Starting phenix.real_space_refine on Thu Feb 13 18:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p00_13140/02_2025/7p00_13140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p00_13140/02_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_13140/02_2025/7p00_13140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p00_13140/02_2025/7p00_13140.map" model { file = "/net/cci-nas-00/data/ceres_data/7p00_13140/02_2025/7p00_13140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p00_13140/02_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-5592/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: 6.66, per 1000 atoms: 0.73 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: 2.56 Conformation dependent library (CDL) restraints added in 1.6 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: 0.95 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: 2.55 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1480 1.32 - 1.44: 2629 1.44 - 1.57: 5125 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9328 Sorted by residual: bond pdb=" C THR R 91 " pdb=" O THR R 91 " ideal model delta sigma weight residual 1.237 1.301 -0.065 1.17e-02 7.31e+03 3.06e+01 bond pdb=" ND1 HIS A 340 " pdb=" CE1 HIS A 340 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.62e+01 bond pdb=" CD2 HIS A 340 " pdb=" NE2 HIS A 340 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.32e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.25e+01 ... (remaining 9323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9292 1.87 - 3.74: 2976 3.74 - 5.61: 359 5.61 - 7.49: 26 7.49 - 9.36: 10 Bond angle restraints: 12663 Sorted by residual: angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" C GLN A 229 " ideal model delta sigma weight residual 111.28 103.41 7.87 1.09e+00 8.42e-01 5.22e+01 angle pdb=" N MET G 38 " pdb=" CA MET G 38 " pdb=" C MET G 38 " ideal model delta sigma weight residual 111.28 104.11 7.17 1.09e+00 8.42e-01 4.33e+01 angle pdb=" CB HIS A 340 " pdb=" CG HIS A 340 " pdb=" CD2 HIS A 340 " ideal model delta sigma weight residual 131.20 122.75 8.45 1.30e+00 5.92e-01 4.22e+01 angle pdb=" N ARG A 224 " pdb=" CA ARG A 224 " pdb=" C ARG A 224 " ideal model delta sigma weight residual 113.16 105.30 7.86 1.24e+00 6.50e-01 4.02e+01 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " ideal model delta sigma weight residual 110.23 119.59 -9.36 1.62e+00 3.81e-01 3.34e+01 ... (remaining 12658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5129 17.34 - 34.68: 350 34.68 - 52.03: 61 52.03 - 69.37: 12 69.37 - 86.71: 7 Dihedral angle restraints: 5559 sinusoidal: 2216 harmonic: 3343 Sorted by residual: dihedral pdb=" C ASP G 36 " pdb=" N ASP G 36 " pdb=" CA ASP G 36 " pdb=" CB ASP G 36 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" C ARG H 208 " pdb=" N ARG H 208 " pdb=" CA ARG H 208 " pdb=" CB ARG H 208 " ideal model delta harmonic sigma weight residual -122.60 -133.96 11.36 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C ASN H 186 " pdb=" N ASN H 186 " pdb=" CA ASN H 186 " pdb=" CB ASN H 186 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 5556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 632 0.078 - 0.155: 544 0.155 - 0.233: 195 0.233 - 0.311: 35 0.311 - 0.388: 8 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA ASP G 36 " pdb=" N ASP G 36 " pdb=" C ASP G 36 " pdb=" CB ASP G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PHE A 212 " pdb=" N PHE A 212 " pdb=" C PHE A 212 " pdb=" CB PHE A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 1411 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 205 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PHE A 205 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE A 205 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN A 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 45 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C MET B 45 " 0.050 2.00e-02 2.50e+03 pdb=" O MET B 45 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 46 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 114 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C CYS B 114 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS B 114 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 115 " -0.015 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1135 2.77 - 3.30: 9199 3.30 - 3.83: 14983 3.83 - 4.37: 20645 4.37 - 4.90: 32283 Nonbonded interactions: 78245 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.236 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 3.040 nonbonded pdb=" O ILE R 273 " pdb=" OD1 ASN R 274 " model vdw 2.334 3.040 nonbonded pdb=" O ARG A 266 " pdb=" ND1 HIS A 340 " model vdw 2.393 3.120 nonbonded pdb=" N PHE B 253 " pdb=" O PHE B 253 " model vdw 2.468 2.496 ... (remaining 78240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- 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 9328 Z= 0.789 Angle : 1.680 9.357 12663 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 *********************** 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 : 1.002 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: 1.3429 time to fit residues: 350.9453 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 : 1.215 ------------------------------------------------------------------------------- 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 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 = 0.130707 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 9328 Z= 0.193 Angle : 0.547 5.659 12663 Z= 0.303 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 *********************** 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 : 1.015 Fit side-chains REVERT: H 23 GLU cc_start: 0.7740 (pm20) cc_final: 0.7512 (pm20) REVERT: H 110 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8551 (ttm) REVERT: H 203 GLN cc_start: 0.8860 (pt0) cc_final: 0.8542 (pp30) REVERT: B 42 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6598 (mmp-170) REVERT: B 129 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7252 (tpt90) REVERT: B 173 THR cc_start: 0.8530 (m) cc_final: 0.8121 (p) REVERT: B 219 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7753 (mtp180) REVERT: A 9 ASP cc_start: 0.8475 (m-30) cc_final: 0.8064 (m-30) REVERT: R 170 THR cc_start: 0.6666 (t) cc_final: 0.6333 (p) REVERT: R 171 THR cc_start: 0.7915 (p) cc_final: 0.7528 (p) REVERT: R 174 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6570 (mtt) REVERT: P 8 PHE cc_start: 0.7902 (m-80) cc_final: 0.7570 (m-80) outliers start: 33 outliers final: 14 residues processed: 181 average time/residue: 1.4007 time to fit residues: 268.8240 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 : 0.942 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.170845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124117 restraints weight = 10293.269| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9328 Z= 0.205 Angle : 0.530 7.227 12663 Z= 0.290 Chirality : 0.042 0.145 1414 Planarity : 0.004 0.043 1596 Dihedral : 4.819 65.193 1319 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.06 % Allowed : 15.84 % 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: 0.76 (0.24), residues: 1126 helix: 1.55 (0.25), residues: 369 sheet: 0.09 (0.30), residues: 262 loop : 0.06 (0.27), residues: 495 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 0.016 0.001 TYR H 207 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.979 Fit side-chains REVERT: H 173 SER cc_start: 0.8107 (m) cc_final: 0.7692 (p) REVERT: H 203 GLN cc_start: 0.8938 (pt0) cc_final: 0.8660 (pp30) REVERT: B 42 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6660 (mmp-170) REVERT: B 129 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7876 (mtp180) REVERT: B 217 MET cc_start: 0.8585 (pmm) cc_final: 0.8335 (pmm) REVERT: B 219 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7687 (mtp180) REVERT: B 259 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (pt0) REVERT: A 24 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7399 (mp10) REVERT: A 290 LYS cc_start: 0.7982 (mptt) cc_final: 0.7757 (mmpt) REVERT: A 373 GLU cc_start: 0.8394 (tt0) cc_final: 0.8124 (tt0) REVERT: R 170 THR cc_start: 0.6804 (t) cc_final: 0.6429 (p) REVERT: R 174 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6545 (mtt) REVERT: P 8 PHE cc_start: 0.7873 (m-80) cc_final: 0.7510 (m-80) outliers start: 40 outliers final: 15 residues processed: 177 average time/residue: 1.3348 time to fit residues: 250.8399 Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117972 restraints weight = 10287.472| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3153 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9328 Z= 0.359 Angle : 0.594 6.371 12663 Z= 0.324 Chirality : 0.046 0.157 1414 Planarity : 0.005 0.052 1596 Dihedral : 5.235 70.622 1319 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.26 % Allowed : 16.45 % Favored : 79.29 % 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: 1.29 (0.25), residues: 368 sheet: -0.10 (0.29), residues: 270 loop : 0.04 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.008 0.002 HIS A 340 PHE 0.019 0.002 PHE R 264 TYR 0.016 0.002 TYR H 207 ARG 0.006 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.050 Fit side-chains REVERT: H 173 SER cc_start: 0.8185 (m) cc_final: 0.7808 (p) REVERT: H 203 GLN cc_start: 0.8898 (pt0) cc_final: 0.8593 (pp30) REVERT: B 42 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6629 (mmp-170) REVERT: B 46 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7623 (mmt180) REVERT: B 70 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9057 (pp) REVERT: B 217 MET cc_start: 0.8603 (pmm) cc_final: 0.8355 (pmm) REVERT: B 219 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7726 (mtp180) REVERT: A 24 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7491 (mp10) REVERT: A 248 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7833 (mtm-85) REVERT: A 373 GLU cc_start: 0.8494 (tt0) cc_final: 0.8262 (tt0) REVERT: R 170 THR cc_start: 0.6801 (t) cc_final: 0.6394 (p) REVERT: R 171 THR cc_start: 0.7952 (p) cc_final: 0.7587 (p) REVERT: R 174 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6524 (mtt) REVERT: R 295 MET cc_start: 0.8711 (mmp) cc_final: 0.8311 (mmp) REVERT: P 6 GLN cc_start: 0.7124 (tt0) cc_final: 0.6735 (tt0) REVERT: P 8 PHE cc_start: 0.7807 (m-80) cc_final: 0.7101 (m-80) outliers start: 42 outliers final: 20 residues processed: 177 average time/residue: 1.3617 time to fit residues: 256.0202 Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 227 SER Chi-restraints excluded: chain B residue 228 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN A 206 GLN A 229 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119728 restraints weight = 10174.655| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.09 r_work: 0.3168 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9328 Z= 0.262 Angle : 0.543 7.195 12663 Z= 0.295 Chirality : 0.043 0.149 1414 Planarity : 0.004 0.049 1596 Dihedral : 5.022 68.038 1319 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.16 % Allowed : 17.26 % Favored : 78.58 % 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: 0.61 (0.24), residues: 1126 helix: 1.37 (0.25), residues: 369 sheet: -0.10 (0.30), residues: 262 loop : 0.10 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 96 *********************** 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 186 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.050 Fit side-chains REVERT: H 23 GLU cc_start: 0.7823 (pm20) cc_final: 0.7537 (pm20) REVERT: H 110 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8626 (ttm) REVERT: H 203 GLN cc_start: 0.8893 (pt0) cc_final: 0.8596 (pp30) REVERT: B 42 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6592 (mmp-170) REVERT: B 46 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7610 (mmt180) REVERT: B 59 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: B 70 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9004 (pp) REVERT: B 75 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: B 134 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7807 (mtm-85) REVERT: B 217 MET cc_start: 0.8602 (pmm) cc_final: 0.8340 (pmm) REVERT: B 219 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7724 (mtp180) REVERT: B 259 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8413 (pt0) REVERT: A 24 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7440 (mp10) REVERT: A 248 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7812 (mtm-85) REVERT: A 373 GLU cc_start: 0.8460 (tt0) cc_final: 0.8137 (tt0) REVERT: R 170 THR cc_start: 0.6849 (t) cc_final: 0.6435 (p) REVERT: R 295 MET cc_start: 0.8663 (mmp) cc_final: 0.8454 (mmp) REVERT: P 6 GLN cc_start: 0.7135 (tt0) cc_final: 0.6742 (tt0) REVERT: P 8 PHE cc_start: 0.7781 (m-80) cc_final: 0.7130 (m-80) outliers start: 41 outliers final: 22 residues processed: 171 average time/residue: 1.3708 time to fit residues: 249.3001 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 : 1.162 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN 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 B residue 336 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN A 206 GLN A 229 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.169106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120481 restraints weight = 10197.950| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.94 r_work: 0.3210 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9328 Z= 0.208 Angle : 0.513 6.364 12663 Z= 0.278 Chirality : 0.042 0.143 1414 Planarity : 0.004 0.050 1596 Dihedral : 4.864 64.407 1319 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.65 % Allowed : 17.87 % Favored : 78.48 % 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: 0.78 (0.24), residues: 1126 helix: 1.45 (0.25), residues: 369 sheet: -0.04 (0.30), residues: 268 loop : 0.29 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 340 PHE 0.014 0.001 PHE R 264 TYR 0.016 0.001 TYR H 207 ARG 0.007 0.000 ARG B 214 *********************** 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: 36 poor density : 145 time to evaluate : 0.938 Fit side-chains REVERT: H 23 GLU cc_start: 0.7785 (pm20) cc_final: 0.7522 (pm20) REVERT: H 110 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8606 (ttm) REVERT: H 167 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (t) REVERT: H 203 GLN cc_start: 0.8889 (pt0) cc_final: 0.8607 (pp30) REVERT: B 42 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6617 (mmp-170) REVERT: B 46 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7647 (mmt180) REVERT: B 59 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: B 134 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7817 (mtm-85) REVERT: B 217 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8360 (pmm) REVERT: B 219 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7747 (mtp180) REVERT: B 259 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: B 334 SER cc_start: 0.8232 (m) cc_final: 0.7770 (t) REVERT: A 24 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7334 (mm110) REVERT: A 248 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7803 (mtm-85) REVERT: A 373 GLU cc_start: 0.8394 (tt0) cc_final: 0.8075 (tt0) REVERT: R 170 THR cc_start: 0.6853 (t) cc_final: 0.6428 (p) REVERT: P 8 PHE cc_start: 0.7776 (m-80) cc_final: 0.7471 (m-80) outliers start: 36 outliers final: 18 residues processed: 168 average time/residue: 1.2867 time to fit residues: 230.1876 Evaluate side-chains 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 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 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 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 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 232 ASN A 340 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124393 restraints weight = 9933.723| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.11 r_work: 0.3195 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9328 Z= 0.249 Angle : 0.528 6.362 12663 Z= 0.286 Chirality : 0.043 0.147 1414 Planarity : 0.004 0.053 1596 Dihedral : 4.835 63.635 1317 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.86 % Allowed : 17.77 % 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: 0.76 (0.24), residues: 1126 helix: 1.41 (0.25), residues: 369 sheet: -0.16 (0.29), residues: 278 loop : 0.39 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 340 PHE 0.016 0.001 PHE R 264 TYR 0.016 0.001 TYR H 207 ARG 0.008 0.000 ARG B 214 *********************** 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: 38 poor density : 143 time to evaluate : 0.944 Fit side-chains REVERT: H 23 GLU cc_start: 0.7789 (pm20) cc_final: 0.7500 (pm20) REVERT: H 63 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: H 110 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (ttm) REVERT: H 167 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7850 (t) REVERT: H 203 GLN cc_start: 0.8913 (pt0) cc_final: 0.8641 (pp30) REVERT: B 42 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6579 (mmp-170) REVERT: B 46 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (mmt180) REVERT: B 59 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: B 70 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9030 (pp) REVERT: B 75 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: B 134 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7906 (mtm-85) REVERT: B 217 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8402 (pmm) REVERT: B 219 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7825 (mtp180) REVERT: A 24 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7603 (mp10) REVERT: A 248 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7860 (mtm-85) REVERT: A 373 GLU cc_start: 0.8442 (tt0) cc_final: 0.8220 (tt0) REVERT: R 170 THR cc_start: 0.6895 (t) cc_final: 0.6462 (p) REVERT: P 6 GLN cc_start: 0.7179 (tt0) cc_final: 0.6783 (tt0) REVERT: P 8 PHE cc_start: 0.7769 (m-80) cc_final: 0.7155 (m-80) outliers start: 38 outliers final: 20 residues processed: 167 average time/residue: 1.3240 time to fit residues: 235.2295 Evaluate side-chains 170 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain B residue 75 GLN 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 217 MET Chi-restraints excluded: chain B residue 227 SER 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 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: 0.1980 chunk 5 optimal weight: 0.0770 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 275 ASN A 368 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126664 restraints weight = 10056.608| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.12 r_work: 0.3234 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9328 Z= 0.159 Angle : 0.484 5.568 12663 Z= 0.263 Chirality : 0.041 0.138 1414 Planarity : 0.004 0.055 1596 Dihedral : 4.566 56.859 1317 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.74 % Allowed : 19.19 % 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: 0.89 (0.24), residues: 1126 helix: 1.60 (0.25), residues: 369 sheet: -0.15 (0.29), residues: 284 loop : 0.45 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 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 *********************** 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 173 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.035 Fit side-chains REVERT: H 23 GLU cc_start: 0.7771 (pm20) cc_final: 0.7474 (pm20) REVERT: H 162 SER cc_start: 0.8252 (m) cc_final: 0.7767 (p) REVERT: H 167 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7908 (t) REVERT: H 203 GLN cc_start: 0.8884 (pt0) cc_final: 0.8626 (pp30) REVERT: B 42 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6515 (mmp-170) REVERT: B 46 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7720 (mmt180) REVERT: B 59 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: B 217 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8458 (pmm) REVERT: B 219 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7829 (mtp180) REVERT: B 259 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: B 334 SER cc_start: 0.8109 (m) cc_final: 0.7624 (t) REVERT: A 24 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7398 (mm110) REVERT: A 373 GLU cc_start: 0.8364 (tt0) cc_final: 0.8125 (tt0) REVERT: R 63 MET cc_start: 0.6837 (mmt) cc_final: 0.6583 (mmt) REVERT: R 170 THR cc_start: 0.6960 (t) cc_final: 0.6530 (p) REVERT: P 6 GLN cc_start: 0.7167 (tt0) cc_final: 0.6829 (tt0) REVERT: P 8 PHE cc_start: 0.7795 (m-80) cc_final: 0.7231 (m-80) outliers start: 27 outliers final: 10 residues processed: 165 average time/residue: 1.3088 time to fit residues: 229.6261 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 B residue 42 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain R residue 94 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: 0.6980 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN ** 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 = 0.3934 r_free = 0.3934 target = 0.170648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124744 restraints weight = 9866.656| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.94 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9328 Z= 0.194 Angle : 0.499 5.774 12663 Z= 0.270 Chirality : 0.042 0.140 1414 Planarity : 0.004 0.052 1596 Dihedral : 4.581 52.951 1317 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.74 % Allowed : 19.09 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.24), residues: 1126 helix: 1.60 (0.25), residues: 368 sheet: -0.19 (0.29), residues: 288 loop : 0.44 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 197 PHE 0.014 0.001 PHE R 264 TYR 0.015 0.001 TYR H 207 ARG 0.009 0.000 ARG B 214 *********************** 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 167 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.940 Fit side-chains REVERT: H 23 GLU cc_start: 0.7805 (pm20) cc_final: 0.7510 (pm20) REVERT: H 63 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: H 162 SER cc_start: 0.8285 (m) cc_final: 0.7790 (p) REVERT: H 167 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7857 (t) REVERT: H 203 GLN cc_start: 0.8896 (pt0) cc_final: 0.8633 (pp30) REVERT: B 42 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6523 (mmp-170) REVERT: B 46 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7721 (mmt180) REVERT: B 217 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8452 (pmm) REVERT: B 219 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7831 (mtp180) REVERT: B 259 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8414 (pt0) REVERT: B 334 SER cc_start: 0.8167 (m) cc_final: 0.7706 (t) REVERT: A 24 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7427 (mm110) REVERT: A 248 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.7868 (mtm-85) REVERT: A 373 GLU cc_start: 0.8389 (tt0) cc_final: 0.8153 (tt0) REVERT: R 63 MET cc_start: 0.6703 (mmt) cc_final: 0.6272 (mmt) REVERT: R 170 THR cc_start: 0.6938 (t) cc_final: 0.6505 (p) REVERT: P 6 GLN cc_start: 0.7214 (tt0) cc_final: 0.6808 (tm-30) REVERT: P 8 PHE cc_start: 0.7773 (m-80) cc_final: 0.7157 (m-80) outliers start: 27 outliers final: 14 residues processed: 157 average time/residue: 1.3868 time to fit residues: 231.1804 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 : 1.006 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain B residue 146 LEU 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 A residue 6 SER 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: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 275 ASN A 368 GLN ** R 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN ** R 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 285 GLN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.168446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122908 restraints weight = 10024.077| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.92 r_work: 0.3184 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9328 Z= 0.293 Angle : 0.552 6.247 12663 Z= 0.298 Chirality : 0.044 0.150 1414 Planarity : 0.004 0.059 1596 Dihedral : 4.811 53.659 1317 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.74 % Allowed : 19.49 % Favored : 77.77 % 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: 0.73 (0.25), residues: 1126 helix: 1.37 (0.25), residues: 373 sheet: -0.21 (0.29), residues: 286 loop : 0.41 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.002 PHE R 264 TYR 0.015 0.002 TYR H 207 ARG 0.008 0.001 ARG B 214 ********************** 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 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.009 Fit side-chains REVERT: H 162 SER cc_start: 0.8283 (m) cc_final: 0.7801 (p) REVERT: H 167 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7881 (t) REVERT: H 203 GLN cc_start: 0.8916 (pt0) cc_final: 0.8641 (pp30) REVERT: B 42 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6566 (mmp-170) REVERT: B 46 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7719 (mmt180) REVERT: B 134 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7937 (mtm-85) REVERT: B 217 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8435 (pmm) REVERT: B 219 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7837 (mtp180) REVERT: B 259 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: A 24 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7627 (mp10) REVERT: A 201 PHE cc_start: 0.6442 (m-10) cc_final: 0.5164 (t80) REVERT: A 248 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7875 (mtm-85) REVERT: A 373 GLU cc_start: 0.8449 (tt0) cc_final: 0.8239 (tt0) REVERT: R 63 MET cc_start: 0.6738 (mmt) cc_final: 0.6248 (mmt) REVERT: R 170 THR cc_start: 0.6921 (t) cc_final: 0.6475 (p) REVERT: P 6 GLN cc_start: 0.7271 (tt0) cc_final: 0.6884 (tt0) REVERT: P 8 PHE cc_start: 0.7744 (m-80) cc_final: 0.7153 (m-80) outliers start: 27 outliers final: 17 residues processed: 152 average time/residue: 1.4678 time to fit residues: 236.9094 Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN A 28 GLN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 368 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125404 restraints weight = 9947.011| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.99 r_work: 0.3213 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9328 Z= 0.237 Angle : 0.525 5.978 12663 Z= 0.283 Chirality : 0.043 0.145 1414 Planarity : 0.004 0.059 1596 Dihedral : 4.721 52.403 1317 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.74 % Allowed : 19.80 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.25), residues: 1126 helix: 1.51 (0.25), residues: 369 sheet: -0.29 (0.29), residues: 288 loop : 0.44 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.015 0.001 PHE R 264 TYR 0.015 0.001 TYR H 207 ARG 0.009 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8595.16 seconds wall clock time: 152 minutes 15.52 seconds (9135.52 seconds total)