.327| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.57 r_work: 0.3326 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9836 Z= 0.165 Angle : 0.620 9.737 13395 Z= 0.286 Chirality : 0.042 0.149 1549 Planarity : 0.004 0.040 1703 Dihedral : 8.501 156.467 1380 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.95 % Allowed : 17.61 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1227 helix: 2.23 (0.20), residues: 667 sheet: -0.06 (0.57), residues: 88 loop : -0.27 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 247 TYR 0.016 0.001 TYR D 155 PHE 0.027 0.002 PHE A 109 TRP 0.016 0.001 TRP A 293 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 9828) covalent geometry : angle 0.58383 / 0.29 (13371) hydrogen bonds : bond 0.04073 / 2.80 ( 545) hydrogen bonds : angle 4.28077 / 3.14 ( 1563) metal coordination : bond 0.00555 / 0.22 ( 8) metal coordination : angle 4.99543 / 3.40 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4172.05 seconds wall clock time: 71 minutes 39.37 seconds (4299.37 seconds total)