Starting phenix.real_space_refine on Wed Sep 17 16:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1w_39738/09_2025/8z1w_39738_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1w_39738/09_2025/8z1w_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_39738/09_2025/8z1w_39738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1w_39738/09_2025/8z1w_39738.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1w_39738/09_2025/8z1w_39738_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1w_39738/09_2025/8z1w_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-2.0-5805/lib/python3.9/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: 2.57, per 1000 atoms: 0.27 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: 0.99 Conformation dependent library (CDL) restraints added in 404.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.57 Time building geometry restraints manager: 1.28 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 - 2.59: 11051 2.59 - 5.18: 2111 5.18 - 7.77: 168 7.77 - 10.35: 36 10.35 - 12.94: 5 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=" C5 AGS D 402 " pdb=" C6 AGS D 402 " pdb=" N1 AGS D 402 " ideal model delta sigma weight residual 117.53 123.05 -5.52 7.63e-01 1.72e+00 5.23e+01 angle pdb=" C4 AGS D 402 " pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " ideal model delta sigma weight residual 110.73 113.92 -3.19 4.52e-01 4.89e+00 4.98e+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 ... (remaining 13366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.87: 5809 29.87 - 59.74: 94 59.74 - 89.60: 13 89.60 - 119.47: 0 119.47 - 149.34: 2 Dihedral angle restraints: 5918 sinusoidal: 2380 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 5915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 1291 0.143 - 0.285: 145 0.285 - 0.428: 31 0.428 - 0.570: 55 0.570 - 0.713: 29 Chirality restraints: 1551 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 1548 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: 3.880 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.180 Find NCS groups from input model: 0.080 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 1.991 15.450 13395 Z= 1.346 Chirality : 0.167 0.713 1551 Planarity : 0.014 0.131 1703 Dihedral : 12.377 149.338 3644 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 aren 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 covalent geometry : bond 0.01820 ( 9828) covalent geometry : angle 1.97813 (13371) hydrogen bonds : bond 0.16931 ( 545) hydrogen bonds : angle 6.70539 ( 1563) metal coordination : bond 0.11906 ( 8) metal coordination : angle 5.69532 ( 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 : 0.249 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: 0.7083 (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: 0.7917 time to fit residues: 245.1629 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 : 0.378 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3563 r_free = 0.3563 target = 0.123462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108092 restraints weight = 12471.572| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.00 r_work: 0.3226 rms_B_bonded: 2.42 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: 0.7771 moved from start: 0.1815 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= 0.176 Angle : 0.652 10.768 13395 Z= 0.320 Chirality : 0.045 0.167 1551 Planarity : 0.005 0.043 1703 Dihedral : 8.342 145.360 1362 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.82 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 aren not related in a simple way. whole: 0.93 (0.24), residues: 1227 helix: 1.35 (0.20), residues: 677 sheet: 0.01 (0.53), residues: 97 loop : -0.27 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 146 TYR 0.013 0.001 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 covalent geometry : bond 0.00422 ( 9828) covalent geometry : angle 0.61568 (13371) hydrogen bonds : bond 0.04934 ( 545) hydrogen bonds : angle 4.77719 ( 1563) metal coordination : bond 0.00860 ( 8) metal coordination : angle 5.11778 ( 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 298 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 24 PHE cc_start: 0.8002 (t80) cc_final: 0.7633 (t80) REVERT: A 74 MET cc_start: 0.7189 (mmm) cc_final: 0.6778 (mmm) REVERT: A 86 ILE cc_start: 0.8570 (mt) cc_final: 0.8276 (mp) REVERT: A 155 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 200 ASP cc_start: 0.7909 (t70) cc_final: 0.7610 (t0) REVERT: A 235 ASP cc_start: 0.7660 (m-30) cc_final: 0.7455 (m-30) REVERT: A 248 MET cc_start: 0.7918 (tpp) cc_final: 0.7695 (tpp) REVERT: B 27 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8282 (mtpt) REVERT: B 131 ASP cc_start: 0.8031 (t70) cc_final: 0.7710 (t0) REVERT: B 216 LEU cc_start: 0.7870 (tp) cc_final: 0.7598 (tt) REVERT: C 67 LYS cc_start: 0.7360 (tttt) cc_final: 0.7117 (tttt) REVERT: C 74 ASP cc_start: 0.7563 (t0) cc_final: 0.7165 (t70) REVERT: C 194 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 198 GLU cc_start: 0.7652 (tt0) cc_final: 0.7409 (tt0) REVERT: C 202 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8102 (ttpp) REVERT: C 216 LEU cc_start: 0.7782 (tp) cc_final: 0.7571 (tt) REVERT: D 86 LEU cc_start: 0.8193 (mt) cc_final: 0.7984 (mp) REVERT: D 115 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7782 (tpp80) REVERT: D 151 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7249 (mtmt) REVERT: D 177 MET cc_start: 0.8413 (mmm) cc_final: 0.8135 (mmm) REVERT: D 221 ASP cc_start: 0.7006 (t0) cc_final: 0.6387 (t0) REVERT: D 273 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7642 (mtm-85) outliers start: 21 outliers final: 11 residues processed: 286 average time/residue: 0.7837 time to fit residues: 236.2454 Evaluate side-chains 281 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU 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: 0.9980 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3587 r_free = 0.3587 target = 0.124725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111521 restraints weight = 12445.243| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.57 r_work: 0.3303 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2209 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 : 0.598 9.561 13395 Z= 0.286 Chirality : 0.042 0.156 1551 Planarity : 0.004 0.037 1703 Dihedral : 7.899 146.464 1362 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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 aren not related in a simple way. whole: 1.28 (0.24), residues: 1227 helix: 1.74 (0.20), residues: 684 sheet: 0.06 (0.54), residues: 88 loop : -0.30 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.011 0.001 TYR B 192 PHE 0.014 0.001 PHE D 303 TRP 0.024 0.002 TRP A 293 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9828) covalent geometry : angle 0.56304 (13371) hydrogen bonds : bond 0.04308 ( 545) hydrogen bonds : angle 4.50251 ( 1563) metal coordination : bond 0.00438 ( 8) metal coordination : angle 4.79712 ( 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 296 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7052 (mmm) cc_final: 0.6669 (mmm) REVERT: A 235 ASP cc_start: 0.7555 (m-30) cc_final: 0.7349 (m-30) REVERT: A 248 MET cc_start: 0.7787 (tpp) cc_final: 0.7573 (tpp) REVERT: A 325 ASP cc_start: 0.6983 (m-30) cc_final: 0.6754 (m-30) REVERT: B 27 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8298 (mtpt) REVERT: B 131 ASP cc_start: 0.7821 (t70) cc_final: 0.7574 (t0) REVERT: B 204 MET cc_start: 0.7999 (mmt) cc_final: 0.7557 (mmt) REVERT: B 216 LEU cc_start: 0.7851 (tp) cc_final: 0.7602 (tt) REVERT: B 294 LEU cc_start: 0.7771 (mm) cc_final: 0.7551 (mp) REVERT: C 24 ASP cc_start: 0.7960 (t0) cc_final: 0.7740 (t70) REVERT: C 74 ASP cc_start: 0.7495 (t0) cc_final: 0.7145 (t0) REVERT: C 130 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6532 (mmt180) REVERT: C 194 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 198 GLU cc_start: 0.7498 (tt0) cc_final: 0.7239 (tt0) REVERT: D 86 LEU cc_start: 0.8195 (mt) cc_final: 0.7975 (mp) REVERT: D 106 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: D 151 LYS cc_start: 0.7410 (mtmt) cc_final: 0.7176 (mtmt) REVERT: D 177 MET cc_start: 0.8391 (mmm) cc_final: 0.7779 (mmm) REVERT: D 221 ASP cc_start: 0.6929 (t0) cc_final: 0.6338 (t0) outliers start: 22 outliers final: 11 residues processed: 280 average time/residue: 0.7605 time to fit residues: 224.4662 Evaluate side-chains 278 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 221 VAL Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 130 ARG 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: 0.9980 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.0060 chunk 82 optimal weight: 0.7980 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.126368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113520 restraints weight = 12593.661| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.51 r_work: 0.3338 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9836 Z= 0.101 Angle : 0.553 8.858 13395 Z= 0.257 Chirality : 0.040 0.143 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.577 147.612 1362 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.85 % Allowed : 12.16 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.25), residues: 1227 helix: 2.07 (0.20), residues: 686 sheet: 0.14 (0.56), residues: 87 loop : -0.28 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.008 0.001 TYR A 236 PHE 0.024 0.001 PHE A 109 TRP 0.018 0.001 TRP A 293 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9828) covalent geometry : angle 0.51440 (13371) hydrogen bonds : bond 0.03589 ( 545) hydrogen bonds : angle 4.27789 ( 1563) metal coordination : bond 0.00244 ( 8) metal coordination : angle 4.84976 ( 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: 19 poor density : 280 time to evaluate : 0.402 Fit side-chains REVERT: A 24 PHE cc_start: 0.8133 (t80) cc_final: 0.7757 (t80) REVERT: A 74 MET cc_start: 0.7044 (mmm) cc_final: 0.6688 (mmm) REVERT: A 248 MET cc_start: 0.7812 (tpp) cc_final: 0.7594 (tpp) REVERT: A 325 ASP cc_start: 0.7154 (m-30) cc_final: 0.6936 (m-30) REVERT: B 27 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8361 (mtpt) REVERT: B 204 MET cc_start: 0.7999 (mmt) cc_final: 0.7574 (mmt) REVERT: B 294 LEU cc_start: 0.7789 (mm) cc_final: 0.7586 (mp) REVERT: C 74 ASP cc_start: 0.7444 (t0) cc_final: 0.7127 (t0) REVERT: C 130 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: C 194 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 198 GLU cc_start: 0.7510 (tt0) cc_final: 0.7266 (tt0) REVERT: D 73 MET cc_start: 0.8135 (mmm) cc_final: 0.7595 (mmm) REVERT: D 102 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: D 177 MET cc_start: 0.8389 (mmm) cc_final: 0.7881 (mmm) REVERT: D 221 ASP cc_start: 0.6838 (t0) cc_final: 0.6326 (t0) REVERT: D 239 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8111 (mtp180) REVERT: D 327 ASP cc_start: 0.7933 (t0) cc_final: 0.7702 (t0) outliers start: 19 outliers final: 11 residues processed: 287 average time/residue: 0.7332 time to fit residues: 222.0792 Evaluate side-chains 284 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 130 ARG Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 102 GLN 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: 2.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3582 r_free = 0.3582 target = 0.124229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111440 restraints weight = 12532.396| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.50 r_work: 0.3319 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9836 Z= 0.165 Angle : 0.610 11.884 13395 Z= 0.281 Chirality : 0.042 0.151 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.589 151.218 1362 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.72 % Allowed : 12.74 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.24), residues: 1227 helix: 2.12 (0.20), residues: 671 sheet: 0.04 (0.56), residues: 88 loop : -0.28 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 115 TYR 0.016 0.001 TYR D 155 PHE 0.019 0.002 PHE A 109 TRP 0.019 0.001 TRP A 293 HIS 0.004 0.001 HIS D 154 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9828) covalent geometry : angle 0.57306 (13371) hydrogen bonds : bond 0.04173 ( 545) hydrogen bonds : angle 4.32401 ( 1563) metal coordination : bond 0.00577 ( 8) metal coordination : angle 4.94473 ( 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 296 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.384 Fit side-chains REVERT: A 74 MET cc_start: 0.7011 (mmm) cc_final: 0.6656 (mmm) REVERT: A 130 ASP cc_start: 0.7928 (t0) cc_final: 0.7711 (t0) REVERT: A 248 MET cc_start: 0.7782 (tpp) cc_final: 0.7561 (tpp) REVERT: A 325 ASP cc_start: 0.7144 (m-30) cc_final: 0.6893 (m-30) REVERT: B 27 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8309 (mtpt) REVERT: B 204 MET cc_start: 0.7974 (mmt) cc_final: 0.7534 (mmt) REVERT: C 74 ASP cc_start: 0.7468 (t0) cc_final: 0.7156 (t70) REVERT: C 171 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7087 (mtm180) REVERT: C 194 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7229 (mt-10) REVERT: C 198 GLU cc_start: 0.7423 (tt0) cc_final: 0.7184 (tt0) REVERT: C 201 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: C 216 LEU cc_start: 0.7830 (tp) cc_final: 0.7617 (tt) REVERT: D 73 MET cc_start: 0.8136 (mmm) cc_final: 0.7608 (mmm) REVERT: D 134 LYS cc_start: 0.7333 (tttp) cc_final: 0.7107 (tttp) REVERT: D 177 MET cc_start: 0.8403 (mmm) cc_final: 0.7793 (mmm) REVERT: D 221 ASP cc_start: 0.6832 (t0) cc_final: 0.6289 (t0) REVERT: D 239 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.8084 (mtp180) REVERT: D 327 ASP cc_start: 0.7927 (t0) cc_final: 0.7669 (t0) outliers start: 28 outliers final: 13 residues processed: 275 average time/residue: 0.7406 time to fit residues: 214.7165 Evaluate side-chains 278 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 163 MET Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain D residue 17 ASP 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: 4.9990 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN C 73 GLN C 201 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 = 0.3568 r_free = 0.3568 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108550 restraints weight = 12556.277| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.99 r_work: 0.3172 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2763 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= 0.152 Angle : 0.592 9.396 13395 Z= 0.273 Chirality : 0.042 0.150 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.563 153.237 1362 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.53 % Allowed : 14.79 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.24), residues: 1227 helix: 2.09 (0.20), residues: 681 sheet: 0.14 (0.56), residues: 87 loop : -0.32 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 115 TYR 0.015 0.001 TYR D 155 PHE 0.018 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 covalent geometry : bond 0.00376 ( 9828) covalent geometry : angle 0.55459 (13371) hydrogen bonds : bond 0.04042 ( 545) hydrogen bonds : angle 4.30917 ( 1563) metal coordination : bond 0.00475 ( 8) metal coordination : angle 4.92579 ( 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 286 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.438 Fit side-chains REVERT: A 20 THR cc_start: 0.8085 (m) cc_final: 0.7657 (p) REVERT: A 74 MET cc_start: 0.7151 (mmm) cc_final: 0.6776 (mmm) REVERT: A 77 ASP cc_start: 0.7537 (t0) cc_final: 0.7102 (t0) REVERT: A 130 ASP cc_start: 0.7969 (t0) cc_final: 0.7735 (t0) REVERT: A 247 ARG cc_start: 0.7461 (tpm170) cc_final: 0.7082 (tpm170) REVERT: A 248 MET cc_start: 0.7903 (tpp) cc_final: 0.7677 (tpp) REVERT: A 325 ASP cc_start: 0.7319 (m-30) cc_final: 0.7092 (m-30) REVERT: B 27 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8255 (mtpt) REVERT: B 204 MET cc_start: 0.8053 (mmt) cc_final: 0.7568 (mmt) REVERT: C 74 ASP cc_start: 0.7641 (t0) cc_final: 0.7310 (t0) REVERT: C 171 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7228 (mtm180) REVERT: C 194 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 198 GLU cc_start: 0.7594 (tt0) cc_final: 0.7349 (tt0) REVERT: C 216 LEU cc_start: 0.7648 (tp) cc_final: 0.7430 (tt) REVERT: C 306 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: D 73 MET cc_start: 0.8292 (mmm) cc_final: 0.7784 (mmm) REVERT: D 134 LYS cc_start: 0.7389 (tttp) cc_final: 0.7188 (tttp) REVERT: D 176 LEU cc_start: 0.8762 (mt) cc_final: 0.8552 (mp) REVERT: D 177 MET cc_start: 0.8369 (mmm) cc_final: 0.7783 (mmm) REVERT: D 221 ASP cc_start: 0.6881 (t0) cc_final: 0.6285 (t0) REVERT: D 243 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (ttmm) REVERT: D 327 ASP cc_start: 0.8094 (t0) cc_final: 0.7830 (t0) outliers start: 26 outliers final: 15 residues processed: 268 average time/residue: 0.7114 time to fit residues: 201.2723 Evaluate side-chains 279 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 C residue 163 MET Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 243 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113242 restraints weight = 12549.099| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.43 r_work: 0.3345 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9836 Z= 0.148 Angle : 0.584 9.231 13395 Z= 0.271 Chirality : 0.041 0.150 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.518 155.586 1362 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 15.27 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1227 helix: 2.12 (0.20), residues: 681 sheet: 0.16 (0.57), residues: 87 loop : -0.34 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.015 0.001 TYR D 155 PHE 0.017 0.001 PHE A 109 TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9828) covalent geometry : angle 0.54686 (13371) hydrogen bonds : bond 0.03986 ( 545) hydrogen bonds : angle 4.28166 ( 1563) metal coordination : bond 0.00457 ( 8) metal coordination : angle 4.89850 ( 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: 26 poor density : 265 time to evaluate : 0.289 Fit side-chains REVERT: A 20 THR cc_start: 0.8293 (m) cc_final: 0.7930 (p) REVERT: A 24 PHE cc_start: 0.8409 (t80) cc_final: 0.8102 (t80) REVERT: A 74 MET cc_start: 0.6975 (mmm) cc_final: 0.6708 (mmm) REVERT: A 77 ASP cc_start: 0.7315 (t0) cc_final: 0.6967 (t0) REVERT: A 248 MET cc_start: 0.7796 (tpp) cc_final: 0.7588 (tpp) REVERT: B 204 MET cc_start: 0.7951 (mmt) cc_final: 0.7629 (mmt) REVERT: C 194 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7335 (mt-10) REVERT: C 198 GLU cc_start: 0.7469 (tt0) cc_final: 0.7246 (tt0) REVERT: D 73 MET cc_start: 0.7976 (mmm) cc_final: 0.7516 (mmm) REVERT: D 102 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: D 176 LEU cc_start: 0.8954 (mt) cc_final: 0.8740 (mp) REVERT: D 221 ASP cc_start: 0.6877 (t0) cc_final: 0.6506 (t0) REVERT: D 327 ASP cc_start: 0.7815 (t0) cc_final: 0.7585 (t0) outliers start: 26 outliers final: 18 residues processed: 275 average time/residue: 0.6697 time to fit residues: 194.8118 Evaluate side-chains 281 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 102 GLN 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: 0.0970 chunk 101 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 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 = 0.3607 r_free = 0.3607 target = 0.125676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113427 restraints weight = 12477.884| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.44 r_work: 0.3345 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9836 Z= 0.140 Angle : 0.593 9.272 13395 Z= 0.274 Chirality : 0.041 0.148 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.489 157.596 1362 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.43 % Allowed : 15.76 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.24), residues: 1227 helix: 2.19 (0.20), residues: 675 sheet: 0.12 (0.57), residues: 87 loop : -0.29 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.015 0.001 TYR D 155 PHE 0.017 0.001 PHE B 170 TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9828) covalent geometry : angle 0.55564 (13371) hydrogen bonds : bond 0.03919 ( 545) hydrogen bonds : angle 4.26059 ( 1563) metal coordination : bond 0.00440 ( 8) metal coordination : angle 4.93929 ( 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 285 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.383 Fit side-chains REVERT: A 20 THR cc_start: 0.8291 (m) cc_final: 0.7933 (p) REVERT: A 24 PHE cc_start: 0.8387 (t80) cc_final: 0.8072 (t80) REVERT: A 74 MET cc_start: 0.6963 (mmm) cc_final: 0.6697 (mmm) REVERT: A 77 ASP cc_start: 0.7405 (t0) cc_final: 0.7055 (t0) REVERT: B 204 MET cc_start: 0.7936 (mmt) cc_final: 0.7614 (mmt) REVERT: C 194 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 198 GLU cc_start: 0.7480 (tt0) cc_final: 0.7263 (tt0) REVERT: D 102 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: D 176 LEU cc_start: 0.8939 (mt) cc_final: 0.8731 (mp) REVERT: D 206 ASP cc_start: 0.7181 (m-30) cc_final: 0.6815 (m-30) REVERT: D 221 ASP cc_start: 0.6800 (t0) cc_final: 0.6441 (t0) REVERT: D 327 ASP cc_start: 0.7812 (t0) cc_final: 0.7578 (t0) outliers start: 25 outliers final: 17 residues processed: 270 average time/residue: 0.7280 time to fit residues: 207.6307 Evaluate side-chains 277 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 102 GLN 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: 0.9980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.0470 chunk 106 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113907 restraints weight = 12367.642| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.44 r_work: 0.3354 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9836 Z= 0.132 Angle : 0.595 9.510 13395 Z= 0.273 Chirality : 0.041 0.146 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.462 160.005 1362 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.85 % Allowed : 16.93 % 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 aren not related in a simple way. whole: 1.71 (0.24), residues: 1227 helix: 2.24 (0.20), residues: 674 sheet: 0.01 (0.56), residues: 88 loop : -0.27 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.014 0.001 TYR D 155 PHE 0.018 0.001 PHE A 96 TRP 0.016 0.001 TRP A 293 HIS 0.002 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9828) covalent geometry : angle 0.55576 (13371) hydrogen bonds : bond 0.03847 ( 545) hydrogen bonds : angle 4.25154 ( 1563) metal coordination : bond 0.00416 ( 8) metal coordination : angle 5.01862 ( 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 281 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.434 Fit side-chains REVERT: A 20 THR cc_start: 0.8293 (m) cc_final: 0.7937 (p) REVERT: A 74 MET cc_start: 0.6952 (mmm) cc_final: 0.6695 (mmm) REVERT: A 77 ASP cc_start: 0.7402 (t0) cc_final: 0.7074 (t0) REVERT: B 204 MET cc_start: 0.7920 (mmt) cc_final: 0.7597 (mmt) REVERT: C 194 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 198 GLU cc_start: 0.7499 (tt0) cc_final: 0.7288 (tt0) REVERT: C 306 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7913 (tpp) REVERT: D 102 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: D 206 ASP cc_start: 0.7163 (m-30) cc_final: 0.6803 (m-30) REVERT: D 221 ASP cc_start: 0.6825 (t0) cc_final: 0.6457 (t0) REVERT: D 327 ASP cc_start: 0.7776 (t0) cc_final: 0.7528 (t0) outliers start: 19 outliers final: 17 residues processed: 271 average time/residue: 0.7308 time to fit residues: 209.3150 Evaluate side-chains 279 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 102 GLN 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: 0.7980 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113698 restraints weight = 12473.172| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.44 r_work: 0.3345 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9836 Z= 0.144 Angle : 0.600 9.561 13395 Z= 0.277 Chirality : 0.042 0.147 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.484 162.890 1362 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.14 % Allowed : 16.83 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.25), residues: 1227 helix: 2.28 (0.20), residues: 667 sheet: -0.03 (0.56), residues: 88 loop : -0.21 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.015 0.001 TYR D 155 PHE 0.016 0.001 PHE A 109 TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9828) covalent geometry : angle 0.56152 (13371) hydrogen bonds : bond 0.03949 ( 545) hydrogen bonds : angle 4.26779 ( 1563) metal coordination : bond 0.00463 ( 8) metal coordination : angle 5.04045 ( 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 285 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 263 time to evaluate : 0.367 Fit side-chains REVERT: A 20 THR cc_start: 0.8285 (m) cc_final: 0.7919 (p) REVERT: A 74 MET cc_start: 0.7000 (mmm) cc_final: 0.6732 (mmm) REVERT: A 77 ASP cc_start: 0.7423 (t0) cc_final: 0.7094 (t0) REVERT: B 204 MET cc_start: 0.7954 (mmt) cc_final: 0.7617 (mmt) REVERT: C 194 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 198 GLU cc_start: 0.7480 (tt0) cc_final: 0.7266 (tt0) REVERT: C 306 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7929 (tpp) REVERT: D 102 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: D 177 MET cc_start: 0.8450 (mmm) cc_final: 0.7752 (mmm) REVERT: D 206 ASP cc_start: 0.7159 (m-30) cc_final: 0.6748 (m-30) REVERT: D 221 ASP cc_start: 0.6844 (t0) cc_final: 0.6458 (t0) REVERT: D 327 ASP cc_start: 0.7783 (t0) cc_final: 0.7534 (t0) outliers start: 22 outliers final: 18 residues processed: 273 average time/residue: 0.7028 time to fit residues: 202.8405 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 : 0.384 ------------------------------------------------------------------------------- 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 57 ILE 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 217 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 102 GLN 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: 0.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 HIS C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110980 restraints weight = 12211.043| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.58 r_work: 0.3307 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9836 Z= 0.230 Angle : 0.660 10.652 13395 Z= 0.307 Chirality : 0.045 0.187 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.629 166.378 1362 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.95 % Allowed : 17.90 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1227 helix: 2.09 (0.20), residues: 667 sheet: -0.12 (0.56), residues: 87 loop : -0.38 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 115 TYR 0.017 0.002 TYR D 155 PHE 0.018 0.002 PHE B 44 TRP 0.016 0.002 TRP A 293 HIS 0.003 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9828) covalent geometry : angle 0.62327 (13371) hydrogen bonds : bond 0.04572 ( 545) hydrogen bonds : angle 4.40828 ( 1563) metal coordination : bond 0.00776 ( 8) metal coordination : angle 5.17066 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.55 seconds wall clock time: 75 minutes 37.10 seconds (4537.10 seconds total)