Starting phenix.real_space_refine on Sun Jun 8 15:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1w_39738/06_2025/8z1w_39738_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1w_39738/06_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_39738/06_2025/8z1w_39738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1w_39738/06_2025/8z1w_39738.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1w_39738/06_2025/8z1w_39738_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1w_39738/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.47, per 1000 atoms: 0.67 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 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: 0.90 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: 2.42 Time building geometry restraints manager: 2.98 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: 2.310 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.280 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16931 ( 545) hydrogen bonds : angle 6.70539 ( 1563) metal coordination : bond 0.11906 ( 8) metal coordination : angle 5.69532 ( 24) covalent geometry : bond 0.01820 ( 9828) covalent geometry : angle 1.97813 (13371) *********************** 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 : 0.899 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: 1.5914 time to fit residues: 494.2061 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 : 1.099 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108304 restraints weight = 12406.712| |-----------------------------------------------------------------------------| 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: 0.3069 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- 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 9836 Z= 0.160 Angle : 0.646 10.968 13395 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 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 545) hydrogen bonds : angle 4.77559 ( 1563) metal coordination : bond 0.00626 ( 8) metal coordination : angle 5.08376 ( 24) covalent geometry : bond 0.00376 ( 9828) covalent geometry : angle 0.60972 (13371) *********************** 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 : 0.960 Fit side-chains REVERT: A 24 PHE cc_start: 0.7981 (t80) cc_final: 0.7601 (t80) REVERT: A 74 MET cc_start: 0.7179 (mmm) cc_final: 0.6770 (mmm) REVERT: A 86 ILE cc_start: 0.8564 (mt) cc_final: 0.8276 (mp) REVERT: A 155 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 200 ASP cc_start: 0.7895 (t70) cc_final: 0.7608 (t0) REVERT: A 235 ASP cc_start: 0.7679 (m-30) cc_final: 0.7460 (m-30) REVERT: A 248 MET cc_start: 0.7893 (tpp) cc_final: 0.7668 (tpp) REVERT: B 27 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8294 (mtpt) REVERT: B 131 ASP cc_start: 0.8035 (t70) cc_final: 0.7706 (t0) REVERT: B 216 LEU cc_start: 0.7859 (tp) cc_final: 0.7588 (tt) REVERT: C 67 LYS cc_start: 0.7357 (tttt) cc_final: 0.7108 (tttt) REVERT: C 74 ASP cc_start: 0.7551 (t0) cc_final: 0.7162 (t70) REVERT: C 194 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7346 (mt-10) REVERT: C 198 GLU cc_start: 0.7668 (tt0) cc_final: 0.7421 (tt0) REVERT: C 202 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8094 (ttpp) REVERT: C 216 LEU cc_start: 0.7768 (tp) cc_final: 0.7553 (tt) REVERT: D 86 LEU cc_start: 0.8181 (mt) cc_final: 0.7970 (mp) REVERT: D 115 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7777 (tpp80) REVERT: D 151 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7246 (mtmt) REVERT: D 221 ASP cc_start: 0.6986 (t0) cc_final: 0.6379 (t0) REVERT: D 273 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7622 (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: 1.4371 time to fit residues: 436.6693 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 : 0.943 ------------------------------------------------------------------------------- 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: 0.6980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.123704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110978 restraints weight = 12559.382| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.48 r_work: 0.3299 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9836 Z= 0.184 Angle : 0.628 10.435 13395 Z= 0.300 Chirality : 0.044 0.178 1551 Planarity : 0.004 0.038 1703 Dihedral : 7.909 147.160 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 : 2.53 % Allowed : 10.31 % 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: 1.14 (0.24), residues: 1227 helix: 1.65 (0.20), residues: 683 sheet: -0.03 (0.54), residues: 88 loop : -0.40 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 293 HIS 0.004 0.001 HIS A 254 PHE 0.017 0.002 PHE A 129 TYR 0.013 0.001 TYR B 192 ARG 0.004 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 545) hydrogen bonds : angle 4.54825 ( 1563) metal coordination : bond 0.00621 ( 8) metal coordination : angle 4.91793 ( 24) covalent geometry : bond 0.00460 ( 9828) covalent geometry : angle 0.59323 (13371) *********************** 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: 26 poor density : 266 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7059 (mmm) cc_final: 0.6693 (mmm) REVERT: A 95 ARG cc_start: 0.8263 (mmt90) cc_final: 0.8009 (mpt180) REVERT: A 130 ASP cc_start: 0.7926 (t0) cc_final: 0.7724 (t0) REVERT: A 325 ASP cc_start: 0.7031 (m-30) cc_final: 0.6809 (m-30) REVERT: B 27 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8370 (mtpt) REVERT: B 131 ASP cc_start: 0.7850 (t70) cc_final: 0.7613 (t0) REVERT: B 204 MET cc_start: 0.8034 (mmt) cc_final: 0.7635 (mmt) REVERT: B 216 LEU cc_start: 0.7993 (tp) cc_final: 0.7765 (tt) REVERT: B 294 LEU cc_start: 0.7879 (mm) cc_final: 0.7646 (mp) REVERT: C 24 ASP cc_start: 0.7940 (t0) cc_final: 0.7738 (t70) REVERT: C 74 ASP cc_start: 0.7456 (t0) cc_final: 0.7148 (t70) REVERT: C 194 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7270 (mt-10) REVERT: C 198 GLU cc_start: 0.7539 (tt0) cc_final: 0.7281 (tt0) REVERT: D 86 LEU cc_start: 0.8253 (mt) cc_final: 0.8053 (mp) REVERT: D 106 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: D 221 ASP cc_start: 0.6945 (t0) cc_final: 0.6412 (t0) REVERT: D 321 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7465 (p) outliers start: 26 outliers final: 10 residues processed: 273 average time/residue: 1.4546 time to fit residues: 420.0174 Evaluate side-chains 269 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 D residue 106 GLN Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 0.0010 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 overall best weight: 0.3524 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.125824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113531 restraints weight = 12337.346| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.43 r_work: 0.3331 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9836 Z= 0.123 Angle : 0.569 9.178 13395 Z= 0.267 Chirality : 0.041 0.148 1551 Planarity : 0.004 0.039 1703 Dihedral : 7.627 147.838 1362 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.43 % Allowed : 11.87 % Favored : 85.70 % 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: 1.39 (0.24), residues: 1227 helix: 1.90 (0.20), residues: 686 sheet: 0.02 (0.54), residues: 87 loop : -0.37 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 293 HIS 0.004 0.001 HIS D 154 PHE 0.012 0.001 PHE B 44 TYR 0.015 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 545) hydrogen bonds : angle 4.34897 ( 1563) metal coordination : bond 0.00332 ( 8) metal coordination : angle 4.79452 ( 24) covalent geometry : bond 0.00290 ( 9828) covalent geometry : angle 0.53250 (13371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 1.101 Fit side-chains REVERT: A 74 MET cc_start: 0.6943 (mmm) cc_final: 0.6648 (mmm) REVERT: A 325 ASP cc_start: 0.7236 (m-30) cc_final: 0.7032 (m-30) REVERT: B 204 MET cc_start: 0.7976 (mmt) cc_final: 0.7657 (mmt) REVERT: B 294 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7769 (mp) REVERT: C 74 ASP cc_start: 0.7353 (t0) cc_final: 0.7141 (t0) REVERT: C 194 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7307 (mt-10) REVERT: C 198 GLU cc_start: 0.7580 (tt0) cc_final: 0.7335 (tt0) REVERT: D 221 ASP cc_start: 0.6856 (t0) cc_final: 0.6522 (t0) REVERT: D 327 ASP cc_start: 0.7871 (t0) cc_final: 0.7637 (t0) outliers start: 25 outliers final: 11 residues processed: 282 average time/residue: 1.3803 time to fit residues: 412.3282 Evaluate side-chains 283 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 91 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 115 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 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 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 = 0.3588 r_free = 0.3588 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111682 restraints weight = 12217.502| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.57 r_work: 0.3327 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2659 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= 0.162 Angle : 0.601 11.807 13395 Z= 0.279 Chirality : 0.042 0.155 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.589 149.804 1362 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.63 % Allowed : 13.42 % Favored : 83.95 % 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: 1.43 (0.24), residues: 1227 helix: 1.98 (0.20), residues: 677 sheet: 0.07 (0.55), residues: 87 loop : -0.39 (0.29), residues: 463 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 0.022 0.002 PHE A 109 TYR 0.017 0.001 TYR D 155 ARG 0.003 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 545) hydrogen bonds : angle 4.35726 ( 1563) metal coordination : bond 0.00544 ( 8) metal coordination : angle 4.83676 ( 24) covalent geometry : bond 0.00403 ( 9828) covalent geometry : angle 0.56540 (13371) *********************** 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 293 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.971 Fit side-chains REVERT: A 29 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7405 (mpp) REVERT: A 74 MET cc_start: 0.7074 (mmm) cc_final: 0.6714 (mmm) REVERT: A 325 ASP cc_start: 0.7182 (m-30) cc_final: 0.6946 (m-30) REVERT: B 62 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7536 (mtt-85) REVERT: B 204 MET cc_start: 0.7926 (mmt) cc_final: 0.7496 (mmt) REVERT: C 74 ASP cc_start: 0.7558 (t0) cc_final: 0.7234 (t0) REVERT: C 194 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7242 (mt-10) REVERT: C 198 GLU cc_start: 0.7491 (tt0) cc_final: 0.7262 (tt0) REVERT: C 201 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: D 221 ASP cc_start: 0.6865 (t0) cc_final: 0.6343 (t0) REVERT: D 239 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.8159 (mtp180) REVERT: D 327 ASP cc_start: 0.7985 (t0) cc_final: 0.7720 (t0) outliers start: 27 outliers final: 15 residues processed: 274 average time/residue: 1.4633 time to fit residues: 423.2306 Evaluate side-chains 282 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 86 LEU 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: 0.8980 chunk 92 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 overall best weight: 0.3054 ------------------------------------------------------------------------------- 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 C 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112583 restraints weight = 12314.297| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.60 r_work: 0.3343 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9836 Z= 0.120 Angle : 0.581 8.902 13395 Z= 0.266 Chirality : 0.040 0.146 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.501 151.537 1362 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.43 % Allowed : 14.88 % 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 (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: 1.58 (0.25), residues: 1227 helix: 2.11 (0.20), residues: 680 sheet: 0.10 (0.56), residues: 87 loop : -0.35 (0.29), residues: 460 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 0.017 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.004 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 545) hydrogen bonds : angle 4.26944 ( 1563) metal coordination : bond 0.00337 ( 8) metal coordination : angle 4.87259 ( 24) covalent geometry : bond 0.00282 ( 9828) covalent geometry : angle 0.54385 (13371) *********************** 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 297 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 1.027 Fit side-chains REVERT: A 20 THR cc_start: 0.8125 (m) cc_final: 0.7685 (p) REVERT: A 24 PHE cc_start: 0.8036 (t80) cc_final: 0.7661 (t80) REVERT: A 74 MET cc_start: 0.7087 (mmm) cc_final: 0.6746 (mmm) REVERT: A 77 ASP cc_start: 0.7454 (t0) cc_final: 0.7018 (t0) REVERT: A 184 PHE cc_start: 0.7469 (m-80) cc_final: 0.6807 (m-80) REVERT: A 325 ASP cc_start: 0.7212 (m-30) cc_final: 0.6990 (m-30) REVERT: B 66 LEU cc_start: 0.8365 (mt) cc_final: 0.8085 (mm) REVERT: B 204 MET cc_start: 0.7919 (mmt) cc_final: 0.7459 (mmt) REVERT: C 74 ASP cc_start: 0.7556 (t0) cc_final: 0.7231 (t0) REVERT: C 194 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7245 (mt-10) REVERT: C 198 GLU cc_start: 0.7502 (tt0) cc_final: 0.7263 (tt0) REVERT: C 306 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8169 (tpp) REVERT: D 221 ASP cc_start: 0.6835 (t0) cc_final: 0.6324 (t0) REVERT: D 327 ASP cc_start: 0.7978 (t0) cc_final: 0.7717 (t0) outliers start: 25 outliers final: 17 residues processed: 281 average time/residue: 1.4833 time to fit residues: 440.1685 Evaluate side-chains 288 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 258 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 77 ARG 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 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: 0.9990 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.125319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113112 restraints weight = 12489.651| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.43 r_work: 0.3335 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9836 Z= 0.159 Angle : 0.599 9.237 13395 Z= 0.277 Chirality : 0.042 0.148 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.499 154.265 1362 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.14 % Allowed : 16.05 % 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 (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: 1.54 (0.24), residues: 1227 helix: 2.07 (0.20), residues: 680 sheet: 0.06 (0.56), residues: 87 loop : -0.35 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 293 HIS 0.002 0.001 HIS A 254 PHE 0.017 0.001 PHE A 109 TYR 0.016 0.001 TYR D 155 ARG 0.005 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 545) hydrogen bonds : angle 4.30474 ( 1563) metal coordination : bond 0.00509 ( 8) metal coordination : angle 4.89532 ( 24) covalent geometry : bond 0.00395 ( 9828) covalent geometry : angle 0.56231 (13371) *********************** 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 295 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 1.804 Fit side-chains REVERT: A 20 THR cc_start: 0.8295 (m) cc_final: 0.7924 (p) REVERT: A 24 PHE cc_start: 0.8396 (t80) cc_final: 0.8048 (t80) REVERT: A 74 MET cc_start: 0.7017 (mmm) cc_final: 0.6738 (mmm) REVERT: A 77 ASP cc_start: 0.7425 (t0) cc_final: 0.7074 (t0) REVERT: B 204 MET cc_start: 0.7939 (mmt) cc_final: 0.7620 (mmt) REVERT: C 194 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 198 GLU cc_start: 0.7568 (tt0) cc_final: 0.7346 (tt0) REVERT: C 216 LEU cc_start: 0.8117 (tp) cc_final: 0.7905 (tt) REVERT: C 306 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7948 (tpp) REVERT: D 221 ASP cc_start: 0.6839 (t0) cc_final: 0.6474 (t0) REVERT: D 239 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.8112 (mtp180) REVERT: D 327 ASP cc_start: 0.7843 (t0) cc_final: 0.7606 (t0) outliers start: 22 outliers final: 16 residues processed: 282 average time/residue: 1.9927 time to fit residues: 595.8272 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 : 1.268 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 156 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 14 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.112136 restraints weight = 12453.781| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.58 r_work: 0.3299 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9836 Z= 0.136 Angle : 0.595 9.143 13395 Z= 0.275 Chirality : 0.041 0.146 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.470 155.416 1362 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.14 % Allowed : 16.15 % 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: 1.68 (0.24), residues: 1227 helix: 2.21 (0.20), residues: 668 sheet: 0.07 (0.57), residues: 87 loop : -0.25 (0.29), residues: 472 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 0.016 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.007 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 545) hydrogen bonds : angle 4.26519 ( 1563) metal coordination : bond 0.00427 ( 8) metal coordination : angle 4.90650 ( 24) covalent geometry : bond 0.00328 ( 9828) covalent geometry : angle 0.55766 (13371) *********************** 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 289 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 1.065 Fit side-chains REVERT: A 20 THR cc_start: 0.8087 (m) cc_final: 0.7657 (p) REVERT: A 24 PHE cc_start: 0.7952 (t80) cc_final: 0.7619 (t80) REVERT: A 74 MET cc_start: 0.7076 (mmm) cc_final: 0.6735 (mmm) REVERT: A 77 ASP cc_start: 0.7538 (t0) cc_final: 0.7107 (t0) REVERT: A 151 MET cc_start: 0.8177 (mmp) cc_final: 0.7942 (mmm) REVERT: A 184 PHE cc_start: 0.7401 (m-80) cc_final: 0.6796 (m-80) REVERT: A 247 ARG cc_start: 0.7149 (tpm170) cc_final: 0.6860 (tpm170) REVERT: B 204 MET cc_start: 0.7928 (mmt) cc_final: 0.7454 (mmt) REVERT: C 146 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7694 (mtp85) REVERT: C 194 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7210 (mt-10) REVERT: C 198 GLU cc_start: 0.7441 (tt0) cc_final: 0.7205 (tt0) REVERT: C 201 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7382 (mt0) REVERT: C 216 LEU cc_start: 0.7651 (tp) cc_final: 0.7434 (tt) REVERT: C 306 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8141 (tpp) REVERT: D 206 ASP cc_start: 0.7133 (m-30) cc_final: 0.6642 (m-30) REVERT: D 221 ASP cc_start: 0.6806 (t0) cc_final: 0.6271 (t0) REVERT: D 239 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8086 (mtp180) REVERT: D 327 ASP cc_start: 0.7953 (t0) cc_final: 0.7675 (t0) outliers start: 22 outliers final: 17 residues processed: 275 average time/residue: 1.5113 time to fit residues: 438.5439 Evaluate side-chains 285 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 201 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 111 SER 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: 0.6980 chunk 99 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 118 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112421 restraints weight = 12380.371| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.48 r_work: 0.3325 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2982 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= 0.144 Angle : 0.593 9.425 13395 Z= 0.274 Chirality : 0.042 0.147 1551 Planarity : 0.004 0.040 1703 Dihedral : 7.452 158.023 1362 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.04 % Allowed : 16.05 % 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: 1.67 (0.24), residues: 1227 helix: 2.21 (0.20), residues: 668 sheet: 0.01 (0.56), residues: 88 loop : -0.25 (0.29), residues: 471 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 0.016 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.008 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 545) hydrogen bonds : angle 4.25465 ( 1563) metal coordination : bond 0.00447 ( 8) metal coordination : angle 4.94525 ( 24) covalent geometry : bond 0.00352 ( 9828) covalent geometry : angle 0.55574 (13371) *********************** 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 288 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 1.059 Fit side-chains REVERT: A 20 THR cc_start: 0.8128 (m) cc_final: 0.7708 (p) REVERT: A 24 PHE cc_start: 0.8046 (t80) cc_final: 0.7721 (t80) REVERT: A 74 MET cc_start: 0.7074 (mmm) cc_final: 0.6746 (mmm) REVERT: A 77 ASP cc_start: 0.7535 (t0) cc_final: 0.7127 (t0) REVERT: A 247 ARG cc_start: 0.7105 (tpm170) cc_final: 0.6827 (tpm170) REVERT: B 204 MET cc_start: 0.7930 (mmt) cc_final: 0.7488 (mmt) REVERT: C 194 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7235 (mt-10) REVERT: C 198 GLU cc_start: 0.7439 (tt0) cc_final: 0.7192 (tt0) REVERT: C 216 LEU cc_start: 0.7758 (tp) cc_final: 0.7548 (tt) REVERT: C 306 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8074 (tpp) REVERT: D 206 ASP cc_start: 0.7164 (m-30) cc_final: 0.6694 (m-30) REVERT: D 221 ASP cc_start: 0.6846 (t0) cc_final: 0.6359 (t0) REVERT: D 239 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8109 (mtp180) REVERT: D 327 ASP cc_start: 0.7919 (t0) cc_final: 0.7647 (t0) outliers start: 21 outliers final: 16 residues processed: 277 average time/residue: 1.4555 time to fit residues: 425.7246 Evaluate side-chains 280 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 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 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: 0.7980 chunk 27 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108549 restraints weight = 12403.304| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.98 r_work: 0.3241 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9836 Z= 0.185 Angle : 0.622 10.072 13395 Z= 0.289 Chirality : 0.043 0.154 1551 Planarity : 0.004 0.041 1703 Dihedral : 7.531 160.596 1362 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.56 % Allowed : 17.12 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.24), residues: 1227 helix: 2.15 (0.20), residues: 668 sheet: -0.07 (0.56), residues: 88 loop : -0.32 (0.28), residues: 471 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 0.017 0.002 PHE A 109 TYR 0.015 0.001 TYR D 155 ARG 0.007 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 545) hydrogen bonds : angle 4.31259 ( 1563) metal coordination : bond 0.00613 ( 8) metal coordination : angle 5.00756 ( 24) covalent geometry : bond 0.00465 ( 9828) covalent geometry : angle 0.58567 (13371) ********************** 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 273 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 0.946 Fit side-chains REVERT: A 20 THR cc_start: 0.8095 (m) cc_final: 0.7667 (p) REVERT: A 24 PHE cc_start: 0.7903 (t80) cc_final: 0.7532 (t80) REVERT: A 74 MET cc_start: 0.7223 (mmm) cc_final: 0.6870 (mmm) REVERT: A 77 ASP cc_start: 0.7666 (t0) cc_final: 0.7266 (t0) REVERT: A 247 ARG cc_start: 0.7371 (tpm170) cc_final: 0.7065 (tpm170) REVERT: B 62 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7502 (mtm-85) REVERT: B 204 MET cc_start: 0.8029 (mmt) cc_final: 0.7553 (mmt) REVERT: C 194 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7347 (mt-10) REVERT: C 198 GLU cc_start: 0.7528 (tt0) cc_final: 0.7311 (tt0) REVERT: C 201 GLN cc_start: 0.7803 (mt0) cc_final: 0.7467 (mt0) REVERT: C 216 LEU cc_start: 0.7695 (tp) cc_final: 0.7481 (tt) REVERT: C 306 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8242 (tpp) REVERT: D 206 ASP cc_start: 0.7253 (m-30) cc_final: 0.6753 (m-30) REVERT: D 239 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.8212 (mtp180) REVERT: D 327 ASP cc_start: 0.8058 (t0) cc_final: 0.7789 (t0) outliers start: 16 outliers final: 15 residues processed: 266 average time/residue: 1.4284 time to fit residues: 402.6458 Evaluate side-chains 273 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 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 163 MET 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: 0.1980 chunk 79 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 117 optimal weight: 0.0370 chunk 118 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.124976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.109849 restraints weight = 12335.081| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.98 r_work: 0.3259 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9836 Z= 0.133 Angle : 0.595 9.632 13395 Z= 0.274 Chirality : 0.041 0.152 1551 Planarity : 0.004 0.042 1703 Dihedral : 7.476 163.495 1362 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.75 % Allowed : 17.22 % 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 (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: 1.70 (0.25), residues: 1227 helix: 2.26 (0.20), residues: 668 sheet: -0.05 (0.56), residues: 88 loop : -0.28 (0.29), residues: 471 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 0.015 0.001 PHE A 109 TYR 0.014 0.001 TYR D 155 ARG 0.007 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 545) hydrogen bonds : angle 4.25320 ( 1563) metal coordination : bond 0.00408 ( 8) metal coordination : angle 4.99285 ( 24) covalent geometry : bond 0.00323 ( 9828) covalent geometry : angle 0.55697 (13371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8975.95 seconds wall clock time: 154 minutes 53.80 seconds (9293.80 seconds total)