Starting phenix.real_space_refine on Thu Jul 2 16:16:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p00_13140/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.map" model { file = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2026/7p00_13140.cif" } 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-6108/lib/python3.11/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: 1.64, per 1000 atoms: 0.18 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: 0.78 Conformation dependent library (CDL) restraints added in 254.7 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: 0.19 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: 1.08 Time building geometry restraints manager: 0.98 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: 5075 17.34 - 34.68: 348 34.68 - 52.03: 61 52.03 - 69.37: 12 69.37 - 86.71: 7 Dihedral angle restraints: 5503 sinusoidal: 2160 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 5500 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: 4.570 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:5.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 12.433 86.708 3338 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/Z covalent geometry : bond 0.01198 / 0.89 ( 9328) covalent geometry : angle 1.67988 / 1.28 (12663) SS BOND : bond 0.01458 / 0.70 ( 3) SS BOND : angle 2.34698 / 1.79 ( 6) hydrogen bonds : bond 0.19545 / 13.30 ( 440) hydrogen bonds : angle 8.23859 / 5.88 ( 1257) Misc. bond : bond 0.10046 / 5.29 ( 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 : 0.241 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: 0.4788 time to fit residues: 125.5982 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 : 0.215 ------------------------------------------------------------------------------- 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... H 203 GLN B 156 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 285 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.172518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125366 restraints weight = 10325.074| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.98 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9332 Z= 0.142 Angle : 0.549 5.487 12669 Z= 0.304 Chirality : 0.043 0.155 1414 Planarity : 0.004 0.040 1596 Dihedral : 4.998 70.591 1263 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.19 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: 0.42 (0.24), residues: 1126 helix: 1.27 (0.25), residues: 376 sheet: 0.01 (0.30), residues: 264 loop : -0.24 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.019 0.002 TYR H 207 PHE 0.013 0.001 PHE B 151 TRP 0.013 0.002 TRP R 30 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9328) covalent geometry : angle 0.54904 / 0.30 (12663) SS BOND : bond 0.00583 / 0.28 ( 3) SS BOND : angle 1.14239 / 0.56 ( 6) hydrogen bonds : bond 0.05006 / 3.40 ( 440) hydrogen bonds : angle 5.46715 / 3.69 ( 1257) Misc. bond : bond 0.00058 / 0.03 ( 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 198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.271 Fit side-chains REVERT: H 203 GLN cc_start: 0.8902 (pt0) cc_final: 0.8609 (pp30) REVERT: B 42 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6607 (mmp-170) REVERT: B 76 ASP cc_start: 0.8538 (p0) cc_final: 0.8336 (p0) REVERT: B 129 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7258 (tpt90) REVERT: B 173 THR cc_start: 0.8516 (m) cc_final: 0.8122 (p) REVERT: B 217 MET cc_start: 0.8386 (ptt) cc_final: 0.8167 (pmm) REVERT: B 219 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7775 (mtp180) REVERT: R 170 THR cc_start: 0.6728 (t) cc_final: 0.6393 (p) REVERT: R 171 THR cc_start: 0.7918 (p) cc_final: 0.7545 (p) REVERT: R 174 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6553 (mtt) REVERT: P 8 PHE cc_start: 0.7907 (m-80) cc_final: 0.7571 (m-80) outliers start: 35 outliers final: 14 residues processed: 185 average time/residue: 0.5115 time to fit residues: 100.4286 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120215 restraints weight = 10285.762| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.95 r_work: 0.3194 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9332 Z= 0.176 Angle : 0.562 7.632 12669 Z= 0.308 Chirality : 0.044 0.152 1414 Planarity : 0.004 0.043 1596 Dihedral : 5.032 67.824 1263 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.37 % Allowed : 15.33 % Favored : 80.30 % 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: 0.58 (0.24), residues: 1126 helix: 1.35 (0.25), residues: 368 sheet: -0.02 (0.30), residues: 262 loop : 0.01 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.016 0.002 TYR H 207 PHE 0.017 0.002 PHE R 264 TRP 0.013 0.002 TRP B 82 HIS 0.007 0.002 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 9328) covalent geometry : angle 0.56202 / 0.31 (12663) SS BOND : bond 0.00750 / 0.36 ( 3) SS BOND : angle 1.08369 / 0.73 ( 6) hydrogen bonds : bond 0.04982 / 3.39 ( 440) hydrogen bonds : angle 5.28732 / 3.56 ( 1257) Misc. bond : bond 0.00085 / 0.04 ( 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 198 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.319 Fit side-chains REVERT: H 173 SER cc_start: 0.8153 (m) cc_final: 0.7745 (p) REVERT: H 203 GLN cc_start: 0.8892 (pt0) cc_final: 0.8592 (pp30) REVERT: B 42 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6598 (mmp-170) REVERT: B 46 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7584 (mmt180) REVERT: B 59 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: B 129 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7619 (mtp-110) REVERT: B 219 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7776 (mtp180) REVERT: B 259 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: A 24 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7408 (mp10) REVERT: R 40 THR cc_start: 0.8044 (t) cc_final: 0.7650 (m) REVERT: R 170 THR cc_start: 0.6807 (t) cc_final: 0.6425 (p) REVERT: R 174 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6552 (mtt) REVERT: P 6 GLN cc_start: 0.7071 (tt0) cc_final: 0.6778 (tt0) REVERT: P 8 PHE cc_start: 0.7841 (m-80) cc_final: 0.7203 (m-80) outliers start: 43 outliers final: 14 residues processed: 182 average time/residue: 0.4960 time to fit residues: 96.3943 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 54 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122634 restraints weight = 10319.117| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.11 r_work: 0.3227 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9332 Z= 0.128 Angle : 0.505 5.282 12669 Z= 0.277 Chirality : 0.042 0.141 1414 Planarity : 0.004 0.046 1596 Dihedral : 4.826 62.949 1263 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.55 % Allowed : 17.77 % Favored : 78.68 % 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: 0.68 (0.24), residues: 1126 helix: 1.47 (0.25), residues: 368 sheet: -0.04 (0.29), residues: 267 loop : 0.08 (0.28), residues: 491 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 0.013 0.001 PHE A 205 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9328) covalent geometry : angle 0.50518 / 0.28 (12663) SS BOND : bond 0.00789 / 0.38 ( 3) SS BOND : angle 0.96985 / 0.61 ( 6) hydrogen bonds : bond 0.04390 / 3.00 ( 440) hydrogen bonds : angle 5.04996 / 3.39 ( 1257) Misc. bond : bond 0.00054 / 0.03 ( 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 183 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.211 Fit side-chains REVERT: H 173 SER cc_start: 0.8151 (m) cc_final: 0.7732 (p) REVERT: H 203 GLN cc_start: 0.8923 (pt0) cc_final: 0.8648 (pp30) REVERT: B 42 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6612 (mmp-170) REVERT: B 59 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: B 219 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7661 (mtp180) REVERT: B 334 SER cc_start: 0.8055 (m) cc_final: 0.7577 (t) REVERT: A 24 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7457 (mp10) REVERT: A 373 GLU cc_start: 0.8445 (tt0) cc_final: 0.8130 (tt0) REVERT: R 40 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7628 (m) REVERT: R 170 THR cc_start: 0.6834 (t) cc_final: 0.6419 (p) REVERT: R 171 THR cc_start: 0.8031 (p) cc_final: 0.7660 (p) REVERT: P 6 GLN cc_start: 0.7070 (tt0) cc_final: 0.6783 (tt0) REVERT: P 8 PHE cc_start: 0.7801 (m-80) cc_final: 0.7209 (m-80) outliers start: 35 outliers final: 15 residues processed: 170 average time/residue: 0.4683 time to fit residues: 85.1867 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 : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER 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 59 TYR Chi-restraints excluded: chain B residue 74 SER 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 203 THR Chi-restraints excluded: chain A residue 228 ILE 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: 5.9990 chunk 85 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.169335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120468 restraints weight = 10334.310| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.14 r_work: 0.3193 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3475 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= 0.157 Angle : 0.522 5.893 12669 Z= 0.283 Chirality : 0.042 0.145 1414 Planarity : 0.004 0.049 1596 Dihedral : 4.814 62.113 1261 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.55 % Allowed : 18.48 % Favored : 77.97 % 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: 0.71 (0.24), residues: 1126 helix: 1.44 (0.25), residues: 368 sheet: -0.02 (0.29), residues: 267 loop : 0.16 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.015 0.001 TYR H 207 PHE 0.015 0.001 PHE R 264 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 9328) covalent geometry : angle 0.52177 / 0.28 (12663) SS BOND : bond 0.00553 / 0.27 ( 3) SS BOND : angle 0.90680 / 0.57 ( 6) hydrogen bonds : bond 0.04485 / 3.06 ( 440) hydrogen bonds : angle 5.06146 / 3.40 ( 1257) Misc. bond : bond 0.00072 / 0.04 ( 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 177 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.313 Fit side-chains REVERT: H 173 SER cc_start: 0.8164 (m) cc_final: 0.7757 (p) REVERT: H 203 GLN cc_start: 0.8932 (pt0) cc_final: 0.8636 (pp30) REVERT: B 42 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6596 (mmp-170) REVERT: B 46 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7635 (mmt180) REVERT: B 219 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7621 (mtp180) REVERT: B 336 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 24 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7448 (mp10) REVERT: A 248 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7821 (mtm-85) REVERT: A 373 GLU cc_start: 0.8468 (tt0) cc_final: 0.8131 (tt0) REVERT: R 170 THR cc_start: 0.6841 (t) cc_final: 0.6420 (p) REVERT: P 8 PHE cc_start: 0.7754 (m-80) cc_final: 0.7405 (m-80) outliers start: 35 outliers final: 18 residues processed: 168 average time/residue: 0.4663 time to fit residues: 83.5333 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER 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 74 SER 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 248 ARG Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 142 LEU 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: 3.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3902 r_free = 0.3902 target = 0.168861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121680 restraints weight = 10330.470| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.99 r_work: 0.3174 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3552 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= 0.159 Angle : 0.523 6.142 12669 Z= 0.285 Chirality : 0.043 0.209 1414 Planarity : 0.004 0.051 1596 Dihedral : 4.805 61.412 1261 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.16 % Allowed : 18.58 % 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: 0.69 (0.24), residues: 1126 helix: 1.37 (0.25), residues: 367 sheet: -0.10 (0.29), residues: 272 loop : 0.24 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.016 0.001 TYR H 207 PHE 0.015 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/Z covalent geometry : bond 0.00356 / 0.16 ( 9328) covalent geometry : angle 0.52295 / 0.28 (12663) SS BOND : bond 0.00600 / 0.29 ( 3) SS BOND : angle 0.91921 / 0.55 ( 6) hydrogen bonds : bond 0.04467 / 3.05 ( 440) hydrogen bonds : angle 5.03510 / 3.39 ( 1257) Misc. bond : bond 0.00074 / 0.04 ( 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 181 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.266 Fit side-chains REVERT: H 63 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: H 110 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (ttm) REVERT: H 203 GLN cc_start: 0.8909 (pt0) cc_final: 0.8612 (pp30) REVERT: B 42 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6610 (mmp-170) REVERT: B 46 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (mmt180) REVERT: B 134 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7816 (mtm-85) REVERT: B 219 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7687 (mtp180) REVERT: B 259 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 24 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7306 (mm110) REVERT: A 248 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7813 (mtm-85) REVERT: A 373 GLU cc_start: 0.8451 (tt0) cc_final: 0.8117 (tt0) REVERT: R 170 THR cc_start: 0.6865 (t) cc_final: 0.6419 (p) REVERT: P 8 PHE cc_start: 0.7768 (m-80) cc_final: 0.7451 (m-80) outliers start: 41 outliers final: 19 residues processed: 166 average time/residue: 0.4594 time to fit residues: 81.6255 Evaluate side-chains 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 74 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 56 GLN 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 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 = 0.3880 r_free = 0.3880 target = 0.166854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119694 restraints weight = 10396.893| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.00 r_work: 0.3155 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9332 Z= 0.225 Angle : 0.574 6.579 12669 Z= 0.312 Chirality : 0.045 0.182 1414 Planarity : 0.005 0.056 1596 Dihedral : 5.106 66.611 1261 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.06 % Allowed : 18.38 % 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: 0.62 (0.24), residues: 1126 helix: 1.19 (0.25), residues: 368 sheet: -0.20 (0.29), residues: 285 loop : 0.37 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 214 TYR 0.016 0.002 TYR H 207 PHE 0.018 0.002 PHE R 264 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 ( 9328) covalent geometry : angle 0.57306 / 0.31 (12663) SS BOND : bond 0.00738 / 0.35 ( 3) SS BOND : angle 1.30626 / 0.73 ( 6) hydrogen bonds : bond 0.04879 / 3.32 ( 440) hydrogen bonds : angle 5.22001 / 3.53 ( 1257) Misc. bond : bond 0.00114 / 0.06 ( 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 181 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.361 Fit side-chains REVERT: H 63 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: H 110 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: H 167 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7798 (t) REVERT: H 203 GLN cc_start: 0.8901 (pt0) cc_final: 0.8593 (pp30) REVERT: B 42 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6580 (mmp-170) REVERT: B 46 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7622 (mmt180) REVERT: B 59 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: B 134 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7820 (mtm-85) REVERT: B 219 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7702 (mtp180) REVERT: B 259 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: A 14 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: A 24 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7486 (mp10) REVERT: A 248 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7813 (mtm-85) REVERT: R 170 THR cc_start: 0.6859 (t) cc_final: 0.6423 (p) REVERT: P 8 PHE cc_start: 0.7761 (m-80) cc_final: 0.7450 (m-80) outliers start: 40 outliers final: 21 residues processed: 166 average time/residue: 0.5353 time to fit residues: 94.5235 Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 74 SER 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 B residue 336 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 204 LYS 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: 3.9990 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3918 r_free = 0.3918 target = 0.169390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119758 restraints weight = 9895.024| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.97 r_work: 0.3173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9332 Z= 0.168 Angle : 0.531 6.237 12669 Z= 0.289 Chirality : 0.043 0.159 1414 Planarity : 0.004 0.059 1596 Dihedral : 4.967 64.704 1261 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.35 % Allowed : 18.68 % Favored : 77.97 % 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: 1.25 (0.25), residues: 368 sheet: -0.24 (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 0.016 0.001 TYR H 207 PHE 0.016 0.002 PHE R 90 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9328) covalent geometry : angle 0.53062 / 0.29 (12663) SS BOND : bond 0.00620 / 0.30 ( 3) SS BOND : angle 1.15832 / 0.62 ( 6) hydrogen bonds : bond 0.04554 / 3.11 ( 440) hydrogen bonds : angle 5.09064 / 3.43 ( 1257) Misc. bond : bond 0.00070 / 0.04 ( 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 177 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.280 Fit side-chains REVERT: H 167 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7843 (t) REVERT: H 203 GLN cc_start: 0.8932 (pt0) cc_final: 0.8657 (pp30) REVERT: B 42 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6555 (mmp-170) REVERT: B 46 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7708 (mmt180) REVERT: B 59 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: B 134 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7933 (mtm-85) REVERT: B 219 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7783 (mtp180) REVERT: B 259 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: B 334 SER cc_start: 0.8321 (m) cc_final: 0.7877 (t) REVERT: A 24 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7467 (mm110) REVERT: A 248 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7901 (mtm-85) REVERT: A 373 GLU cc_start: 0.8559 (tt0) cc_final: 0.8329 (tt0) REVERT: R 170 THR cc_start: 0.6888 (t) cc_final: 0.6443 (p) REVERT: P 6 GLN cc_start: 0.7214 (tt0) cc_final: 0.6842 (tt0) REVERT: P 8 PHE cc_start: 0.7755 (m-80) cc_final: 0.7182 (m-80) outliers start: 33 outliers final: 19 residues processed: 166 average time/residue: 0.5122 time to fit residues: 90.5092 Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 SER 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 B residue 336 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 = 0.3900 r_free = 0.3900 target = 0.167690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118840 restraints weight = 9948.125| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.92 r_work: 0.3176 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3775 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= 0.196 Angle : 0.551 6.385 12669 Z= 0.299 Chirality : 0.044 0.156 1414 Planarity : 0.004 0.059 1596 Dihedral : 5.033 65.361 1261 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.35 % Allowed : 19.09 % 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: 0.62 (0.24), residues: 1126 helix: 1.20 (0.25), residues: 368 sheet: -0.26 (0.28), residues: 285 loop : 0.42 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.016 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/Z covalent geometry : bond 0.00447 / 0.20 ( 9328) covalent geometry : angle 0.55075 / 0.30 (12663) SS BOND : bond 0.00677 / 0.32 ( 3) SS BOND : angle 1.11639 / 0.61 ( 6) hydrogen bonds : bond 0.04702 / 3.21 ( 440) hydrogen bonds : angle 5.12597 / 3.46 ( 1257) Misc. bond : bond 0.00082 / 0.04 ( 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 172 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.338 Fit side-chains REVERT: H 63 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: H 167 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7861 (t) REVERT: H 203 GLN cc_start: 0.8938 (pt0) cc_final: 0.8661 (pp30) REVERT: B 42 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6557 (mmp-170) REVERT: B 46 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7699 (mmt180) REVERT: B 59 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: B 134 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7940 (mtm-85) REVERT: B 219 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7795 (mtp180) REVERT: B 259 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8424 (pt0) REVERT: A 14 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: A 24 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7601 (mp10) REVERT: A 248 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7894 (mtm-85) REVERT: R 170 THR cc_start: 0.6917 (t) cc_final: 0.6465 (p) REVERT: P 6 GLN cc_start: 0.7240 (tt0) cc_final: 0.6849 (tt0) REVERT: P 8 PHE cc_start: 0.7758 (m-80) cc_final: 0.7119 (m-80) outliers start: 33 outliers final: 18 residues processed: 161 average time/residue: 0.4879 time to fit residues: 83.6797 Evaluate side-chains 164 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 74 SER 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 B residue 336 LEU 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: 0.0070 chunk 35 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.170791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122030 restraints weight = 9911.631| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.17 r_work: 0.3198 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9332 Z= 0.131 Angle : 0.509 5.693 12669 Z= 0.278 Chirality : 0.042 0.157 1414 Planarity : 0.004 0.053 1596 Dihedral : 4.773 59.525 1261 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.54 % Allowed : 20.20 % 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: 0.77 (0.25), residues: 1126 helix: 1.43 (0.25), residues: 368 sheet: -0.31 (0.28), residues: 293 loop : 0.53 (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 0.015 0.001 PHE R 90 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS H 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9328) covalent geometry : angle 0.50818 / 0.28 (12663) SS BOND : bond 0.00545 / 0.26 ( 3) SS BOND : angle 1.09005 / 0.56 ( 6) hydrogen bonds : bond 0.04296 / 2.93 ( 440) hydrogen bonds : angle 4.93623 / 3.32 ( 1257) Misc. bond : bond 0.00049 / 0.03 ( 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 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.323 Fit side-chains REVERT: H 162 SER cc_start: 0.8248 (m) cc_final: 0.7749 (p) REVERT: H 167 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7825 (t) REVERT: H 203 GLN cc_start: 0.8941 (pt0) cc_final: 0.8688 (pp30) REVERT: B 42 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6498 (mmp-170) REVERT: B 46 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7732 (mmt180) REVERT: B 59 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: B 134 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: B 219 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7816 (mtp180) REVERT: B 259 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: B 334 SER cc_start: 0.8241 (m) cc_final: 0.7790 (t) REVERT: A 14 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: A 24 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7473 (mm110) REVERT: A 248 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7863 (mtm-85) REVERT: A 373 GLU cc_start: 0.8543 (tt0) cc_final: 0.8289 (tt0) REVERT: R 170 THR cc_start: 0.6901 (t) cc_final: 0.6447 (p) REVERT: P 6 GLN cc_start: 0.7238 (tt0) cc_final: 0.6728 (tm-30) REVERT: P 8 PHE cc_start: 0.7754 (m-80) cc_final: 0.7073 (m-80) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 0.5013 time to fit residues: 85.3524 Evaluate side-chains 159 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 14 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 248 ARG 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: 2.9990 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 89 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118603 restraints weight = 9881.766| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.92 r_work: 0.3174 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9332 Z= 0.213 Angle : 0.572 6.394 12669 Z= 0.310 Chirality : 0.045 0.155 1414 Planarity : 0.005 0.058 1596 Dihedral : 5.024 61.919 1261 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.94 % Allowed : 20.41 % Favored : 76.65 % 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: 0.64 (0.25), residues: 1126 helix: 1.28 (0.25), residues: 368 sheet: -0.37 (0.28), residues: 293 loop : 0.49 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.015 0.002 TYR H 207 PHE 0.017 0.002 PHE R 264 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 9328) covalent geometry : angle 0.57190 / 0.31 (12663) SS BOND : bond 0.00709 / 0.34 ( 3) SS BOND : angle 1.09925 / 0.59 ( 6) hydrogen bonds : bond 0.04784 / 3.25 ( 440) hydrogen bonds : angle 5.13626 / 3.46 ( 1257) Misc. bond : bond 0.00090 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.86 seconds wall clock time: 58 minutes 52.48 seconds (3532.48 seconds total)