Starting phenix.real_space_refine on Sat Aug 23 11:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.map" model { file = "/net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unj_42406/08_2025/8unj_42406.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 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 P 11 5.49 5 Mg 3 5.21 5 S 75 5.16 5 C 7496 2.51 5 N 2087 2.21 5 O 2244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11916 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.17, per 1000 atoms: 0.27 Number of scatterers: 11916 At special positions: 0 Unit cell: (94.392, 110.952, 124.2, 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) S 75 16.00 P 11 15.00 Mg 3 11.99 O 2244 8.00 N 2087 7.00 C 7496 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: 1.01 Conformation dependent library (CDL) restraints added in 516.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 64.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 722 through 743 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.789A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.708A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.649A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.712A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.677A pdb=" N VAL B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O HIS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.616A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.548A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.591A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.915A pdb=" N PHE C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.820A pdb=" N ALA C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.025A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.725A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 161' Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.527A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.693A pdb=" N LEU C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 208 removed outlier: 3.643A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.970A pdb=" N MET C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 271 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.762A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.634A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.569A pdb=" N GLU D 51 " --> pdb=" O CYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.568A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.675A pdb=" N ARG D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 115 through 128 removed outlier: 4.208A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.851A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 170 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.750A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.557A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.759A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.717A pdb=" N ALA D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.544A pdb=" N GLN D 282 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.654A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.279A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 97 through 102 removed outlier: 6.611A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 110 through 117 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 141 through 147 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.905A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.586A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.886A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 328 through 349 removed outlier: 3.593A pdb=" N ASP E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.115A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 73 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.712A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.241A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.807A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4005 1.37 - 1.51: 3171 1.51 - 1.66: 4823 1.66 - 1.80: 76 1.80 - 1.95: 34 Bond restraints: 12109 Sorted by residual: bond pdb=" C GLN D 208 " pdb=" O GLN D 208 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.88e+01 bond pdb=" N ILE E 329 " pdb=" CA ILE E 329 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.08e+00 bond pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.40e+00 bond pdb=" N ALA D 215 " pdb=" CA ALA D 215 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.09e+00 bond pdb=" N LEU D 211 " pdb=" CA LEU D 211 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 ... (remaining 12104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16031 2.01 - 4.03: 315 4.03 - 6.04: 37 6.04 - 8.06: 9 8.06 - 10.07: 2 Bond angle restraints: 16394 Sorted by residual: angle pdb=" N ASN D 181 " pdb=" CA ASN D 181 " pdb=" C ASN D 181 " ideal model delta sigma weight residual 113.16 105.52 7.64 1.24e+00 6.50e-01 3.79e+01 angle pdb=" C GLN D 207 " pdb=" N GLN D 208 " pdb=" CA GLN D 208 " ideal model delta sigma weight residual 120.44 113.54 6.90 1.30e+00 5.92e-01 2.82e+01 angle pdb=" N GLU D 218 " pdb=" CA GLU D 218 " pdb=" C GLU D 218 " ideal model delta sigma weight residual 113.19 107.56 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" N ILE D 214 " pdb=" CA ILE D 214 " pdb=" C ILE D 214 " ideal model delta sigma weight residual 110.42 106.01 4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" N LEU D 211 " pdb=" CA LEU D 211 " pdb=" C LEU D 211 " ideal model delta sigma weight residual 111.82 106.82 5.00 1.16e+00 7.43e-01 1.86e+01 ... (remaining 16389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 7045 23.71 - 47.42: 400 47.42 - 71.13: 68 71.13 - 94.84: 8 94.84 - 118.54: 3 Dihedral angle restraints: 7524 sinusoidal: 3144 harmonic: 4380 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -178.54 118.54 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 52.99 -112.99 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" CA HIS C 241 " pdb=" C HIS C 241 " pdb=" N PRO C 242 " pdb=" CA PRO C 242 " ideal model delta harmonic sigma weight residual -180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1388 0.043 - 0.086: 391 0.086 - 0.129: 112 0.129 - 0.172: 18 0.172 - 0.215: 6 Chirality restraints: 1915 Sorted by residual: chirality pdb=" CA LEU D 212 " pdb=" N LEU D 212 " pdb=" C LEU D 212 " pdb=" CB LEU D 212 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE D 214 " pdb=" N ILE D 214 " pdb=" C ILE D 214 " pdb=" CB ILE D 214 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU E 67 " pdb=" N LEU E 67 " pdb=" C LEU E 67 " pdb=" CB LEU E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1912 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO E 174 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 257 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 258 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 267 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO E 268 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 268 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 268 " 0.031 5.00e-02 4.00e+02 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 167 2.65 - 3.21: 10342 3.21 - 3.77: 19485 3.77 - 4.34: 25332 4.34 - 4.90: 41544 Nonbonded interactions: 96870 Sorted by model distance: nonbonded pdb="MG MG D 401 " pdb=" O2B AGS D 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.087 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.116 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.119 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.197 2.170 ... (remaining 96865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.210 Find NCS groups from input model: 0.090 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 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 : 0.003 0.050 12109 Z= 0.198 Angle : 0.700 10.070 16394 Z= 0.411 Chirality : 0.045 0.215 1915 Planarity : 0.007 0.101 2080 Dihedral : 14.943 118.544 4672 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.51 % Allowed : 9.39 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.19), residues: 1481 helix: -1.30 (0.15), residues: 879 sheet: -0.63 (0.41), residues: 143 loop : -0.63 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 215 TYR 0.020 0.001 TYR E 41 PHE 0.014 0.001 PHE E 339 TRP 0.010 0.002 TRP C 253 HIS 0.005 0.001 HIS E 19 Details of bonding type rmsd covalent geometry : bond 0.00344 (12109) covalent geometry : angle 0.70027 (16394) hydrogen bonds : bond 0.14496 ( 636) hydrogen bonds : angle 6.23379 ( 1866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: -0.2409 (ttm) cc_final: -0.3480 (ptm) REVERT: B 185 CYS cc_start: 0.2644 (m) cc_final: 0.2287 (m) REVERT: C 202 MET cc_start: 0.5514 (tmm) cc_final: 0.5016 (tmm) REVERT: C 206 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6861 (p) REVERT: D 77 TYR cc_start: 0.3767 (p90) cc_final: 0.3195 (p90) REVERT: D 227 ILE cc_start: 0.7255 (tt) cc_final: 0.7053 (tt) REVERT: D 304 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7581 (p) outliers start: 46 outliers final: 12 residues processed: 278 average time/residue: 0.1051 time to fit residues: 42.0368 Evaluate side-chains 179 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 314 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN A 788 GLN A 820 ASN A 839 GLN B 126 GLN B 237 GLN B 268 GLN C 32 ASN C 38 GLN C 135 GLN C 300 HIS D 73 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 126 GLN E 206 ASN E 265 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.222490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.186554 restraints weight = 20393.112| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 3.42 r_work: 0.4214 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12109 Z= 0.137 Angle : 0.603 10.881 16394 Z= 0.301 Chirality : 0.040 0.135 1915 Planarity : 0.005 0.081 2080 Dihedral : 10.050 112.495 1722 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.82 % Allowed : 14.43 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.21), residues: 1481 helix: -0.06 (0.17), residues: 884 sheet: -0.86 (0.40), residues: 150 loop : -0.03 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 854 TYR 0.025 0.002 TYR B 279 PHE 0.014 0.001 PHE C 119 TRP 0.010 0.001 TRP D 40 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00303 (12109) covalent geometry : angle 0.60344 (16394) hydrogen bonds : bond 0.03717 ( 636) hydrogen bonds : angle 4.36249 ( 1866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7919 (pp30) REVERT: A 738 GLN cc_start: 0.7757 (mm110) cc_final: 0.7553 (tp40) REVERT: A 762 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6042 (tp) REVERT: A 820 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6825 (p0) REVERT: B 158 MET cc_start: -0.3423 (ttm) cc_final: -0.3950 (ptm) REVERT: B 185 CYS cc_start: 0.2726 (m) cc_final: 0.2197 (m) REVERT: B 229 MET cc_start: 0.5038 (tpp) cc_final: 0.4487 (tpp) REVERT: B 231 GLN cc_start: 0.8056 (tt0) cc_final: 0.7833 (tt0) REVERT: B 246 ILE cc_start: 0.4547 (mm) cc_final: 0.4273 (mm) REVERT: B 340 LEU cc_start: 0.6514 (tt) cc_final: 0.6300 (tt) REVERT: C 202 MET cc_start: 0.5080 (tmm) cc_final: 0.4758 (tmm) REVERT: D 77 TYR cc_start: 0.4383 (p90) cc_final: 0.3783 (p90) REVERT: D 304 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7797 (p) outliers start: 37 outliers final: 20 residues processed: 209 average time/residue: 0.0922 time to fit residues: 28.6130 Evaluate side-chains 185 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 8.9990 chunk 112 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 135 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.223182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.186689 restraints weight = 20570.838| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.36 r_work: 0.4220 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12109 Z= 0.111 Angle : 0.553 11.017 16394 Z= 0.274 Chirality : 0.039 0.153 1915 Planarity : 0.005 0.074 2080 Dihedral : 9.659 112.690 1707 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.52 % Allowed : 16.18 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1481 helix: 0.54 (0.17), residues: 875 sheet: -0.97 (0.38), residues: 161 loop : 0.23 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.021 0.002 TYR B 279 PHE 0.016 0.001 PHE E 346 TRP 0.009 0.001 TRP D 40 HIS 0.004 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00238 (12109) covalent geometry : angle 0.55341 (16394) hydrogen bonds : bond 0.03464 ( 636) hydrogen bonds : angle 4.16025 ( 1866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.5779 (tp) REVERT: A 815 TYR cc_start: 0.3908 (m-80) cc_final: 0.3216 (m-80) REVERT: B 146 MET cc_start: 0.1970 (ttt) cc_final: 0.1687 (ttp) REVERT: B 158 MET cc_start: -0.3248 (ttm) cc_final: -0.3848 (ptm) REVERT: B 229 MET cc_start: 0.5037 (tpp) cc_final: 0.4539 (tpp) REVERT: B 231 GLN cc_start: 0.8020 (tt0) cc_final: 0.7720 (tt0) REVERT: C 202 MET cc_start: 0.5020 (tmm) cc_final: 0.4735 (tmm) REVERT: D 77 TYR cc_start: 0.4411 (p90) cc_final: 0.3736 (p90) REVERT: D 304 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7761 (p) REVERT: E 4 TRP cc_start: 0.4733 (OUTLIER) cc_final: 0.4514 (m-10) outliers start: 33 outliers final: 20 residues processed: 188 average time/residue: 0.0930 time to fit residues: 26.3027 Evaluate side-chains 174 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 128 optimal weight: 0.0570 chunk 136 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 156 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.222659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.186675 restraints weight = 20517.878| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 3.32 r_work: 0.4214 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12109 Z= 0.108 Angle : 0.536 10.919 16394 Z= 0.265 Chirality : 0.039 0.165 1915 Planarity : 0.004 0.071 2080 Dihedral : 9.380 113.209 1704 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 16.79 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1481 helix: 0.80 (0.18), residues: 876 sheet: -1.03 (0.38), residues: 161 loop : 0.30 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 854 TYR 0.021 0.001 TYR E 155 PHE 0.017 0.001 PHE E 346 TRP 0.010 0.001 TRP E 251 HIS 0.004 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00237 (12109) covalent geometry : angle 0.53612 (16394) hydrogen bonds : bond 0.03232 ( 636) hydrogen bonds : angle 4.03036 ( 1866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5835 (tp) REVERT: A 815 TYR cc_start: 0.3978 (m-80) cc_final: 0.3303 (m-80) REVERT: B 146 MET cc_start: 0.2066 (ttt) cc_final: 0.1734 (tmm) REVERT: B 158 MET cc_start: -0.3543 (ttm) cc_final: -0.4058 (ptm) REVERT: B 229 MET cc_start: 0.4998 (tpp) cc_final: 0.4487 (tpp) REVERT: B 231 GLN cc_start: 0.8129 (tt0) cc_final: 0.7729 (tt0) REVERT: C 202 MET cc_start: 0.5015 (tmm) cc_final: 0.4724 (tmm) REVERT: D 43 LYS cc_start: 0.5640 (OUTLIER) cc_final: 0.5208 (mttt) REVERT: D 77 TYR cc_start: 0.4413 (p90) cc_final: 0.3710 (p90) REVERT: E 4 TRP cc_start: 0.4819 (OUTLIER) cc_final: 0.4575 (m-10) outliers start: 38 outliers final: 21 residues processed: 193 average time/residue: 0.0811 time to fit residues: 23.8933 Evaluate side-chains 178 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 0.0370 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 302 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.218196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.180022 restraints weight = 20433.164| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.50 r_work: 0.4116 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12109 Z= 0.189 Angle : 0.636 10.651 16394 Z= 0.314 Chirality : 0.042 0.149 1915 Planarity : 0.005 0.072 2080 Dihedral : 9.213 118.339 1699 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.44 % Allowed : 17.25 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1481 helix: 0.60 (0.18), residues: 875 sheet: -0.97 (0.40), residues: 145 loop : 0.09 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 114 TYR 0.019 0.002 TYR E 155 PHE 0.018 0.002 PHE E 35 TRP 0.016 0.002 TRP D 40 HIS 0.006 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00432 (12109) covalent geometry : angle 0.63638 (16394) hydrogen bonds : bond 0.03801 ( 636) hydrogen bonds : angle 4.27628 ( 1866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.5720 (tp) REVERT: A 815 TYR cc_start: 0.4083 (m-80) cc_final: 0.3429 (m-80) REVERT: B 158 MET cc_start: -0.3468 (ttm) cc_final: -0.4003 (ptm) REVERT: B 229 MET cc_start: 0.5057 (tpp) cc_final: 0.4602 (tpp) REVERT: B 308 MET cc_start: 0.7172 (mmm) cc_final: 0.6850 (mmt) REVERT: C 122 VAL cc_start: 0.7069 (t) cc_final: 0.6554 (m) REVERT: C 182 MET cc_start: 0.4116 (ptt) cc_final: 0.3891 (ptt) REVERT: C 202 MET cc_start: 0.5202 (tmm) cc_final: 0.4790 (tmm) REVERT: C 292 ASP cc_start: 0.6701 (t0) cc_final: 0.6398 (t0) REVERT: D 77 TYR cc_start: 0.4752 (p90) cc_final: 0.4041 (p90) REVERT: D 304 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7782 (p) REVERT: E 4 TRP cc_start: 0.5273 (OUTLIER) cc_final: 0.4534 (m-10) REVERT: E 108 ILE cc_start: 0.7544 (mm) cc_final: 0.7202 (mt) REVERT: E 110 GLU cc_start: 0.6563 (tp30) cc_final: 0.6346 (mm-30) REVERT: E 214 ARG cc_start: 0.6038 (mtm110) cc_final: 0.5351 (mtt90) outliers start: 45 outliers final: 27 residues processed: 199 average time/residue: 0.0974 time to fit residues: 28.7986 Evaluate side-chains 189 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN E 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.220023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.181778 restraints weight = 20538.375| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.42 r_work: 0.4183 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12109 Z= 0.123 Angle : 0.575 10.812 16394 Z= 0.283 Chirality : 0.039 0.133 1915 Planarity : 0.005 0.068 2080 Dihedral : 8.991 117.624 1699 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.52 % Allowed : 19.01 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.22), residues: 1481 helix: 0.76 (0.18), residues: 875 sheet: -1.10 (0.40), residues: 148 loop : 0.18 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 855 TYR 0.018 0.002 TYR E 279 PHE 0.013 0.001 PHE E 35 TRP 0.012 0.001 TRP D 40 HIS 0.003 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00275 (12109) covalent geometry : angle 0.57531 (16394) hydrogen bonds : bond 0.03288 ( 636) hydrogen bonds : angle 4.12343 ( 1866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 TYR cc_start: 0.4193 (m-80) cc_final: 0.3538 (m-80) REVERT: A 820 ASN cc_start: 0.7110 (p0) cc_final: 0.6558 (p0) REVERT: A 823 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: B 158 MET cc_start: -0.3485 (ttm) cc_final: -0.4027 (ptm) REVERT: B 229 MET cc_start: 0.4943 (tpp) cc_final: 0.4471 (tpp) REVERT: B 231 GLN cc_start: 0.8221 (tt0) cc_final: 0.7995 (tt0) REVERT: B 308 MET cc_start: 0.6970 (mmm) cc_final: 0.4821 (ptt) REVERT: B 341 LEU cc_start: 0.8025 (mp) cc_final: 0.7526 (mt) REVERT: C 126 GLU cc_start: 0.6844 (mp0) cc_final: 0.6215 (tm-30) REVERT: C 202 MET cc_start: 0.5174 (tmm) cc_final: 0.4817 (tmm) REVERT: C 275 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5531 (mt) REVERT: C 292 ASP cc_start: 0.6624 (t0) cc_final: 0.6274 (t0) REVERT: D 43 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5510 (mtmm) REVERT: D 77 TYR cc_start: 0.4655 (p90) cc_final: 0.3927 (p90) REVERT: D 304 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7769 (p) REVERT: D 357 GLN cc_start: 0.7387 (tm-30) cc_final: 0.7077 (tm-30) REVERT: E 108 ILE cc_start: 0.7509 (mm) cc_final: 0.7158 (mt) REVERT: E 110 GLU cc_start: 0.6530 (tp30) cc_final: 0.6312 (mm-30) REVERT: E 281 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7141 (tt) outliers start: 33 outliers final: 21 residues processed: 193 average time/residue: 0.0963 time to fit residues: 27.8885 Evaluate side-chains 185 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 95 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.216858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.185609 restraints weight = 20651.092| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.49 r_work: 0.4288 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.4152 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 12109 Z= 0.308 Angle : 0.805 10.996 16394 Z= 0.401 Chirality : 0.048 0.180 1915 Planarity : 0.006 0.073 2080 Dihedral : 9.314 128.855 1699 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.59 % Allowed : 18.85 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1481 helix: 0.09 (0.17), residues: 881 sheet: -1.22 (0.43), residues: 135 loop : -0.27 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 51 TYR 0.021 0.003 TYR B 279 PHE 0.028 0.003 PHE E 339 TRP 0.027 0.004 TRP D 40 HIS 0.008 0.002 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00707 (12109) covalent geometry : angle 0.80494 (16394) hydrogen bonds : bond 0.04747 ( 636) hydrogen bonds : angle 4.89103 ( 1866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.287 Fit side-chains REVERT: A 738 GLN cc_start: 0.7932 (mm110) cc_final: 0.7634 (tp40) REVERT: A 815 TYR cc_start: 0.4429 (m-80) cc_final: 0.3756 (m-80) REVERT: A 820 ASN cc_start: 0.7332 (p0) cc_final: 0.6867 (p0) REVERT: A 823 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: B 146 MET cc_start: 0.2102 (ttt) cc_final: 0.1810 (tmm) REVERT: B 158 MET cc_start: -0.3497 (ttm) cc_final: -0.4008 (ptm) REVERT: B 229 MET cc_start: 0.5075 (tpp) cc_final: 0.4661 (tpp) REVERT: B 231 GLN cc_start: 0.8307 (tt0) cc_final: 0.8071 (tt0) REVERT: B 308 MET cc_start: 0.7034 (mmm) cc_final: 0.6824 (mmt) REVERT: C 122 VAL cc_start: 0.7572 (t) cc_final: 0.7223 (m) REVERT: C 202 MET cc_start: 0.5709 (tmm) cc_final: 0.5041 (tmm) REVERT: C 292 ASP cc_start: 0.6955 (t0) cc_final: 0.6618 (t0) REVERT: D 77 TYR cc_start: 0.4888 (p90) cc_final: 0.4140 (p90) REVERT: D 304 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7790 (p) REVERT: E 108 ILE cc_start: 0.7636 (mm) cc_final: 0.7361 (mt) REVERT: E 281 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7593 (tt) outliers start: 47 outliers final: 33 residues processed: 208 average time/residue: 0.0953 time to fit residues: 28.9275 Evaluate side-chains 195 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 89 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.217521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.181879 restraints weight = 20524.145| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.91 r_work: 0.4227 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12109 Z= 0.133 Angle : 0.627 11.773 16394 Z= 0.308 Chirality : 0.041 0.170 1915 Planarity : 0.005 0.065 2080 Dihedral : 8.916 122.137 1699 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.67 % Allowed : 20.08 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1481 helix: 0.42 (0.17), residues: 881 sheet: -1.32 (0.42), residues: 138 loop : 0.01 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 214 TYR 0.021 0.002 TYR B 279 PHE 0.015 0.001 PHE E 339 TRP 0.050 0.004 TRP D 40 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00297 (12109) covalent geometry : angle 0.62658 (16394) hydrogen bonds : bond 0.03520 ( 636) hydrogen bonds : angle 4.42181 ( 1866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.5267 (tt) cc_final: 0.5039 (tp) REVERT: A 762 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6313 (tp) REVERT: A 806 GLU cc_start: 0.3877 (mp0) cc_final: 0.3670 (mp0) REVERT: A 815 TYR cc_start: 0.4209 (m-80) cc_final: 0.3629 (m-80) REVERT: A 820 ASN cc_start: 0.7164 (p0) cc_final: 0.6693 (p0) REVERT: A 823 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: B 146 MET cc_start: 0.2049 (ttt) cc_final: 0.1787 (tmm) REVERT: B 158 MET cc_start: -0.3302 (ttm) cc_final: -0.3864 (ptm) REVERT: B 229 MET cc_start: 0.4809 (tpp) cc_final: 0.4321 (tpp) REVERT: B 231 GLN cc_start: 0.8268 (tt0) cc_final: 0.8008 (tt0) REVERT: B 246 ILE cc_start: 0.4779 (mm) cc_final: 0.4526 (mm) REVERT: B 308 MET cc_start: 0.6963 (mmm) cc_final: 0.4822 (ptt) REVERT: B 341 LEU cc_start: 0.8110 (mp) cc_final: 0.7595 (mt) REVERT: C 122 VAL cc_start: 0.7246 (t) cc_final: 0.6877 (m) REVERT: C 126 GLU cc_start: 0.6639 (mp0) cc_final: 0.6078 (tm-30) REVERT: C 202 MET cc_start: 0.5634 (tmm) cc_final: 0.5373 (tmm) REVERT: C 292 ASP cc_start: 0.6673 (t0) cc_final: 0.6428 (t0) REVERT: D 43 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6552 (mtmm) REVERT: D 77 TYR cc_start: 0.4612 (p90) cc_final: 0.3994 (p90) REVERT: D 304 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7820 (p) REVERT: E 108 ILE cc_start: 0.7389 (mm) cc_final: 0.7136 (mt) REVERT: E 281 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7411 (tt) outliers start: 35 outliers final: 24 residues processed: 198 average time/residue: 0.0922 time to fit residues: 27.3919 Evaluate side-chains 188 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.217199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.180815 restraints weight = 20546.771| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.06 r_work: 0.4216 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12109 Z= 0.141 Angle : 0.655 13.917 16394 Z= 0.317 Chirality : 0.041 0.240 1915 Planarity : 0.005 0.066 2080 Dihedral : 8.843 123.559 1699 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.52 % Allowed : 20.23 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1481 helix: 0.51 (0.17), residues: 880 sheet: -1.38 (0.41), residues: 138 loop : 0.09 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 275 TYR 0.030 0.002 TYR B 322 PHE 0.014 0.001 PHE E 339 TRP 0.087 0.005 TRP D 40 HIS 0.003 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.00323 (12109) covalent geometry : angle 0.65475 (16394) hydrogen bonds : bond 0.03539 ( 636) hydrogen bonds : angle 4.37941 ( 1866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 806 GLU cc_start: 0.4060 (mp0) cc_final: 0.3784 (mp0) REVERT: A 815 TYR cc_start: 0.4202 (m-80) cc_final: 0.3665 (m-80) REVERT: A 820 ASN cc_start: 0.7148 (p0) cc_final: 0.6704 (p0) REVERT: A 823 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: B 146 MET cc_start: 0.2107 (ttt) cc_final: 0.1852 (tmm) REVERT: B 158 MET cc_start: -0.3240 (ttm) cc_final: -0.3847 (ptm) REVERT: B 229 MET cc_start: 0.4692 (tpp) cc_final: 0.4256 (tpp) REVERT: B 231 GLN cc_start: 0.8264 (tt0) cc_final: 0.7999 (tt0) REVERT: B 246 ILE cc_start: 0.4772 (mm) cc_final: 0.4515 (mm) REVERT: B 308 MET cc_start: 0.6921 (mmm) cc_final: 0.4822 (ptt) REVERT: C 122 VAL cc_start: 0.7179 (t) cc_final: 0.6813 (m) REVERT: C 126 GLU cc_start: 0.6767 (mp0) cc_final: 0.6456 (tm-30) REVERT: C 202 MET cc_start: 0.5628 (tmm) cc_final: 0.5387 (tmm) REVERT: C 292 ASP cc_start: 0.6640 (t0) cc_final: 0.6434 (t0) REVERT: D 43 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6331 (mtmm) REVERT: D 77 TYR cc_start: 0.4555 (p90) cc_final: 0.3962 (p90) REVERT: D 304 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7845 (p) REVERT: E 281 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7418 (tt) outliers start: 33 outliers final: 25 residues processed: 194 average time/residue: 0.0916 time to fit residues: 26.5677 Evaluate side-chains 190 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 0.0570 chunk 25 optimal weight: 6.9990 chunk 129 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN E 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.223811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.192512 restraints weight = 20627.811| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.85 r_work: 0.4366 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12109 Z= 0.119 Angle : 0.632 12.980 16394 Z= 0.308 Chirality : 0.041 0.319 1915 Planarity : 0.005 0.063 2080 Dihedral : 8.610 121.063 1699 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.06 % Allowed : 20.84 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.22), residues: 1481 helix: 0.70 (0.17), residues: 879 sheet: -1.43 (0.41), residues: 138 loop : 0.23 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 234 TYR 0.030 0.002 TYR B 322 PHE 0.014 0.001 PHE E 35 TRP 0.062 0.005 TRP D 40 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00265 (12109) covalent geometry : angle 0.63191 (16394) hydrogen bonds : bond 0.03310 ( 636) hydrogen bonds : angle 4.21328 ( 1866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.5425 (tt) cc_final: 0.5211 (tp) REVERT: A 806 GLU cc_start: 0.4169 (mp0) cc_final: 0.3909 (mp0) REVERT: A 815 TYR cc_start: 0.4245 (m-80) cc_final: 0.3772 (m-80) REVERT: A 820 ASN cc_start: 0.7133 (p0) cc_final: 0.6712 (p0) REVERT: A 823 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: B 146 MET cc_start: 0.2175 (ttt) cc_final: 0.1880 (tmm) REVERT: B 158 MET cc_start: -0.3463 (ttm) cc_final: -0.4006 (ptm) REVERT: B 229 MET cc_start: 0.4576 (tpp) cc_final: 0.4341 (tpp) REVERT: B 231 GLN cc_start: 0.8277 (tt0) cc_final: 0.8024 (tt0) REVERT: B 246 ILE cc_start: 0.4698 (mm) cc_final: 0.4442 (mm) REVERT: B 308 MET cc_start: 0.6788 (mmm) cc_final: 0.5047 (ptt) REVERT: B 341 LEU cc_start: 0.8086 (mp) cc_final: 0.7654 (mt) REVERT: C 122 VAL cc_start: 0.7235 (t) cc_final: 0.6875 (m) REVERT: C 202 MET cc_start: 0.5638 (tmm) cc_final: 0.5171 (tmm) REVERT: C 213 MET cc_start: 0.7056 (mmp) cc_final: 0.6339 (mmp) REVERT: C 292 ASP cc_start: 0.6554 (t0) cc_final: 0.6216 (t0) REVERT: D 43 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6202 (mttt) REVERT: D 77 TYR cc_start: 0.4462 (p90) cc_final: 0.3920 (p90) REVERT: D 304 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7763 (p) REVERT: E 281 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7242 (tt) outliers start: 27 outliers final: 20 residues processed: 201 average time/residue: 0.0919 time to fit residues: 27.5847 Evaluate side-chains 190 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 254 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 302 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.221983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.190939 restraints weight = 20575.066| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.52 r_work: 0.4361 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4233 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12109 Z= 0.144 Angle : 0.658 12.527 16394 Z= 0.318 Chirality : 0.041 0.206 1915 Planarity : 0.005 0.064 2080 Dihedral : 8.557 123.651 1697 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.06 % Allowed : 21.22 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1481 helix: 0.67 (0.17), residues: 879 sheet: -1.44 (0.41), residues: 138 loop : 0.18 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 234 TYR 0.047 0.002 TYR B 322 PHE 0.019 0.001 PHE E 346 TRP 0.020 0.002 TRP B 38 HIS 0.005 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00328 (12109) covalent geometry : angle 0.65755 (16394) hydrogen bonds : bond 0.03462 ( 636) hydrogen bonds : angle 4.27589 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2977.54 seconds wall clock time: 52 minutes 1.72 seconds (3121.72 seconds total)