Starting phenix.real_space_refine on Sat Aug 23 00:28:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1a_35915/08_2025/8j1a_35915.map" } resolution = 3.24 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= 0.000 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5640 2.51 5 N 1528 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 8845 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1759 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 2.31, per 1000 atoms: 0.26 Number of scatterers: 8845 At special positions: 0 Unit cell: (88.992, 119.48, 124.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1618 8.00 N 1528 7.00 C 5640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.03 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 526.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 39.7% alpha, 22.2% 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 8 through 33 removed outlier: 3.539A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.980A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.359A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.582A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.627A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.625A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 13 through 15 No H-bonds generated for 'chain 'R' and resid 13 through 15' Processing helix chain 'R' and resid 16 through 48 removed outlier: 4.197A pdb=" N TYR R 21 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 Processing helix chain 'R' and resid 53 through 71 removed outlier: 4.033A pdb=" N LEU R 58 " --> pdb=" O ARG R 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 89 through 124 removed outlier: 3.651A pdb=" N ARG R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 133 removed outlier: 3.598A pdb=" N VAL R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 153 removed outlier: 3.557A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 159 Proline residue: R 157 - end of helix No H-bonds generated for 'chain 'R' and resid 154 through 159' Processing helix chain 'R' and resid 175 through 215 removed outlier: 3.734A pdb=" N TYR R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 342 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 347 through 349 No H-bonds generated for 'chain 'R' and resid 347 through 349' Processing helix chain 'R' and resid 350 through 371 removed outlier: 3.838A pdb=" N LEU R 354 " --> pdb=" O VAL R 350 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP R 360 " --> pdb=" O ALA R 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU R 361 " --> pdb=" O ASN R 357 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 387 Processing helix chain 'R' and resid 387 through 392 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.168A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.951A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.562A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.650A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.147A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.818A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.665A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.739A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 161 through 162 removed outlier: 4.159A pdb=" N VAL R 162 " --> pdb=" O THR R 167 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR R 167 " --> pdb=" O VAL R 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.916A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.486A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1242 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: 1.61 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1552 1.33 - 1.45: 2399 1.45 - 1.57: 4996 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9029 Sorted by residual: bond pdb=" C TYR A 287 " pdb=" O TYR A 287 " ideal model delta sigma weight residual 1.244 1.203 0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" C ASN G 59 " pdb=" N PRO G 60 " ideal model delta sigma weight residual 1.336 1.369 -0.034 9.80e-03 1.04e+04 1.17e+01 bond pdb=" CA ARG R 176 " pdb=" C ARG R 176 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" C ASP B 163 " pdb=" N THR B 164 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.24e-02 6.50e+03 9.02e+00 bond pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.35e-02 5.49e+03 6.82e+00 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 11882 1.52 - 3.03: 280 3.03 - 4.55: 57 4.55 - 6.07: 8 6.07 - 7.58: 8 Bond angle restraints: 12235 Sorted by residual: angle pdb=" N TYR R 332 " pdb=" CA TYR R 332 " pdb=" C TYR R 332 " ideal model delta sigma weight residual 113.12 120.45 -7.33 1.25e+00 6.40e-01 3.43e+01 angle pdb=" CA ASP B 163 " pdb=" C ASP B 163 " pdb=" O ASP B 163 " ideal model delta sigma weight residual 120.55 114.60 5.95 1.21e+00 6.83e-01 2.42e+01 angle pdb=" N GLU A 289 " pdb=" CA GLU A 289 " pdb=" C GLU A 289 " ideal model delta sigma weight residual 110.97 105.99 4.98 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 111.22 104.32 6.90 1.58e+00 4.01e-01 1.91e+01 angle pdb=" N SER A 293 " pdb=" CA SER A 293 " pdb=" C SER A 293 " ideal model delta sigma weight residual 109.46 102.24 7.22 1.66e+00 3.63e-01 1.89e+01 ... (remaining 12230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4749 17.58 - 35.16: 456 35.16 - 52.74: 108 52.74 - 70.32: 30 70.32 - 87.90: 8 Dihedral angle restraints: 5351 sinusoidal: 2061 harmonic: 3290 Sorted by residual: dihedral pdb=" N SER B 331 " pdb=" C SER B 331 " pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta harmonic sigma weight residual 122.80 113.84 8.96 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 40.06 49.94 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " pdb=" CG ASP B 290 " pdb=" OD1 ASP B 290 " ideal model delta sinusoidal sigma weight residual -30.00 -90.91 60.91 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1174 0.054 - 0.107: 180 0.107 - 0.161: 35 0.161 - 0.215: 6 0.215 - 0.268: 4 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA TYR R 332 " pdb=" N TYR R 332 " pdb=" C TYR R 332 " pdb=" CB TYR R 332 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG R 176 " pdb=" N ARG R 176 " pdb=" C ARG R 176 " pdb=" CB ARG R 176 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA SER A 293 " pdb=" N SER A 293 " pdb=" C SER A 293 " pdb=" CB SER A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1396 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.057 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO S 14 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 333 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ASP B 333 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP B 333 " 0.021 2.00e-02 2.50e+03 pdb=" N SER B 334 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C GLY R 175 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.016 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 82 2.56 - 3.15: 7341 3.15 - 3.73: 13430 3.73 - 4.32: 18841 4.32 - 4.90: 33050 Nonbonded interactions: 72744 Sorted by model distance: nonbonded pdb=" CD1 LEU R 98 " pdb=" CE3 TRP R 156 " model vdw 1.976 3.760 nonbonded pdb=" CD2 LEU R 98 " pdb=" CE2 TYR R 159 " model vdw 2.136 3.760 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.174 3.040 nonbonded pdb=" CD1 LEU R 98 " pdb=" CZ3 TRP R 156 " model vdw 2.189 3.760 nonbonded pdb=" OH TYR R 12 " pdb=" OE2 GLU R 14 " model vdw 2.268 3.040 ... (remaining 72739 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: 1.040 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.058 9032 Z= 0.214 Angle : 0.615 7.584 12241 Z= 0.371 Chirality : 0.044 0.268 1399 Planarity : 0.005 0.084 1543 Dihedral : 15.324 87.901 3222 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.63 % Allowed : 16.37 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.26), residues: 1119 helix: 1.87 (0.28), residues: 370 sheet: -0.56 (0.30), residues: 287 loop : -0.48 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.016 0.001 TYR S 227 PHE 0.013 0.001 PHE S 32 TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9029) covalent geometry : angle 0.61537 (12235) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.78411 ( 6) hydrogen bonds : bond 0.12777 ( 444) hydrogen bonds : angle 5.95467 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7603 (mt0) REVERT: B 259 GLN cc_start: 0.8480 (pt0) cc_final: 0.8270 (pt0) REVERT: B 260 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: S 160 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7036 (mtp85) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.1430 time to fit residues: 18.4154 Evaluate side-chains 95 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain R residue 359 THR Chi-restraints excluded: chain R residue 390 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 132 ASN R 61 ASN R 352 HIS R 362 ASN S 82 GLN S 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.177295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133203 restraints weight = 9828.149| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.14 r_work: 0.3177 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9032 Z= 0.164 Angle : 0.562 7.273 12241 Z= 0.301 Chirality : 0.042 0.152 1399 Planarity : 0.004 0.049 1543 Dihedral : 5.009 61.997 1244 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.31 % Allowed : 15.74 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.26), residues: 1119 helix: 1.75 (0.27), residues: 383 sheet: -0.50 (0.30), residues: 281 loop : -0.45 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.015 0.001 TYR B 59 PHE 0.014 0.002 PHE R 96 TRP 0.010 0.002 TRP B 169 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9029) covalent geometry : angle 0.56187 (12235) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.69848 ( 6) hydrogen bonds : bond 0.04048 ( 444) hydrogen bonds : angle 4.96149 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7609 (mt0) outliers start: 22 outliers final: 13 residues processed: 126 average time/residue: 0.1130 time to fit residues: 19.1477 Evaluate side-chains 108 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.180926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135750 restraints weight = 9775.562| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.11 r_work: 0.3235 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.138 Angle : 0.530 7.802 12241 Z= 0.282 Chirality : 0.041 0.140 1399 Planarity : 0.004 0.037 1543 Dihedral : 4.609 60.265 1237 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.73 % Allowed : 17.73 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.42 (0.26), residues: 1119 helix: 1.86 (0.27), residues: 380 sheet: -0.53 (0.31), residues: 282 loop : -0.46 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.014 0.001 TYR R 159 PHE 0.018 0.002 PHE S 68 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9029) covalent geometry : angle 0.52959 (12235) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.61615 ( 6) hydrogen bonds : bond 0.03659 ( 444) hydrogen bonds : angle 4.83125 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7630 (mt0) REVERT: S 160 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7077 (mtp85) outliers start: 26 outliers final: 16 residues processed: 118 average time/residue: 0.1205 time to fit residues: 19.0262 Evaluate side-chains 110 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 97 optimal weight: 0.0170 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137585 restraints weight = 9828.653| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.14 r_work: 0.3311 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9032 Z= 0.111 Angle : 0.499 7.345 12241 Z= 0.266 Chirality : 0.040 0.161 1399 Planarity : 0.003 0.036 1543 Dihedral : 4.430 55.868 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.04 % Allowed : 18.36 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.26), residues: 1119 helix: 1.97 (0.27), residues: 377 sheet: -0.63 (0.30), residues: 279 loop : -0.41 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.011 0.001 TYR R 159 PHE 0.012 0.001 PHE B 292 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9029) covalent geometry : angle 0.49850 (12235) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.56115 ( 6) hydrogen bonds : bond 0.03336 ( 444) hydrogen bonds : angle 4.65462 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8403 (mm-40) cc_final: 0.7640 (mt0) REVERT: B 86 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8534 (p) REVERT: S 160 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7165 (mtp85) outliers start: 29 outliers final: 17 residues processed: 126 average time/residue: 0.1029 time to fit residues: 17.3766 Evaluate side-chains 115 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 32 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.176023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132384 restraints weight = 9680.649| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.09 r_work: 0.3210 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9032 Z= 0.151 Angle : 0.528 8.000 12241 Z= 0.279 Chirality : 0.042 0.140 1399 Planarity : 0.004 0.037 1543 Dihedral : 3.996 18.061 1234 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.73 % Allowed : 19.31 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1119 helix: 1.93 (0.27), residues: 377 sheet: -0.72 (0.30), residues: 279 loop : -0.43 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.010 0.001 TYR R 159 PHE 0.014 0.002 PHE R 96 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9029) covalent geometry : angle 0.52796 (12235) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.73591 ( 6) hydrogen bonds : bond 0.03507 ( 444) hydrogen bonds : angle 4.69937 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: R 191 LEU cc_start: 0.7456 (tt) cc_final: 0.7213 (tp) REVERT: S 82 GLN cc_start: 0.7558 (tp40) cc_final: 0.7263 (tp40) REVERT: S 160 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7107 (mtp85) outliers start: 26 outliers final: 22 residues processed: 124 average time/residue: 0.0992 time to fit residues: 16.8437 Evaluate side-chains 123 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 119 ASN R 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.182567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138172 restraints weight = 9694.057| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.21 r_work: 0.3348 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9032 Z= 0.101 Angle : 0.489 8.161 12241 Z= 0.259 Chirality : 0.040 0.135 1399 Planarity : 0.003 0.037 1543 Dihedral : 3.786 17.927 1234 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.52 % Allowed : 19.94 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.25), residues: 1119 helix: 2.03 (0.27), residues: 378 sheet: -0.75 (0.30), residues: 274 loop : -0.42 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.010 0.001 TYR S 60 PHE 0.011 0.001 PHE B 292 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9029) covalent geometry : angle 0.48913 (12235) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.65872 ( 6) hydrogen bonds : bond 0.03109 ( 444) hydrogen bonds : angle 4.47992 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7618 (mt0) REVERT: B 86 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8450 (p) REVERT: B 96 ARG cc_start: 0.8352 (mtt180) cc_final: 0.8144 (mtt180) REVERT: S 82 GLN cc_start: 0.7509 (tp40) cc_final: 0.7107 (tp-100) outliers start: 24 outliers final: 18 residues processed: 121 average time/residue: 0.1052 time to fit residues: 17.3986 Evaluate side-chains 115 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN R 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.175114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131532 restraints weight = 9756.546| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.13 r_work: 0.3286 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9032 Z= 0.167 Angle : 0.539 8.569 12241 Z= 0.284 Chirality : 0.042 0.139 1399 Planarity : 0.004 0.042 1543 Dihedral : 3.993 18.287 1234 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.73 % Allowed : 19.73 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.30 (0.25), residues: 1119 helix: 1.91 (0.27), residues: 378 sheet: -0.85 (0.30), residues: 274 loop : -0.47 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.012 0.001 TYR R 159 PHE 0.022 0.002 PHE S 68 TRP 0.008 0.001 TRP S 36 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9029) covalent geometry : angle 0.53853 (12235) SS BOND : bond 0.00488 ( 3) SS BOND : angle 1.00970 ( 6) hydrogen bonds : bond 0.03520 ( 444) hydrogen bonds : angle 4.64822 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6896 (tp) REVERT: A 306 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7497 (mt0) REVERT: B 86 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8486 (p) REVERT: R 191 LEU cc_start: 0.7391 (tt) cc_final: 0.7170 (tp) REVERT: S 82 GLN cc_start: 0.7516 (tp40) cc_final: 0.7106 (tp-100) outliers start: 26 outliers final: 18 residues processed: 124 average time/residue: 0.1088 time to fit residues: 18.3555 Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 65 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 269 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.179661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135846 restraints weight = 9665.321| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.08 r_work: 0.3323 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9032 Z= 0.126 Angle : 0.513 8.788 12241 Z= 0.271 Chirality : 0.041 0.137 1399 Planarity : 0.003 0.040 1543 Dihedral : 3.903 18.259 1234 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.31 % Allowed : 20.25 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.32 (0.25), residues: 1119 helix: 1.94 (0.27), residues: 378 sheet: -0.84 (0.30), residues: 274 loop : -0.48 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.010 0.001 TYR R 159 PHE 0.019 0.001 PHE S 68 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9029) covalent geometry : angle 0.51252 (12235) SS BOND : bond 0.00420 ( 3) SS BOND : angle 0.70207 ( 6) hydrogen bonds : bond 0.03273 ( 444) hydrogen bonds : angle 4.56508 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6951 (tp) REVERT: B 86 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8482 (p) REVERT: R 191 LEU cc_start: 0.7383 (tt) cc_final: 0.7162 (tp) REVERT: S 82 GLN cc_start: 0.7507 (tp40) cc_final: 0.7105 (tp-100) outliers start: 22 outliers final: 17 residues processed: 120 average time/residue: 0.1005 time to fit residues: 16.8315 Evaluate side-chains 118 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139137 restraints weight = 9726.893| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.22 r_work: 0.3350 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9032 Z= 0.101 Angle : 0.496 9.028 12241 Z= 0.261 Chirality : 0.040 0.193 1399 Planarity : 0.003 0.040 1543 Dihedral : 3.739 18.218 1234 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.20 % Allowed : 20.25 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.40 (0.25), residues: 1119 helix: 2.01 (0.27), residues: 380 sheet: -0.77 (0.30), residues: 274 loop : -0.46 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.009 0.001 TYR S 60 PHE 0.016 0.001 PHE S 68 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9029) covalent geometry : angle 0.49593 (12235) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.75128 ( 6) hydrogen bonds : bond 0.03057 ( 444) hydrogen bonds : angle 4.41931 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 276 GLU cc_start: 0.7381 (pm20) cc_final: 0.7022 (pm20) REVERT: B 86 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8456 (p) REVERT: S 68 PHE cc_start: 0.7876 (m-10) cc_final: 0.7631 (m-10) REVERT: S 82 GLN cc_start: 0.7511 (tp40) cc_final: 0.7122 (tp-100) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.1050 time to fit residues: 17.3844 Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.136670 restraints weight = 9714.819| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.19 r_work: 0.3317 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9032 Z= 0.130 Angle : 0.521 9.143 12241 Z= 0.274 Chirality : 0.042 0.345 1399 Planarity : 0.003 0.043 1543 Dihedral : 3.819 18.447 1234 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.20 % Allowed : 20.36 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.40 (0.25), residues: 1119 helix: 1.99 (0.27), residues: 380 sheet: -0.78 (0.30), residues: 274 loop : -0.44 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.009 0.001 TYR R 159 PHE 0.018 0.001 PHE S 68 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9029) covalent geometry : angle 0.51992 (12235) SS BOND : bond 0.00287 ( 3) SS BOND : angle 1.41322 ( 6) hydrogen bonds : bond 0.03210 ( 444) hydrogen bonds : angle 4.49462 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 273 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6910 (tp) REVERT: A 276 GLU cc_start: 0.7407 (pm20) cc_final: 0.7047 (pm20) REVERT: A 306 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7676 (mt0) REVERT: B 86 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8536 (p) REVERT: R 191 LEU cc_start: 0.7414 (tt) cc_final: 0.7195 (tp) REVERT: S 82 GLN cc_start: 0.7522 (tp40) cc_final: 0.7138 (tp-100) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.1046 time to fit residues: 16.7409 Evaluate side-chains 117 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.2980 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN A 304 GLN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.183915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138542 restraints weight = 9643.688| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.12 r_work: 0.3352 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9032 Z= 0.103 Angle : 0.502 9.094 12241 Z= 0.263 Chirality : 0.041 0.208 1399 Planarity : 0.003 0.040 1543 Dihedral : 3.739 18.325 1234 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.10 % Allowed : 20.67 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.25), residues: 1119 helix: 2.04 (0.27), residues: 381 sheet: -0.72 (0.30), residues: 274 loop : -0.46 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.009 0.001 TYR S 60 PHE 0.016 0.001 PHE S 68 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9029) covalent geometry : angle 0.50099 (12235) SS BOND : bond 0.00238 ( 3) SS BOND : angle 1.23677 ( 6) hydrogen bonds : bond 0.03034 ( 444) hydrogen bonds : angle 4.40378 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.72 seconds wall clock time: 47 minutes 8.81 seconds (2828.81 seconds total)