Starting phenix.real_space_refine on Tue Mar 3 23:27:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p00_13140/03_2026/7p00_13140.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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 63 5.16 5 C 5837 2.51 5 N 1547 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9110 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 405 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1879 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2359 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.25 Number of scatterers: 9110 At special positions: 0 Unit cell: (87.234, 121.737, 122.388, 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 63 16.00 O 1663 8.00 N 1547 7.00 C 5837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.05 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 356.7 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 17 sheets defined 38.7% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'H' and resid 70 through 73 removed outlier: 4.320A pdb=" N GLY H 73 " --> pdb=" O SER H 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 70 through 73' Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 237 through 241 removed outlier: 3.597A pdb=" N VAL H 241 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 13 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.512A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.552A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.580A pdb=" N GLN A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.884A pdb=" N ARG A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 267 " --> pdb=" O TRP A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.603A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.670A pdb=" N ALA A 299 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.546A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 68 through 84 Processing helix chain 'R' and resid 84 through 96 removed outlier: 3.570A pdb=" N THR R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 136 removed outlier: 4.074A pdb=" N TYR R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 205 Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 237 through 274 removed outlier: 4.007A pdb=" N VAL R 247 " --> pdb=" O LYS R 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 282 through 296 Processing helix chain 'R' and resid 296 through 309 removed outlier: 3.833A pdb=" N TYR R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN R 301 " --> pdb=" O SER R 297 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 319 removed outlier: 3.551A pdb=" N GLY R 315 " --> pdb=" O ARG R 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 24 Processing sheet with id=AA2, first strand: chain 'H' and resid 28 through 29 removed outlier: 6.175A pdb=" N ARG H 55 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP H 64 " --> pdb=" O ARG H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 28 through 29 removed outlier: 4.152A pdb=" N PHE H 127 " --> pdb=" O ARG H 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AA5, first strand: chain 'H' and resid 163 through 165 removed outlier: 3.548A pdb=" N GLU H 263 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU H 195 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU H 204 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.031A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.885A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.387A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.916A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.707A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.545A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 294 through 298 removed outlier: 6.436A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.108A pdb=" N HIS A 34 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 215 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 36 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AB7, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.175A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 169 through 173 445 hydrogen bonds defined for protein. 1257 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: 1.52 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1480 1.32 - 1.44: 2629 1.44 - 1.57: 5125 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9328 Sorted by residual: bond pdb=" C THR R 91 " pdb=" O THR R 91 " ideal model delta sigma weight residual 1.237 1.301 -0.065 1.17e-02 7.31e+03 3.06e+01 bond pdb=" ND1 HIS A 340 " pdb=" CE1 HIS A 340 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.62e+01 bond pdb=" CD2 HIS A 340 " pdb=" NE2 HIS A 340 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.32e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.25e+01 ... (remaining 9323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9292 1.87 - 3.74: 2976 3.74 - 5.61: 359 5.61 - 7.49: 26 7.49 - 9.36: 10 Bond angle restraints: 12663 Sorted by residual: angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" C GLN A 229 " ideal model delta sigma weight residual 111.28 103.41 7.87 1.09e+00 8.42e-01 5.22e+01 angle pdb=" N MET G 38 " pdb=" CA MET G 38 " pdb=" C MET G 38 " ideal model delta sigma weight residual 111.28 104.11 7.17 1.09e+00 8.42e-01 4.33e+01 angle pdb=" CB HIS A 340 " pdb=" CG HIS A 340 " pdb=" CD2 HIS A 340 " ideal model delta sigma weight residual 131.20 122.75 8.45 1.30e+00 5.92e-01 4.22e+01 angle pdb=" N ARG A 224 " pdb=" CA ARG A 224 " pdb=" C ARG A 224 " ideal model delta sigma weight residual 113.16 105.30 7.86 1.24e+00 6.50e-01 4.02e+01 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " ideal model delta sigma weight residual 110.23 119.59 -9.36 1.62e+00 3.81e-01 3.34e+01 ... (remaining 12658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5129 17.34 - 34.68: 350 34.68 - 52.03: 61 52.03 - 69.37: 12 69.37 - 86.71: 7 Dihedral angle restraints: 5559 sinusoidal: 2216 harmonic: 3343 Sorted by residual: dihedral pdb=" C ASP G 36 " pdb=" N ASP G 36 " pdb=" CA ASP G 36 " pdb=" CB ASP G 36 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C ARG H 208 " pdb=" N ARG H 208 " pdb=" CA ARG H 208 " pdb=" CB ARG H 208 " ideal model delta harmonic sigma weight residual -122.60 -133.96 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C ASN H 186 " pdb=" N ASN H 186 " pdb=" CA ASN H 186 " pdb=" CB ASN H 186 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 632 0.078 - 0.155: 544 0.155 - 0.233: 195 0.233 - 0.311: 35 0.311 - 0.388: 8 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ASP G 36 " pdb=" N ASP G 36 " pdb=" C ASP G 36 " pdb=" CB ASP G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PHE A 212 " pdb=" N PHE A 212 " pdb=" C PHE A 212 " pdb=" CB PHE A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1411 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 205 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PHE A 205 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE A 205 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN A 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 45 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C MET B 45 " 0.050 2.00e-02 2.50e+03 pdb=" O MET B 45 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 114 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C CYS B 114 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS B 114 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 115 " -0.015 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1135 2.77 - 3.30: 9199 3.30 - 3.83: 14983 3.83 - 4.37: 20645 4.37 - 4.90: 32283 Nonbonded interactions: 78245 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.236 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 3.040 nonbonded pdb=" O ILE R 273 " pdb=" OD1 ASN R 274 " model vdw 2.334 3.040 nonbonded pdb=" O ARG A 266 " pdb=" ND1 HIS A 340 " model vdw 2.393 3.120 nonbonded pdb=" N PHE B 253 " pdb=" O PHE B 253 " model vdw 2.468 2.496 ... (remaining 78240 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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.040 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:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.012 0.100 9332 Z= 0.901 Angle : 1.680 9.357 12669 Z= 1.284 Chirality : 0.115 0.388 1414 Planarity : 0.006 0.037 1596 Dihedral : 12.349 86.708 3394 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.81 % Allowed : 7.92 % Favored : 91.27 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.50 (0.24), residues: 1126 helix: 0.29 (0.26), residues: 373 sheet: -0.44 (0.32), residues: 248 loop : -0.62 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 89 TYR 0.022 0.002 TYR H 207 PHE 0.030 0.003 PHE A 205 TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.01198 ( 9328) covalent geometry : angle 1.67988 (12663) SS BOND : bond 0.01458 ( 3) SS BOND : angle 2.34698 ( 6) hydrogen bonds : bond 0.19545 ( 440) hydrogen bonds : angle 8.23859 ( 1257) Misc. bond : bond 0.10046 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 239 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 188 MET cc_start: 0.8172 (mmm) cc_final: 0.7715 (mmp) REVERT: B 325 MET cc_start: 0.7846 (tpp) cc_final: 0.7628 (mmm) REVERT: R 279 LEU cc_start: 0.8203 (mt) cc_final: 0.7977 (mt) REVERT: P 8 PHE cc_start: 0.7850 (m-80) cc_final: 0.7583 (m-80) outliers start: 8 outliers final: 1 residues processed: 246 average time/residue: 0.6435 time to fit residues: 167.8066 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 GLN B 266 HIS B 293 ASN B 340 ASN A 206 GLN A 229 GLN A 354 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.172541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125356 restraints weight = 10321.477| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.98 r_work: 0.3242 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9332 Z= 0.144 Angle : 0.550 5.378 12669 Z= 0.303 Chirality : 0.043 0.152 1414 Planarity : 0.004 0.041 1596 Dihedral : 4.954 69.853 1319 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.55 % Allowed : 14.52 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.41 (0.24), residues: 1126 helix: 1.28 (0.25), residues: 376 sheet: 0.00 (0.31), residues: 258 loop : -0.26 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.019 0.002 TYR B 105 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.002 TRP A 227 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9328) covalent geometry : angle 0.54916 (12663) SS BOND : bond 0.00587 ( 3) SS BOND : angle 1.12989 ( 6) hydrogen bonds : bond 0.04934 ( 440) hydrogen bonds : angle 5.45127 ( 1257) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.370 Fit side-chains REVERT: H 203 GLN cc_start: 0.8894 (pt0) cc_final: 0.8589 (pp30) REVERT: B 42 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6593 (mmp-170) REVERT: B 129 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7231 (tpt90) REVERT: B 173 THR cc_start: 0.8505 (m) cc_final: 0.8106 (p) REVERT: B 217 MET cc_start: 0.8389 (ptt) cc_final: 0.8180 (pmm) REVERT: B 219 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7759 (mtp180) REVERT: R 170 THR cc_start: 0.6677 (t) cc_final: 0.6345 (p) REVERT: R 171 THR cc_start: 0.7908 (p) cc_final: 0.7520 (p) REVERT: R 174 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6515 (mtt) REVERT: P 8 PHE cc_start: 0.7865 (m-80) cc_final: 0.7545 (m-80) outliers start: 35 outliers final: 14 residues processed: 186 average time/residue: 0.6768 time to fit residues: 133.3195 Evaluate side-chains 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN B 176 GLN B 259 GLN B 293 ASN A 28 GLN A 206 GLN A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120016 restraints weight = 10274.779| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.09 r_work: 0.3184 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9332 Z= 0.189 Angle : 0.574 7.744 12669 Z= 0.314 Chirality : 0.044 0.154 1414 Planarity : 0.005 0.045 1596 Dihedral : 5.080 68.879 1319 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.26 % Allowed : 15.53 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.54 (0.24), residues: 1126 helix: 1.28 (0.25), residues: 369 sheet: -0.03 (0.30), residues: 262 loop : 0.01 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.017 0.002 TYR H 207 PHE 0.018 0.002 PHE R 264 TRP 0.013 0.002 TRP B 82 HIS 0.008 0.002 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9328) covalent geometry : angle 0.57355 (12663) SS BOND : bond 0.00901 ( 3) SS BOND : angle 1.06906 ( 6) hydrogen bonds : bond 0.05069 ( 440) hydrogen bonds : angle 5.33065 ( 1257) Misc. bond : bond 0.00090 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.383 Fit side-chains REVERT: H 173 SER cc_start: 0.8177 (m) cc_final: 0.7780 (p) REVERT: H 203 GLN cc_start: 0.8910 (pt0) cc_final: 0.8608 (pp30) REVERT: B 42 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6607 (mmp-170) REVERT: B 46 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7626 (mmt180) REVERT: B 59 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: B 129 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7638 (mtp-110) REVERT: B 219 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7801 (mtp180) REVERT: B 259 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: A 24 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7454 (mp10) REVERT: R 40 THR cc_start: 0.8085 (t) cc_final: 0.7678 (m) REVERT: R 170 THR cc_start: 0.6799 (t) cc_final: 0.6411 (p) REVERT: R 174 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6567 (mtt) REVERT: P 8 PHE cc_start: 0.7856 (m-80) cc_final: 0.7521 (m-80) outliers start: 42 outliers final: 16 residues processed: 178 average time/residue: 0.6262 time to fit residues: 118.3531 Evaluate side-chains 164 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 340 ASN G 59 ASN A 28 GLN A 206 GLN A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.169055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123453 restraints weight = 10317.786| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.03 r_work: 0.3179 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9332 Z= 0.163 Angle : 0.536 5.660 12669 Z= 0.293 Chirality : 0.043 0.147 1414 Planarity : 0.004 0.049 1596 Dihedral : 4.958 66.312 1319 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.06 % Allowed : 17.56 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.56 (0.24), residues: 1126 helix: 1.32 (0.25), residues: 368 sheet: -0.06 (0.30), residues: 262 loop : 0.03 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.015 0.002 PHE R 264 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9328) covalent geometry : angle 0.53560 (12663) SS BOND : bond 0.00484 ( 3) SS BOND : angle 1.00950 ( 6) hydrogen bonds : bond 0.04662 ( 440) hydrogen bonds : angle 5.18037 ( 1257) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.384 Fit side-chains REVERT: H 110 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: H 173 SER cc_start: 0.8159 (m) cc_final: 0.7759 (p) REVERT: H 203 GLN cc_start: 0.8921 (pt0) cc_final: 0.8623 (pp30) REVERT: B 42 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6604 (mmp-170) REVERT: B 46 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7585 (mmt180) REVERT: B 219 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7663 (mtp180) REVERT: A 24 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7444 (mp10) REVERT: A 248 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7811 (mtm-85) REVERT: A 373 GLU cc_start: 0.8494 (tt0) cc_final: 0.8156 (tt0) REVERT: R 40 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7602 (m) REVERT: R 170 THR cc_start: 0.6824 (t) cc_final: 0.6413 (p) REVERT: R 171 THR cc_start: 0.7965 (p) cc_final: 0.7592 (p) REVERT: R 295 MET cc_start: 0.8730 (mmp) cc_final: 0.8521 (mmp) REVERT: P 8 PHE cc_start: 0.7765 (m-80) cc_final: 0.7440 (m-80) outliers start: 40 outliers final: 20 residues processed: 172 average time/residue: 0.6178 time to fit residues: 112.9613 Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN B 17 GLN B 293 ASN B 340 ASN G 59 ASN A 28 GLN A 206 GLN A 229 GLN A 340 HIS ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119769 restraints weight = 10353.054| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.10 r_work: 0.3173 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9332 Z= 0.164 Angle : 0.531 6.610 12669 Z= 0.288 Chirality : 0.043 0.146 1414 Planarity : 0.004 0.051 1596 Dihedral : 4.934 64.899 1319 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.06 % Allowed : 17.77 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.66 (0.24), residues: 1126 helix: 1.36 (0.25), residues: 368 sheet: -0.02 (0.29), residues: 262 loop : 0.14 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.015 0.001 PHE R 264 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9328) covalent geometry : angle 0.53097 (12663) SS BOND : bond 0.00598 ( 3) SS BOND : angle 0.92811 ( 6) hydrogen bonds : bond 0.04568 ( 440) hydrogen bonds : angle 5.10968 ( 1257) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.370 Fit side-chains REVERT: H 63 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: H 173 SER cc_start: 0.8174 (m) cc_final: 0.7779 (p) REVERT: H 203 GLN cc_start: 0.8915 (pt0) cc_final: 0.8625 (pp30) REVERT: B 42 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6582 (mmp-170) REVERT: B 46 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7632 (mmt180) REVERT: B 134 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7832 (mtm-85) REVERT: B 219 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7646 (mtp180) REVERT: B 259 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: A 24 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7494 (mp10) REVERT: A 248 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7836 (mtm-85) REVERT: A 373 GLU cc_start: 0.8491 (tt0) cc_final: 0.8182 (tt0) REVERT: R 40 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7608 (m) REVERT: R 170 THR cc_start: 0.6856 (t) cc_final: 0.6440 (p) REVERT: P 8 PHE cc_start: 0.7819 (m-80) cc_final: 0.7536 (m-80) outliers start: 40 outliers final: 19 residues processed: 166 average time/residue: 0.6544 time to fit residues: 115.4297 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN A 206 GLN A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.169900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121330 restraints weight = 10347.492| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.95 r_work: 0.3209 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9332 Z= 0.124 Angle : 0.496 5.795 12669 Z= 0.270 Chirality : 0.041 0.137 1414 Planarity : 0.004 0.050 1596 Dihedral : 4.714 60.055 1319 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.05 % Allowed : 19.39 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.76 (0.24), residues: 1126 helix: 1.47 (0.25), residues: 368 sheet: -0.14 (0.29), residues: 278 loop : 0.31 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.013 0.001 PHE A 205 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9328) covalent geometry : angle 0.49585 (12663) SS BOND : bond 0.00480 ( 3) SS BOND : angle 0.88862 ( 6) hydrogen bonds : bond 0.04224 ( 440) hydrogen bonds : angle 4.95626 ( 1257) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.294 Fit side-chains REVERT: H 110 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8584 (ttm) REVERT: H 173 SER cc_start: 0.8144 (m) cc_final: 0.7737 (p) REVERT: H 203 GLN cc_start: 0.8904 (pt0) cc_final: 0.8620 (pp30) REVERT: B 42 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6626 (mmp-170) REVERT: B 46 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7660 (mmt180) REVERT: B 59 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: B 219 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7681 (mtp180) REVERT: B 334 SER cc_start: 0.8098 (m) cc_final: 0.7630 (t) REVERT: A 24 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7331 (mm110) REVERT: A 373 GLU cc_start: 0.8469 (tt0) cc_final: 0.8162 (tt0) REVERT: R 170 THR cc_start: 0.6856 (t) cc_final: 0.6424 (p) REVERT: P 8 PHE cc_start: 0.7797 (m-80) cc_final: 0.7460 (m-80) outliers start: 30 outliers final: 14 residues processed: 162 average time/residue: 0.5764 time to fit residues: 99.3460 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN B 293 ASN B 340 ASN G 59 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 232 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125698 restraints weight = 10033.231| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.88 r_work: 0.3203 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9332 Z= 0.166 Angle : 0.527 6.015 12669 Z= 0.286 Chirality : 0.043 0.238 1414 Planarity : 0.004 0.051 1596 Dihedral : 4.761 60.162 1317 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.35 % Allowed : 19.39 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.75 (0.24), residues: 1126 helix: 1.36 (0.25), residues: 368 sheet: -0.14 (0.29), residues: 285 loop : 0.40 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.016 0.001 PHE R 264 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9328) covalent geometry : angle 0.52656 (12663) SS BOND : bond 0.00612 ( 3) SS BOND : angle 0.90773 ( 6) hydrogen bonds : bond 0.04477 ( 440) hydrogen bonds : angle 5.03700 ( 1257) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.370 Fit side-chains REVERT: H 63 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: H 110 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8629 (ttm) REVERT: H 203 GLN cc_start: 0.8886 (pt0) cc_final: 0.8629 (pp30) REVERT: B 42 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6612 (mmp-170) REVERT: B 46 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (mmt180) REVERT: B 59 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8284 (m-80) REVERT: B 134 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7942 (mtm-85) REVERT: B 219 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7822 (mtp180) REVERT: B 259 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: B 334 SER cc_start: 0.8282 (m) cc_final: 0.7842 (t) REVERT: A 24 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7522 (mm110) REVERT: A 248 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7891 (mtm-85) REVERT: A 373 GLU cc_start: 0.8506 (tt0) cc_final: 0.8219 (tt0) REVERT: R 170 THR cc_start: 0.6923 (t) cc_final: 0.6489 (p) REVERT: P 8 PHE cc_start: 0.7827 (m-80) cc_final: 0.7563 (m-80) outliers start: 33 outliers final: 17 residues processed: 161 average time/residue: 0.6469 time to fit residues: 110.8063 Evaluate side-chains 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.170251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125413 restraints weight = 9880.961| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.99 r_work: 0.3213 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9332 Z= 0.151 Angle : 0.516 5.706 12669 Z= 0.280 Chirality : 0.042 0.183 1414 Planarity : 0.004 0.059 1596 Dihedral : 4.742 58.700 1317 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.25 % Allowed : 19.19 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.77 (0.24), residues: 1126 helix: 1.39 (0.25), residues: 368 sheet: -0.17 (0.29), residues: 286 loop : 0.43 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.015 0.001 TYR H 207 PHE 0.014 0.001 PHE R 264 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9328) covalent geometry : angle 0.51520 (12663) SS BOND : bond 0.00614 ( 3) SS BOND : angle 1.20348 ( 6) hydrogen bonds : bond 0.04374 ( 440) hydrogen bonds : angle 4.99878 ( 1257) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.385 Fit side-chains REVERT: H 63 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: H 167 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7865 (t) REVERT: H 203 GLN cc_start: 0.8901 (pt0) cc_final: 0.8638 (pp30) REVERT: B 42 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6549 (mmp-170) REVERT: B 46 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7706 (mmt180) REVERT: B 59 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: B 134 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7920 (mtm-85) REVERT: B 219 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7795 (mtp180) REVERT: B 259 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: B 334 SER cc_start: 0.8258 (m) cc_final: 0.7811 (t) REVERT: A 14 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: A 24 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7473 (mm110) REVERT: A 248 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7884 (mtm-85) REVERT: A 373 GLU cc_start: 0.8505 (tt0) cc_final: 0.8248 (tt0) REVERT: R 170 THR cc_start: 0.6895 (t) cc_final: 0.6461 (p) REVERT: P 6 GLN cc_start: 0.7198 (tt0) cc_final: 0.6844 (tt0) REVERT: P 8 PHE cc_start: 0.7777 (m-80) cc_final: 0.7172 (m-80) outliers start: 32 outliers final: 16 residues processed: 160 average time/residue: 0.6622 time to fit residues: 112.6291 Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 232 ASN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 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 = 0.3879 r_free = 0.3879 target = 0.166274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119520 restraints weight = 9978.310| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.06 r_work: 0.3172 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9332 Z= 0.195 Angle : 0.551 6.056 12669 Z= 0.298 Chirality : 0.044 0.177 1414 Planarity : 0.004 0.058 1596 Dihedral : 4.907 60.894 1317 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 19.59 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.70 (0.24), residues: 1126 helix: 1.28 (0.25), residues: 368 sheet: -0.20 (0.28), residues: 290 loop : 0.45 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.015 0.002 TYR H 207 PHE 0.017 0.002 PHE R 264 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 9328) covalent geometry : angle 0.55034 (12663) SS BOND : bond 0.00657 ( 3) SS BOND : angle 1.17539 ( 6) hydrogen bonds : bond 0.04661 ( 440) hydrogen bonds : angle 5.10727 ( 1257) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.405 Fit side-chains REVERT: H 63 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: H 167 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (t) REVERT: H 203 GLN cc_start: 0.8928 (pt0) cc_final: 0.8648 (pp30) REVERT: B 42 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6536 (mmp-170) REVERT: B 46 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7710 (mmt180) REVERT: B 59 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 134 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7921 (mtm-85) REVERT: B 219 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7796 (mtp180) REVERT: B 259 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: A 14 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: A 24 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7477 (mm110) REVERT: A 201 PHE cc_start: 0.6386 (m-10) cc_final: 0.5119 (t80) REVERT: A 248 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: A 373 GLU cc_start: 0.8549 (tt0) cc_final: 0.8151 (tt0) REVERT: R 170 THR cc_start: 0.6901 (t) cc_final: 0.6456 (p) REVERT: P 6 GLN cc_start: 0.7208 (tt0) cc_final: 0.6831 (tt0) REVERT: P 8 PHE cc_start: 0.7737 (m-80) cc_final: 0.7164 (m-80) outliers start: 29 outliers final: 16 residues processed: 155 average time/residue: 0.6457 time to fit residues: 106.0788 Evaluate side-chains 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 94 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.170680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121733 restraints weight = 9915.411| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.94 r_work: 0.3196 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9332 Z= 0.132 Angle : 0.505 5.731 12669 Z= 0.275 Chirality : 0.042 0.165 1414 Planarity : 0.004 0.054 1596 Dihedral : 4.680 56.201 1317 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.23 % Allowed : 20.41 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.78 (0.24), residues: 1126 helix: 1.45 (0.25), residues: 368 sheet: -0.25 (0.28), residues: 293 loop : 0.47 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.014 0.001 PHE R 90 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9328) covalent geometry : angle 0.50486 (12663) SS BOND : bond 0.00539 ( 3) SS BOND : angle 1.12430 ( 6) hydrogen bonds : bond 0.04236 ( 440) hydrogen bonds : angle 4.92860 ( 1257) Misc. bond : bond 0.00048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: H 63 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: H 162 SER cc_start: 0.8250 (m) cc_final: 0.7748 (p) REVERT: H 167 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7898 (t) REVERT: H 203 GLN cc_start: 0.8919 (pt0) cc_final: 0.8659 (pp30) REVERT: B 42 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6524 (mmp-170) REVERT: B 46 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7731 (mmt180) REVERT: B 134 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7957 (mtm-85) REVERT: B 217 MET cc_start: 0.8803 (pmm) cc_final: 0.8564 (pmm) REVERT: B 219 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7810 (mtp180) REVERT: B 259 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: B 334 SER cc_start: 0.8238 (m) cc_final: 0.7754 (t) REVERT: A 14 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 24 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7438 (mm110) REVERT: A 201 PHE cc_start: 0.6355 (m-10) cc_final: 0.5254 (t80) REVERT: A 373 GLU cc_start: 0.8490 (tt0) cc_final: 0.8250 (tt0) REVERT: R 170 THR cc_start: 0.6932 (t) cc_final: 0.6498 (p) REVERT: P 6 GLN cc_start: 0.7283 (tt0) cc_final: 0.6788 (tm-30) REVERT: P 8 PHE cc_start: 0.7745 (m-80) cc_final: 0.7070 (m-80) outliers start: 22 outliers final: 14 residues processed: 157 average time/residue: 0.6440 time to fit residues: 107.1683 Evaluate side-chains 160 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.0970 chunk 89 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 ASN B 293 ASN B 340 ASN G 59 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124491 restraints weight = 9812.008| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.15 r_work: 0.3217 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9332 Z= 0.110 Angle : 0.484 5.418 12669 Z= 0.263 Chirality : 0.041 0.159 1414 Planarity : 0.004 0.051 1596 Dihedral : 4.478 49.077 1317 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.03 % Allowed : 20.71 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.88 (0.25), residues: 1126 helix: 1.58 (0.25), residues: 368 sheet: -0.23 (0.28), residues: 298 loop : 0.53 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.016 0.001 TYR H 207 PHE 0.015 0.001 PHE A 205 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9328) covalent geometry : angle 0.48394 (12663) SS BOND : bond 0.00476 ( 3) SS BOND : angle 1.10767 ( 6) hydrogen bonds : bond 0.03985 ( 440) hydrogen bonds : angle 4.79696 ( 1257) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.06 seconds wall clock time: 74 minutes 47.53 seconds (4487.53 seconds total)