Starting phenix.real_space_refine on Sat Aug 23 00:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.map" model { file = "/net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efb_28077/08_2025/8efb_28077.cif" } resolution = 3.2 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= 0.007 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 73 5.16 5 C 5701 2.51 5 N 1508 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s 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: 8947 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2290 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 273} Chain: "A" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1826 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 436 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1792 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'WH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.19 Number of scatterers: 8947 At special positions: 0 Unit cell: (125.28, 113.4, 108, 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 73 16.00 O 1665 8.00 N 1508 7.00 C 5701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 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: 0.98 Conformation dependent library (CDL) restraints added in 351.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 39.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 69 through 98 Processing helix chain 'R' and resid 103 through 133 Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 3.911A pdb=" N LEU R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 removed outlier: 3.569A pdb=" N ALA R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 226 through 264 removed outlier: 4.758A pdb=" N MET R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 340 Proline residue: R 335 - end of helix Processing helix chain 'R' and resid 342 through 352 removed outlier: 3.515A pdb=" N PHE R 352 " --> pdb=" O CYS R 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.210A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.605A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.553A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.045A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.948A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.888A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.230A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.151A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 213 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.729A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.817A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.994A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.681A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.707A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.025A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.878A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.660A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.660A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.062A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1404 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: 1.37 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2721 1.34 - 1.46: 2195 1.46 - 1.59: 4114 1.59 - 1.71: 0 1.71 - 1.83: 107 Bond restraints: 9137 Sorted by residual: bond pdb=" C22 WH2 R 500 " pdb=" O02 WH2 R 500 " ideal model delta sigma weight residual 1.428 1.557 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C ALA E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.18e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.75e+00 bond pdb=" C LEU R 123 " pdb=" N PRO R 124 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.36e-02 5.41e+03 5.40e+00 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.23e-02 6.61e+03 4.81e+00 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11785 1.93 - 3.86: 517 3.86 - 5.79: 53 5.79 - 7.72: 19 7.72 - 9.65: 4 Bond angle restraints: 12378 Sorted by residual: angle pdb=" CA ARG E 219 " pdb=" CB ARG E 219 " pdb=" CG ARG E 219 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 angle pdb=" C ALA R 104 " pdb=" N THR R 105 " pdb=" CA THR R 105 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.85e+01 angle pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta sigma weight residual 125.66 133.36 -7.70 1.85e+00 2.92e-01 1.73e+01 angle pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " pdb=" CG PHE R 206 " ideal model delta sigma weight residual 113.80 117.91 -4.11 1.00e+00 1.00e+00 1.69e+01 angle pdb=" N PHE R 206 " pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " ideal model delta sigma weight residual 110.16 115.12 -4.96 1.48e+00 4.57e-01 1.12e+01 ... (remaining 12373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.23: 5004 11.23 - 22.47: 365 22.47 - 33.70: 58 33.70 - 44.94: 17 44.94 - 56.17: 5 Dihedral angle restraints: 5449 sinusoidal: 2147 harmonic: 3302 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" N PHE R 206 " pdb=" C PHE R 206 " pdb=" CA PHE R 206 " pdb=" CB PHE R 206 " ideal model delta harmonic sigma weight residual 122.80 131.76 -8.96 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 5446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1052 0.057 - 0.114: 272 0.114 - 0.171: 67 0.171 - 0.228: 13 0.228 - 0.285: 2 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA PHE R 206 " pdb=" N PHE R 206 " pdb=" C PHE R 206 " pdb=" CB PHE R 206 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE R 140 " pdb=" CA ILE R 140 " pdb=" CG1 ILE R 140 " pdb=" CG2 ILE R 140 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1403 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 206 " 0.025 2.00e-02 2.50e+03 2.05e-02 7.32e+00 pdb=" CG PHE R 206 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE R 206 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE R 206 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 206 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE R 206 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 158 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C TRP R 158 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP R 158 " 0.017 2.00e-02 2.50e+03 pdb=" N THR R 159 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 197 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C SER R 197 " 0.044 2.00e-02 2.50e+03 pdb=" O SER R 197 " -0.017 2.00e-02 2.50e+03 pdb=" N SER R 198 " -0.015 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1318 2.78 - 3.31: 8464 3.31 - 3.84: 14836 3.84 - 4.37: 16974 4.37 - 4.90: 30493 Nonbonded interactions: 72085 Sorted by model distance: nonbonded pdb=" OG SER E 205 " pdb=" OG1 THR E 216 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.294 3.040 nonbonded pdb=" O ARG R 260 " pdb=" OG SER R 263 " model vdw 2.331 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.349 3.120 ... (remaining 72080 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: 0.300 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.030 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.005 0.129 9139 Z= 0.270 Angle : 0.909 9.648 12382 Z= 0.539 Chirality : 0.056 0.285 1406 Planarity : 0.007 0.049 1554 Dihedral : 8.311 56.169 3313 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.18 (0.24), residues: 1122 helix: 2.62 (0.24), residues: 413 sheet: 0.17 (0.29), residues: 283 loop : -0.63 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 22 TYR 0.037 0.003 TYR R 151 PHE 0.042 0.003 PHE R 206 TRP 0.030 0.003 TRP E 111 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9137) covalent geometry : angle 0.90825 (12378) SS BOND : bond 0.00485 ( 2) SS BOND : angle 2.44801 ( 4) hydrogen bonds : bond 0.12245 ( 486) hydrogen bonds : angle 5.90809 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 MET cc_start: 0.6703 (mmm) cc_final: 0.6449 (mmt) REVERT: R 223 PHE cc_start: 0.6558 (m-80) cc_final: 0.6263 (m-10) REVERT: R 268 SER cc_start: 0.6932 (m) cc_final: 0.6722 (p) REVERT: A 28 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5904 (mp0) REVERT: A 207 GLU cc_start: 0.6510 (tt0) cc_final: 0.6137 (tt0) REVERT: A 298 GLU cc_start: 0.6951 (tt0) cc_final: 0.6327 (mt-10) REVERT: A 337 ASP cc_start: 0.7986 (m-30) cc_final: 0.7674 (m-30) REVERT: B 36 ASN cc_start: 0.7609 (m-40) cc_final: 0.7333 (p0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.0849 time to fit residues: 30.7109 Evaluate side-chains 159 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN A 244 HIS A 322 HIS B 35 ASN B 91 HIS B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127286 restraints weight = 10106.155| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.08 r_work: 0.3259 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9139 Z= 0.171 Angle : 0.579 11.511 12382 Z= 0.308 Chirality : 0.043 0.152 1406 Planarity : 0.005 0.047 1554 Dihedral : 4.346 39.021 1271 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.86 % Allowed : 8.27 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.54 (0.24), residues: 1122 helix: 2.96 (0.24), residues: 408 sheet: 0.23 (0.29), residues: 290 loop : -0.32 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 219 TYR 0.019 0.002 TYR R 108 PHE 0.027 0.002 PHE R 206 TRP 0.020 0.002 TRP E 111 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9137) covalent geometry : angle 0.57850 (12378) SS BOND : bond 0.00365 ( 2) SS BOND : angle 1.17204 ( 4) hydrogen bonds : bond 0.04008 ( 486) hydrogen bonds : angle 4.83988 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 102 LYS cc_start: 0.7930 (pttt) cc_final: 0.7700 (pttp) REVERT: R 132 MET cc_start: 0.7424 (mmm) cc_final: 0.7052 (mmt) REVERT: R 223 PHE cc_start: 0.6662 (m-80) cc_final: 0.6283 (m-10) REVERT: R 257 MET cc_start: 0.8653 (ttp) cc_final: 0.8412 (ttt) REVERT: A 18 MET cc_start: 0.8633 (tpp) cc_final: 0.8394 (mtp) REVERT: A 244 HIS cc_start: 0.7885 (m90) cc_final: 0.7682 (m170) REVERT: A 308 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 316 THR cc_start: 0.8106 (m) cc_final: 0.7805 (p) REVERT: B 32 GLN cc_start: 0.8189 (mt0) cc_final: 0.7531 (mp10) REVERT: B 36 ASN cc_start: 0.7919 (m-40) cc_final: 0.7442 (p0) REVERT: B 43 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7905 (mt) REVERT: B 46 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7572 (mpt90) REVERT: B 98 SER cc_start: 0.8520 (m) cc_final: 0.8202 (t) REVERT: E 187 GLN cc_start: 0.8679 (pt0) cc_final: 0.8435 (pt0) REVERT: E 247 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6290 (mp0) outliers start: 28 outliers final: 18 residues processed: 195 average time/residue: 0.0820 time to fit residues: 21.7325 Evaluate side-chains 172 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN R 173 HIS R 334 ASN B 295 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106902 restraints weight = 10260.348| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.05 r_work: 0.3108 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9139 Z= 0.157 Angle : 0.536 10.751 12382 Z= 0.288 Chirality : 0.042 0.166 1406 Planarity : 0.004 0.045 1554 Dihedral : 4.228 32.617 1271 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.57 % Allowed : 10.51 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.46 (0.24), residues: 1122 helix: 2.83 (0.24), residues: 410 sheet: 0.15 (0.29), residues: 277 loop : -0.25 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.018 0.002 TYR R 229 PHE 0.018 0.001 PHE R 206 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9137) covalent geometry : angle 0.53580 (12378) SS BOND : bond 0.00382 ( 2) SS BOND : angle 0.77795 ( 4) hydrogen bonds : bond 0.03929 ( 486) hydrogen bonds : angle 4.61376 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.206 Fit side-chains REVERT: R 132 MET cc_start: 0.7490 (mmm) cc_final: 0.7133 (mmt) REVERT: R 223 PHE cc_start: 0.6661 (m-80) cc_final: 0.6423 (m-10) REVERT: R 229 TYR cc_start: 0.7435 (t80) cc_final: 0.6918 (t80) REVERT: R 257 MET cc_start: 0.8719 (ttp) cc_final: 0.8436 (ttt) REVERT: A 244 HIS cc_start: 0.8082 (m90) cc_final: 0.7878 (m90) REVERT: A 298 GLU cc_start: 0.7402 (tt0) cc_final: 0.6752 (mt-10) REVERT: A 308 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: B 36 ASN cc_start: 0.7740 (m-40) cc_final: 0.7353 (p0) REVERT: B 43 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 46 ARG cc_start: 0.8583 (mtp180) cc_final: 0.7922 (mpt90) REVERT: B 59 TYR cc_start: 0.9094 (m-80) cc_final: 0.8601 (m-80) REVERT: E 187 GLN cc_start: 0.8862 (pt0) cc_final: 0.8642 (pt0) outliers start: 35 outliers final: 25 residues processed: 183 average time/residue: 0.0825 time to fit residues: 20.5315 Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain R residue 333 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 GLN R 152 ASN A 213 HIS B 32 GLN B 88 ASN B 295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102900 restraints weight = 10462.542| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.05 r_work: 0.3055 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9139 Z= 0.178 Angle : 0.540 10.205 12382 Z= 0.288 Chirality : 0.042 0.177 1406 Planarity : 0.004 0.046 1554 Dihedral : 4.328 28.347 1271 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.47 % Allowed : 11.73 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.23 (0.24), residues: 1122 helix: 2.51 (0.24), residues: 416 sheet: 0.02 (0.29), residues: 283 loop : -0.28 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.013 0.002 TYR E 191 PHE 0.017 0.002 PHE R 223 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9137) covalent geometry : angle 0.53969 (12378) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.74043 ( 4) hydrogen bonds : bond 0.03963 ( 486) hydrogen bonds : angle 4.66373 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7363 (mmm) cc_final: 0.6968 (mmt) REVERT: R 229 TYR cc_start: 0.7683 (t80) cc_final: 0.7346 (t80) REVERT: A 9 ASP cc_start: 0.8346 (m-30) cc_final: 0.7924 (t0) REVERT: A 244 HIS cc_start: 0.8110 (m90) cc_final: 0.7694 (m90) REVERT: A 273 LEU cc_start: 0.8244 (mt) cc_final: 0.8015 (mp) REVERT: A 289 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8049 (pm20) REVERT: A 298 GLU cc_start: 0.7429 (tt0) cc_final: 0.6760 (mt-10) REVERT: A 308 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 313 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7861 (ttm170) REVERT: B 36 ASN cc_start: 0.7821 (m-40) cc_final: 0.7421 (p0) REVERT: B 46 ARG cc_start: 0.8676 (mtp180) cc_final: 0.8161 (mtt90) REVERT: B 59 TYR cc_start: 0.9031 (m-80) cc_final: 0.8707 (m-80) REVERT: B 217 MET cc_start: 0.8436 (ppp) cc_final: 0.8194 (ppp) REVERT: E 187 GLN cc_start: 0.8924 (pt0) cc_final: 0.8696 (pt0) REVERT: E 247 GLU cc_start: 0.6759 (mp0) cc_final: 0.6347 (mp0) outliers start: 34 outliers final: 26 residues processed: 179 average time/residue: 0.0828 time to fit residues: 20.1398 Evaluate side-chains 166 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain R residue 329 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103824 restraints weight = 10334.983| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.96 r_work: 0.2961 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9139 Z= 0.161 Angle : 0.522 10.964 12382 Z= 0.278 Chirality : 0.042 0.208 1406 Planarity : 0.004 0.044 1554 Dihedral : 4.232 26.865 1271 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.67 % Allowed : 13.27 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.22 (0.24), residues: 1122 helix: 2.55 (0.25), residues: 410 sheet: -0.03 (0.29), residues: 294 loop : -0.27 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.013 0.002 TYR R 130 PHE 0.012 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9137) covalent geometry : angle 0.52230 (12378) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.66928 ( 4) hydrogen bonds : bond 0.03829 ( 486) hydrogen bonds : angle 4.62276 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.275 Fit side-chains REVERT: R 132 MET cc_start: 0.7249 (mmm) cc_final: 0.6838 (mmt) REVERT: R 213 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.6077 (ptp-110) REVERT: R 283 MET cc_start: 0.7131 (tmm) cc_final: 0.6643 (tpt) REVERT: A 9 ASP cc_start: 0.8270 (m-30) cc_final: 0.7787 (t0) REVERT: A 231 ASP cc_start: 0.7076 (t70) cc_final: 0.6700 (t0) REVERT: A 244 HIS cc_start: 0.7816 (m90) cc_final: 0.7361 (m90) REVERT: A 273 LEU cc_start: 0.8104 (mt) cc_final: 0.7849 (mp) REVERT: A 308 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 36 ASN cc_start: 0.7946 (m-40) cc_final: 0.7445 (p0) REVERT: B 43 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8143 (mt) REVERT: B 46 ARG cc_start: 0.8518 (mtp180) cc_final: 0.7832 (mtt-85) REVERT: B 59 TYR cc_start: 0.9053 (m-80) cc_final: 0.8583 (m-80) REVERT: B 217 MET cc_start: 0.8374 (ppp) cc_final: 0.8040 (ppp) REVERT: B 292 PHE cc_start: 0.8924 (m-10) cc_final: 0.8362 (m-80) REVERT: E 247 GLU cc_start: 0.6555 (mp0) cc_final: 0.6257 (mp0) outliers start: 36 outliers final: 27 residues processed: 178 average time/residue: 0.0815 time to fit residues: 19.8153 Evaluate side-chains 174 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 210 THR Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 88 ASN E 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102990 restraints weight = 10333.903| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.02 r_work: 0.2935 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9139 Z= 0.152 Angle : 0.521 11.250 12382 Z= 0.276 Chirality : 0.042 0.218 1406 Planarity : 0.004 0.043 1554 Dihedral : 4.190 26.739 1271 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.88 % Allowed : 13.16 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.15 (0.25), residues: 1122 helix: 2.47 (0.25), residues: 416 sheet: -0.06 (0.30), residues: 279 loop : -0.33 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.020 0.002 TYR B 264 PHE 0.011 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9137) covalent geometry : angle 0.52123 (12378) SS BOND : bond 0.00320 ( 2) SS BOND : angle 0.62181 ( 4) hydrogen bonds : bond 0.03770 ( 486) hydrogen bonds : angle 4.56715 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7256 (mmm) cc_final: 0.6828 (mmt) REVERT: R 213 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.6072 (ptp-170) REVERT: R 283 MET cc_start: 0.7118 (tmm) cc_final: 0.6643 (tpt) REVERT: A 9 ASP cc_start: 0.8293 (m-30) cc_final: 0.7826 (t0) REVERT: A 231 ASP cc_start: 0.7273 (t70) cc_final: 0.6912 (t0) REVERT: A 308 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: B 36 ASN cc_start: 0.7875 (m-40) cc_final: 0.7351 (p0) REVERT: B 43 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8205 (mt) REVERT: B 59 TYR cc_start: 0.8986 (m-80) cc_final: 0.8535 (m-80) REVERT: B 217 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8140 (ppp) REVERT: B 292 PHE cc_start: 0.8926 (m-10) cc_final: 0.8362 (m-80) REVERT: E 87 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7435 (mpp80) REVERT: E 247 GLU cc_start: 0.6488 (mp0) cc_final: 0.6184 (mp0) outliers start: 38 outliers final: 27 residues processed: 173 average time/residue: 0.0729 time to fit residues: 17.2147 Evaluate side-chains 172 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102281 restraints weight = 10490.262| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.01 r_work: 0.3067 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9139 Z= 0.161 Angle : 0.529 10.904 12382 Z= 0.280 Chirality : 0.042 0.178 1406 Planarity : 0.004 0.044 1554 Dihedral : 4.157 25.597 1271 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.67 % Allowed : 13.98 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.10 (0.24), residues: 1122 helix: 2.47 (0.25), residues: 409 sheet: -0.10 (0.30), residues: 283 loop : -0.34 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 219 TYR 0.021 0.002 TYR B 264 PHE 0.012 0.001 PHE A 189 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9137) covalent geometry : angle 0.52855 (12378) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.67040 ( 4) hydrogen bonds : bond 0.03838 ( 486) hydrogen bonds : angle 4.60096 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7360 (mmm) cc_final: 0.6908 (mmt) REVERT: R 213 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6060 (ptp-170) REVERT: A 9 ASP cc_start: 0.8288 (m-30) cc_final: 0.7830 (t0) REVERT: A 231 ASP cc_start: 0.7291 (t70) cc_final: 0.6955 (t0) REVERT: A 244 HIS cc_start: 0.7943 (m90) cc_final: 0.7466 (m90) REVERT: A 308 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 36 ASN cc_start: 0.7840 (m-40) cc_final: 0.7351 (p0) REVERT: B 59 TYR cc_start: 0.8988 (m-80) cc_final: 0.8591 (m-80) REVERT: B 217 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8167 (ppp) REVERT: C 47 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7911 (mp0) REVERT: E 87 ARG cc_start: 0.8081 (ptp-170) cc_final: 0.7579 (mpp80) REVERT: E 247 GLU cc_start: 0.6405 (mp0) cc_final: 0.6062 (mp0) outliers start: 36 outliers final: 26 residues processed: 171 average time/residue: 0.0822 time to fit residues: 19.4135 Evaluate side-chains 172 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099803 restraints weight = 10445.203| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.89 r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9139 Z= 0.184 Angle : 0.550 11.624 12382 Z= 0.290 Chirality : 0.043 0.223 1406 Planarity : 0.004 0.045 1554 Dihedral : 4.251 24.933 1271 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.57 % Allowed : 14.29 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.06 (0.25), residues: 1122 helix: 2.43 (0.25), residues: 410 sheet: -0.22 (0.29), residues: 288 loop : -0.27 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.024 0.002 TYR B 264 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9137) covalent geometry : angle 0.54946 (12378) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.76198 ( 4) hydrogen bonds : bond 0.03975 ( 486) hydrogen bonds : angle 4.68298 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7432 (mmm) cc_final: 0.6985 (mmt) REVERT: R 213 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5992 (ptp-110) REVERT: R 283 MET cc_start: 0.7184 (tmm) cc_final: 0.6734 (tpt) REVERT: A 9 ASP cc_start: 0.8321 (m-30) cc_final: 0.7865 (t0) REVERT: A 231 ASP cc_start: 0.7329 (t70) cc_final: 0.7035 (t0) REVERT: A 308 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: B 36 ASN cc_start: 0.7863 (m-40) cc_final: 0.7370 (p0) REVERT: B 59 TYR cc_start: 0.8960 (m-80) cc_final: 0.8571 (m-80) REVERT: B 217 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: B 292 PHE cc_start: 0.8982 (m-10) cc_final: 0.8359 (m-80) REVERT: C 47 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7883 (mp0) REVERT: E 247 GLU cc_start: 0.6490 (mp0) cc_final: 0.6127 (mp0) outliers start: 35 outliers final: 27 residues processed: 169 average time/residue: 0.0775 time to fit residues: 18.1157 Evaluate side-chains 171 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103382 restraints weight = 10303.514| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.86 r_work: 0.2971 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9139 Z= 0.122 Angle : 0.515 11.744 12382 Z= 0.270 Chirality : 0.041 0.242 1406 Planarity : 0.004 0.045 1554 Dihedral : 4.068 25.622 1271 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.65 % Allowed : 15.92 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.06 (0.25), residues: 1122 helix: 2.37 (0.25), residues: 413 sheet: -0.20 (0.29), residues: 288 loop : -0.23 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.018 0.001 TYR B 264 PHE 0.010 0.001 PHE R 206 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9137) covalent geometry : angle 0.51458 (12378) SS BOND : bond 0.00381 ( 2) SS BOND : angle 0.69700 ( 4) hydrogen bonds : bond 0.03600 ( 486) hydrogen bonds : angle 4.51897 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7880 (p) REVERT: R 132 MET cc_start: 0.7371 (mmm) cc_final: 0.6922 (mmt) REVERT: R 206 PHE cc_start: 0.6778 (p90) cc_final: 0.4987 (m-80) REVERT: R 213 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.6017 (ptp-170) REVERT: R 266 MET cc_start: 0.7612 (tmm) cc_final: 0.7146 (tmm) REVERT: R 283 MET cc_start: 0.7194 (tmm) cc_final: 0.6721 (tpt) REVERT: A 9 ASP cc_start: 0.8243 (m-30) cc_final: 0.7787 (t0) REVERT: A 231 ASP cc_start: 0.7246 (t70) cc_final: 0.6992 (t0) REVERT: A 308 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: B 36 ASN cc_start: 0.7859 (m-40) cc_final: 0.7378 (p0) REVERT: B 59 TYR cc_start: 0.8906 (m-80) cc_final: 0.8512 (m-80) REVERT: B 217 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8083 (ppp) REVERT: B 292 PHE cc_start: 0.8896 (m-10) cc_final: 0.8293 (m-80) REVERT: C 47 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7746 (mp0) REVERT: E 113 GLN cc_start: 0.8368 (tp40) cc_final: 0.7845 (mm-40) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.0706 time to fit residues: 16.6412 Evaluate side-chains 167 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097850 restraints weight = 10389.614| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.13 r_work: 0.2895 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9139 Z= 0.173 Angle : 0.546 12.149 12382 Z= 0.286 Chirality : 0.042 0.229 1406 Planarity : 0.004 0.046 1554 Dihedral : 4.200 24.444 1271 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.55 % Allowed : 16.22 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.02 (0.25), residues: 1122 helix: 2.33 (0.25), residues: 413 sheet: -0.29 (0.29), residues: 288 loop : -0.20 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 219 TYR 0.022 0.002 TYR B 264 PHE 0.013 0.001 PHE R 206 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9137) covalent geometry : angle 0.54622 (12378) SS BOND : bond 0.00379 ( 2) SS BOND : angle 0.74069 ( 4) hydrogen bonds : bond 0.03867 ( 486) hydrogen bonds : angle 4.63769 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: R 132 MET cc_start: 0.7296 (mmm) cc_final: 0.6842 (mmt) REVERT: R 213 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5980 (ptp-170) REVERT: R 266 MET cc_start: 0.7700 (tmm) cc_final: 0.7273 (tmm) REVERT: R 283 MET cc_start: 0.7163 (tmm) cc_final: 0.6749 (tpt) REVERT: A 9 ASP cc_start: 0.8278 (m-30) cc_final: 0.7801 (t0) REVERT: A 231 ASP cc_start: 0.7444 (t70) cc_final: 0.7185 (t0) REVERT: A 308 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 36 ASN cc_start: 0.8004 (m-40) cc_final: 0.7483 (p0) REVERT: B 59 TYR cc_start: 0.8973 (m-80) cc_final: 0.8506 (m-80) REVERT: B 217 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8024 (ppp) REVERT: B 292 PHE cc_start: 0.9002 (m-10) cc_final: 0.8379 (m-80) REVERT: C 47 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7709 (mp0) REVERT: E 113 GLN cc_start: 0.8471 (tp40) cc_final: 0.7949 (mm-40) REVERT: E 198 SER cc_start: 0.9116 (t) cc_final: 0.8851 (p) REVERT: E 247 GLU cc_start: 0.6277 (mp0) cc_final: 0.5747 (mp0) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.0737 time to fit residues: 16.6956 Evaluate side-chains 164 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 314 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 244 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105158 restraints weight = 10188.942| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.99 r_work: 0.3113 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9139 Z= 0.107 Angle : 0.504 11.981 12382 Z= 0.264 Chirality : 0.041 0.212 1406 Planarity : 0.004 0.045 1554 Dihedral : 3.968 25.433 1271 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 16.63 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.17 (0.25), residues: 1122 helix: 2.44 (0.25), residues: 412 sheet: -0.21 (0.29), residues: 294 loop : -0.09 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.015 0.001 TYR B 264 PHE 0.011 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 321 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9137) covalent geometry : angle 0.50408 (12378) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.55023 ( 4) hydrogen bonds : bond 0.03434 ( 486) hydrogen bonds : angle 4.44781 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.97 seconds wall clock time: 37 minutes 43.09 seconds (2263.09 seconds total)