Starting phenix.real_space_refine on Fri Feb 14 03:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1w_39738/02_2025/8z1w_39738_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1w_39738/02_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_39738/02_2025/8z1w_39738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1w_39738/02_2025/8z1w_39738.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1w_39738/02_2025/8z1w_39738_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1w_39738/02_2025/8z1w_39738_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.82, per 1000 atoms: 0.71 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.12 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: 2.96 Time building geometry restraints manager: 2.85 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: 2.560 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.770 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- 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 : 0.018 0.144 9828 Z= 1.199 Angle : 1.978 12.943 13371 Z= 1.347 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.142 0.022 TRP A 293 HIS 0.015 0.003 HIS D 255 PHE 0.052 0.011 PHE C 70 TYR 0.090 0.015 TYR B 96 ARG 0.009 0.001 ARG C 62 *********************** 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 : 1.021 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 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: 1.6714 time to fit residues: 518.5836 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 : 1.143 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.123696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108304 restraints weight = 12406.685| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.99 r_work: 0.3229 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9828 Z= 0.249 Angle : 0.610 7.752 13371 Z= 0.318 Chirality : 0.043 0.165 1551 Planarity : 0.005 0.044 1703 Dihedral : 8.339 144.926 1362 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.04 % Allowed : 6.61 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1227 helix: 1.39 (0.20), residues: 677 sheet: 0.12 (0.53), residues: 96 loop : -0.26 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 293 HIS 0.004 0.001 HIS A 204 PHE 0.016 0.002 PHE D 303 TYR 0.013 0.001 TYR B 192 ARG 0.004 0.001 ARG C 146 *********************** 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 300 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 1.029 Fit side-chains REVERT: A 24 PHE cc_start: 0.7994 (t80) cc_final: 0.7615 (t80) REVERT: A 74 MET cc_start: 0.7177 (mmm) cc_final: 0.6769 (mmm) REVERT: A 86 ILE cc_start: 0.8563 (mt) cc_final: 0.8274 (mp) REVERT: A 155 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7518 (tp) REVERT: A 200 ASP cc_start: 0.7896 (t70) cc_final: 0.7608 (t0) REVERT: A 235 ASP cc_start: 0.7676 (m-30) cc_final: 0.7456 (m-30) REVERT: A 248 MET cc_start: 0.7891 (tpp) cc_final: 0.7666 (tpp) REVERT: B 27 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8295 (mtpt) REVERT: B 131 ASP cc_start: 0.8033 (t70) cc_final: 0.7705 (t0) REVERT: B 216 LEU cc_start: 0.7858 (tp) cc_final: 0.7589 (tt) REVERT: C 67 LYS cc_start: 0.7355 (tttt) cc_final: 0.7106 (tttt) REVERT: C 74 ASP cc_start: 0.7550 (t0) cc_final: 0.7159 (t70) REVERT: C 194 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 198 GLU cc_start: 0.7664 (tt0) cc_final: 0.7417 (tt0) REVERT: C 202 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8097 (ttpp) REVERT: C 216 LEU cc_start: 0.7769 (tp) cc_final: 0.7555 (tt) REVERT: D 86 LEU cc_start: 0.8179 (mt) cc_final: 0.7970 (mp) REVERT: D 115 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7779 (tpp80) REVERT: D 151 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7242 (mtmt) REVERT: D 221 ASP cc_start: 0.6990 (t0) cc_final: 0.6383 (t0) REVERT: D 273 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: D 327 ASP cc_start: 0.8068 (t0) cc_final: 0.7737 (t0) outliers start: 21 outliers final: 11 residues processed: 288 average time/residue: 1.5670 time to fit residues: 475.9960 Evaluate side-chains 276 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 163 MET 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 27 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.124514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111656 restraints weight = 12565.782| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.50 r_work: 0.3307 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9828 Z= 0.234 Angle : 0.566 8.293 13371 Z= 0.287 Chirality : 0.042 0.158 1551 Planarity : 0.004 0.037 1703 Dihedral : 7.879 146.479 1362 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.72 % Allowed : 10.12 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1227 helix: 1.75 (0.20), residues: 684 sheet: 0.03 (0.54), residues: 88 loop : -0.32 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 293 HIS 0.003 0.001 HIS A 254 PHE 0.018 0.001 PHE A 129 TYR 0.011 0.001 TYR B 192 ARG 0.003 0.000 ARG C 146 *********************** 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 292 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7058 (mmm) cc_final: 0.6686 (mmm) REVERT: A 95 ARG cc_start: 0.8264 (mmt90) cc_final: 0.7998 (mpt180) REVERT: A 248 MET cc_start: 0.7811 (tpp) cc_final: 0.7603 (tpp) REVERT: A 325 ASP cc_start: 0.7028 (m-30) cc_final: 0.6816 (m-30) REVERT: B 27 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8376 (mtpt) REVERT: B 131 ASP cc_start: 0.7789 (t70) cc_final: 0.7553 (t0) REVERT: B 204 MET cc_start: 0.8010 (mmt) cc_final: 0.7610 (mmt) REVERT: B 216 LEU cc_start: 0.7941 (tp) cc_final: 0.7710 (tt) REVERT: B 294 LEU cc_start: 0.7873 (mm) cc_final: 0.7636 (mp) REVERT: C 74 ASP cc_start: 0.7463 (t0) cc_final: 0.7139 (t70) REVERT: C 194 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7235 (mt-10) REVERT: C 198 GLU cc_start: 0.7546 (tt0) cc_final: 0.7293 (tt0) REVERT: D 70 MET cc_start: 0.7961 (mtm) cc_final: 0.7759 (mtm) REVERT: D 86 LEU cc_start: 0.8232 (mt) cc_final: 0.8024 (mp) REVERT: D 106 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: D 221 ASP cc_start: 0.6938 (t0) cc_final: 0.6395 (t0) outliers start: 28 outliers final: 12 residues processed: 271 average time/residue: 1.4827 time to fit residues: 424.6064 Evaluate side-chains 274 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 312 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 = 0.3575 r_free = 0.3575 target = 0.123785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110956 restraints weight = 12368.584| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.49 r_work: 0.3303 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9828 Z= 0.284 Angle : 0.562 8.198 13371 Z= 0.282 Chirality : 0.043 0.160 1551 Planarity : 0.004 0.039 1703 Dihedral : 7.692 148.088 1362 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.33 % Allowed : 11.77 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1227 helix: 1.81 (0.20), residues: 684 sheet: -0.03 (0.54), residues: 87 loop : -0.38 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 293 HIS 0.005 0.001 HIS D 154 PHE 0.014 0.002 PHE D 303 TYR 0.017 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 *********************** 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 292 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 1.058 Fit side-chains REVERT: A 24 PHE cc_start: 0.8101 (t80) cc_final: 0.7767 (t80) REVERT: A 74 MET cc_start: 0.7046 (mmm) cc_final: 0.6691 (mmm) REVERT: A 130 ASP cc_start: 0.7927 (t0) cc_final: 0.7695 (t0) REVERT: A 325 ASP cc_start: 0.7138 (m-30) cc_final: 0.6912 (m-30) REVERT: B 27 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 204 MET cc_start: 0.8013 (mmt) cc_final: 0.7590 (mmt) REVERT: B 216 LEU cc_start: 0.7953 (tp) cc_final: 0.7745 (tt) REVERT: B 294 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7579 (mp) REVERT: C 74 ASP cc_start: 0.7471 (t0) cc_final: 0.7163 (t70) REVERT: C 194 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7236 (mt-10) REVERT: C 198 GLU cc_start: 0.7509 (tt0) cc_final: 0.7247 (tt0) REVERT: D 221 ASP cc_start: 0.6910 (t0) cc_final: 0.6407 (t0) REVERT: D 327 ASP cc_start: 0.7960 (t0) cc_final: 0.7682 (t0) outliers start: 24 outliers final: 13 residues processed: 274 average time/residue: 1.4800 time to fit residues: 428.5576 Evaluate side-chains 275 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 261 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 55 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 201 GLN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108564 restraints weight = 12259.167| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.97 r_work: 0.3240 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9828 Z= 0.236 Angle : 0.542 7.893 13371 Z= 0.271 Chirality : 0.041 0.153 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.594 149.716 1362 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.63 % Allowed : 12.74 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1227 helix: 1.93 (0.20), residues: 686 sheet: -0.00 (0.55), residues: 87 loop : -0.45 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 293 HIS 0.003 0.001 HIS D 154 PHE 0.026 0.001 PHE A 109 TYR 0.016 0.001 TYR D 155 ARG 0.002 0.000 ARG C 324 *********************** 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 294 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 1.033 Fit side-chains REVERT: A 24 PHE cc_start: 0.7954 (t80) cc_final: 0.7577 (t80) REVERT: A 29 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7402 (mpp) REVERT: A 74 MET cc_start: 0.7164 (mmm) cc_final: 0.6789 (mmm) REVERT: A 130 ASP cc_start: 0.7952 (t0) cc_final: 0.7714 (t0) REVERT: A 325 ASP cc_start: 0.7281 (m-30) cc_final: 0.7040 (m-30) REVERT: B 27 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8274 (mtpt) REVERT: B 204 MET cc_start: 0.8032 (mmt) cc_final: 0.7591 (mmt) REVERT: B 216 LEU cc_start: 0.7829 (tp) cc_final: 0.7600 (tt) REVERT: C 74 ASP cc_start: 0.7647 (t0) cc_final: 0.7292 (t0) REVERT: C 194 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7329 (mt-10) REVERT: C 198 GLU cc_start: 0.7560 (tt0) cc_final: 0.7332 (tt0) REVERT: C 201 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: D 221 ASP cc_start: 0.6900 (t0) cc_final: 0.6318 (t0) REVERT: D 327 ASP cc_start: 0.8081 (t0) cc_final: 0.7816 (t0) outliers start: 27 outliers final: 14 residues processed: 278 average time/residue: 1.4861 time to fit residues: 437.5205 Evaluate side-chains 283 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 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 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 42 optimal weight: 0.0980 chunk 92 optimal weight: 0.0000 chunk 41 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 201 GLN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111936 restraints weight = 12320.088| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.59 r_work: 0.3332 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9828 Z= 0.220 Angle : 0.546 8.324 13371 Z= 0.269 Chirality : 0.041 0.148 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.534 151.469 1362 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.14 % Allowed : 14.79 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1227 helix: 1.99 (0.20), residues: 687 sheet: 0.05 (0.55), residues: 87 loop : -0.42 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 293 HIS 0.002 0.001 HIS A 254 PHE 0.021 0.001 PHE A 109 TYR 0.015 0.001 TYR D 155 ARG 0.004 0.000 ARG D 115 *********************** 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: 22 poor density : 272 time to evaluate : 1.009 Fit side-chains REVERT: A 24 PHE cc_start: 0.8139 (t80) cc_final: 0.7767 (t80) REVERT: A 74 MET cc_start: 0.7070 (mmm) cc_final: 0.6730 (mmm) REVERT: A 77 ASP cc_start: 0.7463 (t0) cc_final: 0.7055 (t0) REVERT: A 130 ASP cc_start: 0.7881 (t0) cc_final: 0.7656 (t0) REVERT: A 325 ASP cc_start: 0.7257 (m-30) cc_final: 0.7051 (m-30) REVERT: B 27 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8331 (mtpt) REVERT: B 204 MET cc_start: 0.7954 (mmt) cc_final: 0.7529 (mmt) REVERT: C 74 ASP cc_start: 0.7557 (t0) cc_final: 0.7268 (t0) REVERT: C 194 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7278 (mt-10) REVERT: C 198 GLU cc_start: 0.7535 (tt0) cc_final: 0.7292 (tt0) REVERT: C 306 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: D 221 ASP cc_start: 0.6844 (t0) cc_final: 0.6346 (t0) REVERT: D 239 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8154 (mtp180) REVERT: D 327 ASP cc_start: 0.7976 (t0) cc_final: 0.7717 (t0) outliers start: 22 outliers final: 15 residues processed: 281 average time/residue: 1.4878 time to fit residues: 441.2196 Evaluate side-chains 283 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 163 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.0470 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN C 137 GLN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111696 restraints weight = 12357.703| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.59 r_work: 0.3302 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9828 Z= 0.273 Angle : 0.575 12.451 13371 Z= 0.279 Chirality : 0.042 0.149 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.526 153.944 1362 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.33 % Allowed : 15.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1227 helix: 2.03 (0.20), residues: 681 sheet: 0.03 (0.56), residues: 87 loop : -0.38 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS D 21 PHE 0.021 0.002 PHE A 109 TYR 0.015 0.001 TYR D 155 ARG 0.004 0.000 ARG D 115 *********************** 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: 24 poor density : 267 time to evaluate : 1.168 Fit side-chains REVERT: A 20 THR cc_start: 0.8101 (m) cc_final: 0.7684 (p) REVERT: A 24 PHE cc_start: 0.7952 (t80) cc_final: 0.7590 (t80) REVERT: A 74 MET cc_start: 0.7098 (mmm) cc_final: 0.6754 (mmm) REVERT: A 77 ASP cc_start: 0.7522 (t0) cc_final: 0.7103 (t0) REVERT: A 130 ASP cc_start: 0.7865 (t0) cc_final: 0.7639 (t0) REVERT: A 151 MET cc_start: 0.8175 (mmp) cc_final: 0.7937 (mmm) REVERT: A 325 ASP cc_start: 0.7249 (m-30) cc_final: 0.7043 (m-30) REVERT: B 27 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8270 (mtpt) REVERT: B 204 MET cc_start: 0.7931 (mmt) cc_final: 0.7461 (mmt) REVERT: C 74 ASP cc_start: 0.7590 (t0) cc_final: 0.7252 (t0) REVERT: C 194 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7271 (mt-10) REVERT: C 198 GLU cc_start: 0.7491 (tt0) cc_final: 0.7256 (tt0) REVERT: C 306 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8107 (tpp) REVERT: D 221 ASP cc_start: 0.6863 (t0) cc_final: 0.6328 (t0) REVERT: D 239 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8145 (mtp180) REVERT: D 327 ASP cc_start: 0.7991 (t0) cc_final: 0.7708 (t0) outliers start: 24 outliers final: 19 residues processed: 278 average time/residue: 1.5085 time to fit residues: 443.0369 Evaluate side-chains 286 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 163 MET 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 C residue 306 MET Chi-restraints excluded: chain D residue 111 SER 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 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.0270 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 85 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3578 r_free = 0.3578 target = 0.124409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109200 restraints weight = 12446.478| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.99 r_work: 0.3249 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9828 Z= 0.211 Angle : 0.548 8.775 13371 Z= 0.269 Chirality : 0.041 0.144 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.463 155.936 1362 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.95 % Allowed : 16.34 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1227 helix: 2.12 (0.20), residues: 681 sheet: 0.06 (0.57), residues: 87 loop : -0.34 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS C 12 PHE 0.020 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 *********************** 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 290 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 1.229 Fit side-chains REVERT: A 20 THR cc_start: 0.8014 (m) cc_final: 0.7579 (p) REVERT: A 24 PHE cc_start: 0.7890 (t80) cc_final: 0.7506 (t80) REVERT: A 74 MET cc_start: 0.7169 (mmm) cc_final: 0.6819 (mmm) REVERT: A 77 ASP cc_start: 0.7624 (t0) cc_final: 0.7218 (t0) REVERT: A 130 ASP cc_start: 0.7922 (t0) cc_final: 0.7696 (t0) REVERT: A 151 MET cc_start: 0.8243 (mmp) cc_final: 0.7989 (mmm) REVERT: A 325 ASP cc_start: 0.7368 (m-30) cc_final: 0.7154 (m-30) REVERT: B 27 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8232 (mtpt) REVERT: B 204 MET cc_start: 0.8008 (mmt) cc_final: 0.7533 (mmt) REVERT: B 242 MET cc_start: 0.8802 (mmm) cc_final: 0.8598 (mmp) REVERT: C 74 ASP cc_start: 0.7678 (t0) cc_final: 0.7324 (t0) REVERT: C 194 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7354 (mt-10) REVERT: C 198 GLU cc_start: 0.7553 (tt0) cc_final: 0.7314 (tt0) REVERT: C 216 LEU cc_start: 0.7707 (tp) cc_final: 0.7491 (tt) REVERT: C 306 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: D 206 ASP cc_start: 0.7213 (m-30) cc_final: 0.6716 (m-30) REVERT: D 221 ASP cc_start: 0.6834 (t0) cc_final: 0.6298 (t0) REVERT: D 239 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8182 (mtp180) REVERT: D 327 ASP cc_start: 0.8060 (t0) cc_final: 0.7786 (t0) outliers start: 20 outliers final: 16 residues processed: 278 average time/residue: 1.5079 time to fit residues: 443.0196 Evaluate side-chains 284 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 267 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 217 VAL 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 70 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 118 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3570 r_free = 0.3570 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108923 restraints weight = 12366.341| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.95 r_work: 0.3246 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9828 Z= 0.257 Angle : 0.567 9.043 13371 Z= 0.277 Chirality : 0.042 0.150 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.481 158.180 1362 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.24 % Allowed : 16.25 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1227 helix: 2.21 (0.20), residues: 667 sheet: 0.01 (0.56), residues: 87 loop : -0.31 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.002 0.001 HIS D 21 PHE 0.019 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 *********************** 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 286 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 1.069 Fit side-chains REVERT: A 20 THR cc_start: 0.8087 (m) cc_final: 0.7655 (p) REVERT: A 24 PHE cc_start: 0.7905 (t80) cc_final: 0.7514 (t80) REVERT: A 29 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7413 (mpp) REVERT: A 74 MET cc_start: 0.7160 (mmm) cc_final: 0.6818 (mmm) REVERT: A 77 ASP cc_start: 0.7650 (t0) cc_final: 0.7235 (t0) REVERT: A 130 ASP cc_start: 0.7916 (t0) cc_final: 0.7690 (t0) REVERT: B 27 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8224 (mtpt) REVERT: B 204 MET cc_start: 0.8025 (mmt) cc_final: 0.7544 (mmt) REVERT: C 74 ASP cc_start: 0.7680 (t0) cc_final: 0.7328 (t0) REVERT: C 194 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7318 (mt-10) REVERT: C 198 GLU cc_start: 0.7529 (tt0) cc_final: 0.7285 (tt0) REVERT: C 216 LEU cc_start: 0.7596 (tp) cc_final: 0.7380 (tt) REVERT: C 306 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8240 (tpp) REVERT: D 206 ASP cc_start: 0.7217 (m-30) cc_final: 0.6729 (m-30) REVERT: D 221 ASP cc_start: 0.6876 (t0) cc_final: 0.6328 (t0) REVERT: D 239 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8190 (mtp180) REVERT: D 327 ASP cc_start: 0.8062 (t0) cc_final: 0.7785 (t0) outliers start: 23 outliers final: 18 residues processed: 272 average time/residue: 1.5470 time to fit residues: 443.9699 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 163 MET 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 C residue 306 MET Chi-restraints excluded: chain D residue 111 SER 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 3 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109031 restraints weight = 12403.460| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.98 r_work: 0.3248 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.004 0.049 9828 Z= 0.248 Angle : 0.561 9.310 13371 Z= 0.275 Chirality : 0.042 0.153 1551 Planarity : 0.004 0.040 1703 Dihedral : 7.481 160.514 1362 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.14 % Allowed : 16.44 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1227 helix: 2.21 (0.20), residues: 667 sheet: -0.01 (0.56), residues: 87 loop : -0.31 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS D 21 PHE 0.019 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 ********************** 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 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 1.047 Fit side-chains REVERT: A 20 THR cc_start: 0.8089 (m) cc_final: 0.7652 (p) REVERT: A 24 PHE cc_start: 0.7902 (t80) cc_final: 0.7519 (t80) REVERT: A 74 MET cc_start: 0.7184 (mmm) cc_final: 0.6839 (mmm) REVERT: A 77 ASP cc_start: 0.7650 (t0) cc_final: 0.7255 (t0) REVERT: A 86 ILE cc_start: 0.8576 (mt) cc_final: 0.8277 (mp) REVERT: A 130 ASP cc_start: 0.7934 (t0) cc_final: 0.7710 (t0) REVERT: A 325 ASP cc_start: 0.7447 (m-30) cc_final: 0.7151 (m-30) REVERT: B 27 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8210 (mtpt) REVERT: B 204 MET cc_start: 0.8031 (mmt) cc_final: 0.7551 (mmt) REVERT: C 32 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (tp-100) REVERT: C 194 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7314 (mt-10) REVERT: C 198 GLU cc_start: 0.7541 (tt0) cc_final: 0.7301 (tt0) REVERT: C 216 LEU cc_start: 0.7583 (tp) cc_final: 0.7381 (tt) REVERT: C 306 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: D 206 ASP cc_start: 0.7275 (m-30) cc_final: 0.6765 (m-30) REVERT: D 221 ASP cc_start: 0.6876 (t0) cc_final: 0.6340 (t0) REVERT: D 239 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8202 (mtp180) REVERT: D 327 ASP cc_start: 0.8055 (t0) cc_final: 0.7782 (t0) outliers start: 22 outliers final: 18 residues processed: 272 average time/residue: 1.5029 time to fit residues: 432.6596 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE 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 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 86 LEU 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 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 111 SER 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 36 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.0050 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 118 optimal weight: 0.0030 overall best weight: 0.2204 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.124298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109153 restraints weight = 12367.420| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.98 r_work: 0.3243 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 9828 Z= 0.251 Angle : 0.893 59.186 13371 Z= 0.507 Chirality : 0.048 0.998 1551 Planarity : 0.004 0.040 1703 Dihedral : 7.494 160.528 1362 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.65 % Allowed : 17.32 % Favored : 81.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1227 helix: 2.22 (0.20), residues: 667 sheet: -0.01 (0.56), residues: 87 loop : -0.30 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 293 HIS 0.002 0.001 HIS A 254 PHE 0.018 0.001 PHE A 109 TYR 0.013 0.001 TYR D 155 ARG 0.003 0.000 ARG D 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8655.72 seconds wall clock time: 152 minutes 52.09 seconds (9172.09 seconds total)