Starting phenix.real_space_refine on Sun Jul 27 09:57:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p00_13140/07_2025/7p00_13140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p00_13140/07_2025/7p00_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_2025/7p00_13140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2025/7p00_13140.map" model { file = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2025/7p00_13140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p00_13140/07_2025/7p00_13140.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.88, per 1000 atoms: 0.76 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.79 Time building geometry restraints manager: 2.80 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: 8.890 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- 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 : 4.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 PHE 0.030 0.003 PHE A 205 TYR 0.022 0.002 TYR H 207 ARG 0.005 0.001 ARG H 89 Details of bonding type rmsd hydrogen bonds : bond 0.19545 ( 440) hydrogen bonds : angle 8.23859 ( 1257) SS BOND : bond 0.01458 ( 3) SS BOND : angle 2.34698 ( 6) covalent geometry : bond 0.01198 ( 9328) covalent geometry : angle 1.67988 (12663) 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 : 1.046 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: 0.7847 (tpp) cc_final: 0.7629 (mmm) REVERT: R 279 LEU cc_start: 0.8203 (mt) cc_final: 0.7982 (mt) REVERT: P 8 PHE cc_start: 0.7850 (m-80) cc_final: 0.7649 (m-80) outliers start: 8 outliers final: 1 residues processed: 246 average time/residue: 1.4296 time to fit residues: 374.1902 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 : 0.970 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3949 r_free = 0.3949 target = 0.172856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130708 restraints weight = 10275.846| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.97 r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9332 Z= 0.139 Angle : 0.547 5.659 12669 Z= 0.304 Chirality : 0.043 0.153 1414 Planarity : 0.004 0.043 1596 Dihedral : 4.922 71.338 1319 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.35 % Allowed : 14.82 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1126 helix: 1.30 (0.25), residues: 376 sheet: 0.02 (0.30), residues: 264 loop : -0.21 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 30 HIS 0.008 0.001 HIS A 340 PHE 0.013 0.001 PHE B 151 TYR 0.018 0.002 TYR B 105 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05118 ( 440) hydrogen bonds : angle 5.44886 ( 1257) SS BOND : bond 0.00419 ( 3) SS BOND : angle 1.13636 ( 6) covalent geometry : bond 0.00294 ( 9328) covalent geometry : angle 0.54674 (12663) Misc. bond : bond 0.00037 ( 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 194 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.059 Fit side-chains REVERT: H 23 GLU cc_start: 0.7740 (pm20) cc_final: 0.7511 (pm20) REVERT: H 110 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8551 (ttm) REVERT: H 203 GLN cc_start: 0.8859 (pt0) cc_final: 0.8542 (pp30) REVERT: B 42 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6599 (mmp-170) REVERT: B 129 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7252 (tpt90) REVERT: B 173 THR cc_start: 0.8529 (m) cc_final: 0.8119 (p) REVERT: B 219 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7753 (mtp180) REVERT: A 9 ASP cc_start: 0.8474 (m-30) cc_final: 0.8063 (m-30) REVERT: R 170 THR cc_start: 0.6664 (t) cc_final: 0.6330 (p) REVERT: R 171 THR cc_start: 0.7914 (p) cc_final: 0.7526 (p) REVERT: R 174 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6570 (mtt) REVERT: P 8 PHE cc_start: 0.7900 (m-80) cc_final: 0.7567 (m-80) outliers start: 33 outliers final: 14 residues processed: 181 average time/residue: 1.6919 time to fit residues: 323.9880 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 LYS 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 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 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 176 GLN B 259 GLN B 293 ASN A 28 GLN A 206 GLN A 229 GLN A 368 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125142 restraints weight = 10299.123| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.97 r_work: 0.3232 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3114 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= 0.137 Angle : 0.525 7.034 12669 Z= 0.288 Chirality : 0.042 0.146 1414 Planarity : 0.004 0.041 1596 Dihedral : 4.779 63.857 1319 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.16 % Allowed : 15.74 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1126 helix: 1.59 (0.25), residues: 369 sheet: 0.08 (0.30), residues: 267 loop : 0.08 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS A 340 PHE 0.014 0.001 PHE R 264 TYR 0.017 0.001 TYR H 207 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 440) hydrogen bonds : angle 5.13851 ( 1257) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.98286 ( 6) covalent geometry : bond 0.00295 ( 9328) covalent geometry : angle 0.52511 (12663) Misc. bond : bond 0.00060 ( 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 197 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.956 Fit side-chains REVERT: H 173 SER cc_start: 0.8099 (m) cc_final: 0.7688 (p) REVERT: H 203 GLN cc_start: 0.8910 (pt0) cc_final: 0.8636 (pp30) REVERT: B 42 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6658 (mmp-170) REVERT: B 129 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7865 (mtp180) REVERT: B 217 MET cc_start: 0.8587 (pmm) cc_final: 0.8291 (pmm) REVERT: B 219 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7691 (mtp180) REVERT: B 259 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: A 24 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7391 (mp10) REVERT: A 290 LYS cc_start: 0.7996 (mptt) cc_final: 0.7778 (mmpt) REVERT: A 373 GLU cc_start: 0.8352 (tt0) cc_final: 0.8086 (tt0) REVERT: R 170 THR cc_start: 0.6814 (t) cc_final: 0.6444 (p) REVERT: R 174 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6573 (mtt) REVERT: P 8 PHE cc_start: 0.7872 (m-80) cc_final: 0.7505 (m-80) outliers start: 41 outliers final: 15 residues processed: 180 average time/residue: 1.2807 time to fit residues: 245.3870 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 40 THR 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 82 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 A 28 GLN A 206 GLN A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120482 restraints weight = 10279.041| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.11 r_work: 0.3146 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9332 Z= 0.178 Angle : 0.546 5.730 12669 Z= 0.298 Chirality : 0.043 0.149 1414 Planarity : 0.004 0.049 1596 Dihedral : 4.955 64.788 1319 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.16 % Allowed : 16.95 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1126 helix: 1.51 (0.25), residues: 369 sheet: -0.03 (0.30), residues: 267 loop : 0.12 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS A 340 PHE 0.016 0.002 PHE R 264 TYR 0.015 0.002 TYR H 207 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 440) hydrogen bonds : angle 5.17272 ( 1257) SS BOND : bond 0.01264 ( 3) SS BOND : angle 1.12315 ( 6) covalent geometry : bond 0.00401 ( 9328) covalent geometry : angle 0.54537 (12663) Misc. bond : bond 0.00086 ( 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 187 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.030 Fit side-chains REVERT: H 173 SER cc_start: 0.8170 (m) cc_final: 0.7764 (p) REVERT: H 203 GLN cc_start: 0.8941 (pt0) cc_final: 0.8651 (pp30) REVERT: B 42 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6603 (mmp-170) REVERT: B 46 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7584 (mmt180) REVERT: B 70 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 217 MET cc_start: 0.8621 (pmm) cc_final: 0.8326 (pmm) REVERT: B 219 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7740 (mtp180) REVERT: A 24 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7489 (mp10) REVERT: A 248 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7859 (mtm-85) REVERT: A 373 GLU cc_start: 0.8415 (tt0) cc_final: 0.8112 (tt0) REVERT: R 170 THR cc_start: 0.6835 (t) cc_final: 0.6426 (p) REVERT: R 171 THR cc_start: 0.8008 (p) cc_final: 0.7637 (p) REVERT: R 295 MET cc_start: 0.8701 (mmp) cc_final: 0.8451 (mmp) REVERT: P 8 PHE cc_start: 0.7839 (m-80) cc_final: 0.7491 (m-80) outliers start: 41 outliers final: 18 residues processed: 176 average time/residue: 1.2408 time to fit residues: 233.2628 Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 143 THR 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 A residue 235 THR 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 19 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 A 28 GLN A 206 GLN A 229 GLN A 340 HIS A 368 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121731 restraints weight = 10169.416| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.96 r_work: 0.3202 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9332 Z= 0.178 Angle : 0.540 6.762 12669 Z= 0.293 Chirality : 0.043 0.149 1414 Planarity : 0.004 0.047 1596 Dihedral : 4.941 64.949 1319 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.76 % Allowed : 17.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1126 helix: 1.46 (0.25), residues: 369 sheet: -0.07 (0.29), residues: 267 loop : 0.19 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 340 PHE 0.016 0.002 PHE R 264 TYR 0.016 0.001 TYR H 207 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 440) hydrogen bonds : angle 5.13138 ( 1257) SS BOND : bond 0.00850 ( 3) SS BOND : angle 0.97565 ( 6) covalent geometry : bond 0.00402 ( 9328) covalent geometry : angle 0.53971 (12663) Misc. bond : bond 0.00090 ( 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 176 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.046 Fit side-chains REVERT: H 110 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8624 (ttm) REVERT: H 173 SER cc_start: 0.8179 (m) cc_final: 0.7787 (p) REVERT: H 203 GLN cc_start: 0.8907 (pt0) cc_final: 0.8611 (pp30) REVERT: B 42 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6603 (mmp-170) REVERT: B 46 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7575 (mmt180) REVERT: B 70 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9008 (pp) REVERT: B 217 MET cc_start: 0.8609 (pmm) cc_final: 0.8361 (pmm) REVERT: B 219 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7756 (mtp180) REVERT: B 334 SER cc_start: 0.8290 (m) cc_final: 0.7826 (t) REVERT: A 24 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7480 (mp10) REVERT: A 248 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7809 (mtm-85) REVERT: A 373 GLU cc_start: 0.8419 (tt0) cc_final: 0.8111 (tt0) REVERT: R 170 THR cc_start: 0.6897 (t) cc_final: 0.6502 (p) REVERT: P 8 PHE cc_start: 0.7865 (m-80) cc_final: 0.7529 (m-80) outliers start: 37 outliers final: 20 residues processed: 165 average time/residue: 1.4128 time to fit residues: 248.3804 Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 70 LEU 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 227 SER 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 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 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN G 59 ASN A 28 GLN A 206 GLN A 229 GLN A 275 ASN A 368 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122339 restraints weight = 10163.146| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.92 r_work: 0.3236 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3615 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 : 0.494 5.727 12669 Z= 0.269 Chirality : 0.041 0.139 1414 Planarity : 0.004 0.044 1596 Dihedral : 4.685 59.549 1319 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.55 % Allowed : 18.58 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1126 helix: 1.59 (0.25), residues: 369 sheet: -0.10 (0.29), residues: 282 loop : 0.33 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE A 205 TYR 0.016 0.001 TYR H 207 ARG 0.008 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 440) hydrogen bonds : angle 4.95020 ( 1257) SS BOND : bond 0.00504 ( 3) SS BOND : angle 0.88079 ( 6) covalent geometry : bond 0.00266 ( 9328) covalent geometry : angle 0.49397 (12663) Misc. bond : bond 0.00049 ( 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 178 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.086 Fit side-chains REVERT: H 110 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8579 (ttm) REVERT: H 173 SER cc_start: 0.8139 (m) cc_final: 0.7736 (p) REVERT: H 203 GLN cc_start: 0.8898 (pt0) cc_final: 0.8612 (pp30) REVERT: B 42 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6589 (mmp-170) REVERT: B 46 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7569 (mmt180) REVERT: B 134 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: B 217 MET cc_start: 0.8638 (pmm) cc_final: 0.8403 (pmm) REVERT: B 219 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7748 (mtp180) REVERT: B 259 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: B 334 SER cc_start: 0.8118 (m) cc_final: 0.7642 (t) REVERT: A 24 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7300 (mm-40) REVERT: A 373 GLU cc_start: 0.8381 (tt0) cc_final: 0.8152 (tt0) REVERT: R 78 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7234 (tp30) REVERT: R 170 THR cc_start: 0.6940 (t) cc_final: 0.6519 (p) REVERT: P 8 PHE cc_start: 0.7752 (m-80) cc_final: 0.7439 (m-80) outliers start: 35 outliers final: 16 residues processed: 164 average time/residue: 1.3311 time to fit residues: 232.9647 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 227 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 A 275 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.171073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126234 restraints weight = 9923.293| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.01 r_work: 0.3216 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3669 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= 0.143 Angle : 0.506 5.903 12669 Z= 0.275 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.058 1596 Dihedral : 4.633 57.489 1317 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.25 % Allowed : 18.88 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1126 helix: 1.57 (0.25), residues: 369 sheet: -0.11 (0.29), residues: 286 loop : 0.43 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE R 264 TYR 0.016 0.001 TYR H 207 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 440) hydrogen bonds : angle 4.94942 ( 1257) SS BOND : bond 0.00523 ( 3) SS BOND : angle 1.18006 ( 6) covalent geometry : bond 0.00315 ( 9328) covalent geometry : angle 0.50568 (12663) Misc. bond : bond 0.00061 ( 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 173 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.929 Fit side-chains REVERT: H 63 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: H 110 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8614 (ttm) REVERT: H 167 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7842 (t) REVERT: H 173 SER cc_start: 0.8157 (m) cc_final: 0.7775 (p) REVERT: H 203 GLN cc_start: 0.8901 (pt0) cc_final: 0.8629 (pp30) REVERT: B 42 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6608 (mmp-170) REVERT: B 46 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7634 (mmt180) REVERT: B 134 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7913 (mtm-85) REVERT: B 217 MET cc_start: 0.8666 (pmm) cc_final: 0.8444 (pmm) REVERT: B 219 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7842 (mtp180) REVERT: B 259 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8369 (pt0) REVERT: B 334 SER cc_start: 0.8233 (m) cc_final: 0.7783 (t) REVERT: A 24 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7465 (mm-40) REVERT: A 248 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7864 (mtm-85) REVERT: A 373 GLU cc_start: 0.8425 (tt0) cc_final: 0.8183 (tt0) REVERT: R 170 THR cc_start: 0.6925 (t) cc_final: 0.6490 (p) REVERT: P 6 GLN cc_start: 0.7143 (tt0) cc_final: 0.6769 (tt0) REVERT: P 8 PHE cc_start: 0.7791 (m-80) cc_final: 0.7204 (m-80) outliers start: 32 outliers final: 17 residues processed: 162 average time/residue: 1.2911 time to fit residues: 222.8178 Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 227 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 232 ASN A 368 GLN R 89 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3865 r_free = 0.3865 target = 0.165339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116522 restraints weight = 10403.402| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.94 r_work: 0.3082 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.007 0.061 9332 Z= 0.304 Angle : 0.637 7.105 12669 Z= 0.343 Chirality : 0.048 0.178 1414 Planarity : 0.005 0.059 1596 Dihedral : 5.306 70.433 1317 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.76 % Allowed : 18.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1126 helix: 1.06 (0.25), residues: 375 sheet: -0.28 (0.28), residues: 298 loop : 0.41 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.002 HIS B 54 PHE 0.020 0.002 PHE B 151 TYR 0.016 0.002 TYR H 120 ARG 0.009 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 440) hydrogen bonds : angle 5.38416 ( 1257) SS BOND : bond 0.00856 ( 3) SS BOND : angle 1.24543 ( 6) covalent geometry : bond 0.00706 ( 9328) covalent geometry : angle 0.63634 (12663) Misc. bond : bond 0.00148 ( 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: 37 poor density : 140 time to evaluate : 0.980 Fit side-chains REVERT: H 63 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: H 167 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7827 (t) REVERT: H 203 GLN cc_start: 0.8936 (pt0) cc_final: 0.8704 (pp30) REVERT: B 42 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6561 (mmp-170) REVERT: B 46 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7617 (mmt180) REVERT: B 59 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: B 70 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9096 (pp) REVERT: B 134 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7859 (mtm-85) REVERT: B 217 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8287 (pmm) REVERT: B 219 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7738 (mtp180) REVERT: B 259 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: A 24 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7553 (mp10) REVERT: A 248 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7835 (mtm-85) REVERT: A 373 GLU cc_start: 0.8569 (tt0) cc_final: 0.8320 (tt0) REVERT: R 170 THR cc_start: 0.6891 (t) cc_final: 0.6447 (p) REVERT: R 299 MET cc_start: 0.8253 (mtm) cc_final: 0.8045 (mtm) REVERT: P 6 GLN cc_start: 0.7241 (tt0) cc_final: 0.6774 (tt0) REVERT: P 8 PHE cc_start: 0.7725 (m-80) cc_final: 0.7088 (m-80) outliers start: 37 outliers final: 18 residues processed: 164 average time/residue: 1.2919 time to fit residues: 225.6241 Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 A 368 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123074 restraints weight = 9864.803| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.93 r_work: 0.3227 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.002 0.027 9332 Z= 0.115 Angle : 0.493 5.454 12669 Z= 0.268 Chirality : 0.041 0.137 1414 Planarity : 0.004 0.052 1596 Dihedral : 4.671 58.492 1317 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.13 % Allowed : 19.80 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1126 helix: 1.57 (0.25), residues: 369 sheet: -0.21 (0.28), residues: 288 loop : 0.47 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 227 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE A 205 TYR 0.017 0.001 TYR H 207 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 440) hydrogen bonds : angle 4.91021 ( 1257) SS BOND : bond 0.00503 ( 3) SS BOND : angle 1.08447 ( 6) covalent geometry : bond 0.00239 ( 9328) covalent geometry : angle 0.49228 (12663) Misc. bond : bond 0.00038 ( 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 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: H 162 SER cc_start: 0.8230 (m) cc_final: 0.7750 (p) REVERT: H 167 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7880 (t) REVERT: H 203 GLN cc_start: 0.8910 (pt0) cc_final: 0.8649 (pp30) REVERT: B 42 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6528 (mmp-170) REVERT: B 46 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7719 (mmt180) REVERT: B 134 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7941 (mtm-85) REVERT: B 217 MET cc_start: 0.8666 (pmm) cc_final: 0.8456 (pmm) REVERT: B 219 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7816 (mtp180) REVERT: B 259 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: B 334 SER cc_start: 0.8134 (m) cc_final: 0.7699 (t) REVERT: A 24 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7414 (mm110) REVERT: A 248 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: R 170 THR cc_start: 0.6948 (t) cc_final: 0.6520 (p) REVERT: P 6 GLN cc_start: 0.7325 (tt0) cc_final: 0.6949 (tt0) REVERT: P 8 PHE cc_start: 0.7738 (m-80) cc_final: 0.7124 (m-80) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 1.3122 time to fit residues: 216.4520 Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG 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 227 SER 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 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 69 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 275 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121874 restraints weight = 9976.540| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.13 r_work: 0.3183 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3853 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= 0.144 Angle : 0.518 6.045 12669 Z= 0.281 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.055 1596 Dihedral : 4.673 55.902 1317 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.13 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1126 helix: 1.55 (0.25), residues: 369 sheet: -0.22 (0.29), residues: 288 loop : 0.49 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS H 52 PHE 0.014 0.001 PHE A 205 TYR 0.016 0.001 TYR H 207 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 440) hydrogen bonds : angle 4.93302 ( 1257) SS BOND : bond 0.00553 ( 3) SS BOND : angle 1.07186 ( 6) covalent geometry : bond 0.00318 ( 9328) covalent geometry : angle 0.51781 (12663) Misc. bond : bond 0.00061 ( 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 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.092 Fit side-chains REVERT: H 63 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: H 162 SER cc_start: 0.8237 (m) cc_final: 0.7742 (p) REVERT: H 167 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7825 (t) REVERT: H 203 GLN cc_start: 0.8936 (pt0) cc_final: 0.8669 (pp30) REVERT: B 42 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6510 (mmp-170) REVERT: B 46 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7698 (mmt180) REVERT: B 134 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7966 (mtm-85) REVERT: B 217 MET cc_start: 0.8672 (pmm) cc_final: 0.8452 (pmm) REVERT: B 219 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7820 (mtp180) REVERT: B 259 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8378 (pt0) REVERT: B 334 SER cc_start: 0.8262 (m) cc_final: 0.7783 (t) REVERT: A 24 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 248 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7856 (mtm-85) REVERT: R 170 THR cc_start: 0.6955 (t) cc_final: 0.6518 (p) REVERT: P 6 GLN cc_start: 0.7300 (tt0) cc_final: 0.6904 (tt0) REVERT: P 8 PHE cc_start: 0.7689 (m-80) cc_final: 0.7082 (m-80) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 1.3748 time to fit residues: 216.1813 Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 GLU 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 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 227 SER 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 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 68 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.168906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120591 restraints weight = 9920.684| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.15 r_work: 0.3142 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9332 Z= 0.179 Angle : 0.544 6.427 12669 Z= 0.294 Chirality : 0.043 0.148 1414 Planarity : 0.004 0.059 1596 Dihedral : 4.794 55.217 1317 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.23 % Allowed : 20.10 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1126 helix: 1.47 (0.25), residues: 369 sheet: -0.27 (0.29), residues: 288 loop : 0.51 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.016 0.002 PHE R 90 TYR 0.016 0.001 TYR H 207 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 440) hydrogen bonds : angle 5.01763 ( 1257) SS BOND : bond 0.00640 ( 3) SS BOND : angle 1.07003 ( 6) covalent geometry : bond 0.00405 ( 9328) covalent geometry : angle 0.54352 (12663) Misc. bond : bond 0.00083 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9165.42 seconds wall clock time: 161 minutes 7.83 seconds (9667.83 seconds total)