Starting phenix.real_space_refine on Wed Sep 17 13:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lre_63327/09_2025/9lre_63327.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.126 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 58 5.16 5 C 5663 2.51 5 N 1489 2.21 5 O 1635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8845 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1697 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2319 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 8845 At special positions: 0 Unit cell: (92.96, 119.105, 122.01, 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 58 16.00 O 1635 8.00 N 1489 7.00 C 5663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 334.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.025A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.964A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.591A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.779A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.791A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.787A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.007A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.699A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 44 removed outlier: 3.673A pdb=" N ASN R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS R 44 " --> pdb=" O PHE R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 67 Processing helix chain 'R' and resid 67 through 77 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 125 Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.926A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix removed outlier: 3.554A pdb=" N VAL R 153 " --> pdb=" O PRO R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 171 through 183 removed outlier: 3.651A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 205 Processing helix chain 'R' and resid 290 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 337 through 358 removed outlier: 4.042A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 362 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.715A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.759A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.871A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.267A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.915A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.826A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.531A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.532A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.960A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.960A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.962A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 214 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.962A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2814 1.35 - 1.47: 2324 1.47 - 1.59: 3821 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 9043 Sorted by residual: bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ALA A 11 " pdb=" CA ALA A 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N LEU R 10 " pdb=" CA LEU R 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N VAL E 2 " pdb=" CA VAL E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 11676 1.10 - 2.20: 486 2.20 - 3.30: 70 3.30 - 4.40: 13 4.40 - 5.50: 4 Bond angle restraints: 12249 Sorted by residual: angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.67 5.50 1.14e+00 7.69e-01 2.33e+01 angle pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N SER B 331 " ideal model delta sigma weight residual 114.74 117.70 -2.96 1.13e+00 7.83e-01 6.84e+00 angle pdb=" CA GLY E 213 " pdb=" C GLY E 213 " pdb=" N VAL E 214 " ideal model delta sigma weight residual 114.52 117.31 -2.79 1.09e+00 8.42e-01 6.53e+00 angle pdb=" N ALA E 92 " pdb=" CA ALA E 92 " pdb=" C ALA E 92 " ideal model delta sigma weight residual 107.73 111.01 -3.28 1.61e+00 3.86e-01 4.14e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 109.14 106.14 3.00 1.49e+00 4.50e-01 4.06e+00 ... (remaining 12244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 4814 16.44 - 32.88: 404 32.88 - 49.32: 90 49.32 - 65.76: 15 65.76 - 82.20: 3 Dihedral angle restraints: 5326 sinusoidal: 2075 harmonic: 3251 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual 93.00 127.89 -34.89 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 888 0.029 - 0.057: 317 0.057 - 0.086: 89 0.086 - 0.115: 58 0.115 - 0.143: 24 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA PRO E 107 " pdb=" N PRO E 107 " pdb=" C PRO E 107 " pdb=" CB PRO E 107 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1373 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO E 107 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 358 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.82e+00 pdb=" N PRO R 359 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO R 359 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 359 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 185 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO R 186 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 186 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 186 " -0.021 5.00e-02 4.00e+02 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 946 2.75 - 3.29: 8542 3.29 - 3.82: 14781 3.82 - 4.36: 18350 4.36 - 4.90: 31847 Nonbonded interactions: 74466 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.261 3.040 nonbonded pdb=" N HSM R 701 " pdb=" O HOH R 801 " model vdw 2.332 3.120 nonbonded pdb=" OD2 ASP A 229 " pdb=" NH2 ARG A 242 " model vdw 2.351 3.120 nonbonded pdb=" O SER E 105 " pdb=" NH2 ARG E 179 " model vdw 2.352 3.120 ... (remaining 74461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.003 0.041 9046 Z= 0.138 Angle : 0.521 5.502 12255 Z= 0.305 Chirality : 0.039 0.143 1376 Planarity : 0.003 0.055 1538 Dihedral : 12.896 82.198 3217 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.31 % Allowed : 7.98 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1098 helix: 1.44 (0.27), residues: 408 sheet: -0.23 (0.29), residues: 291 loop : -0.97 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 364 TYR 0.012 0.001 TYR R 358 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9043) covalent geometry : angle 0.52020 (12249) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.13975 ( 6) hydrogen bonds : bond 0.19014 ( 461) hydrogen bonds : angle 6.81906 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8333 (m-30) cc_final: 0.8068 (m-30) REVERT: A 207 GLU cc_start: 0.7459 (tt0) cc_final: 0.7065 (tp30) REVERT: A 249 LEU cc_start: 0.8299 (tp) cc_final: 0.8039 (tt) REVERT: A 284 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7558 (t) REVERT: A 350 ASP cc_start: 0.7879 (m-30) cc_final: 0.7402 (m-30) REVERT: B 303 ASP cc_start: 0.7611 (m-30) cc_final: 0.7212 (m-30) REVERT: E 93 MET cc_start: 0.8139 (tpp) cc_final: 0.7710 (mmm) REVERT: G 46 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7268 (pmtt) REVERT: R 61 ASP cc_start: 0.7562 (m-30) cc_final: 0.7288 (m-30) REVERT: R 136 MET cc_start: 0.8086 (mtp) cc_final: 0.7877 (mtp) REVERT: R 370 LEU cc_start: 0.8417 (mt) cc_final: 0.8209 (mp) outliers start: 3 outliers final: 0 residues processed: 201 average time/residue: 0.6019 time to fit residues: 128.3028 Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 294 ASN A 331 ASN B 6 GLN B 75 GLN B 119 ASN B 175 GLN B 220 GLN B 239 ASN B 259 GLN B 266 HIS E 130 GLN E 167 GLN E 220 HIS G 44 HIS G 59 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.173441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.138252 restraints weight = 9917.646| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.70 r_work: 0.3157 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9046 Z= 0.272 Angle : 0.696 9.237 12255 Z= 0.369 Chirality : 0.048 0.180 1376 Planarity : 0.005 0.067 1538 Dihedral : 6.039 56.078 1217 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.25 % Allowed : 13.58 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1098 helix: 1.75 (0.26), residues: 403 sheet: -0.15 (0.29), residues: 291 loop : -0.90 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.023 0.002 TYR R 358 PHE 0.018 0.002 PHE B 151 TRP 0.025 0.002 TRP B 99 HIS 0.009 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 9043) covalent geometry : angle 0.69488 (12249) SS BOND : bond 0.00701 ( 3) SS BOND : angle 1.55730 ( 6) hydrogen bonds : bond 0.05702 ( 461) hydrogen bonds : angle 5.23431 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7724 (tt0) cc_final: 0.7038 (tp30) REVERT: A 249 LEU cc_start: 0.8209 (tp) cc_final: 0.7928 (tt) REVERT: A 252 SER cc_start: 0.8539 (t) cc_final: 0.8136 (m) REVERT: A 308 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 350 ASP cc_start: 0.8030 (m-30) cc_final: 0.7571 (m-30) REVERT: B 66 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7127 (t70) REVERT: B 217 MET cc_start: 0.8438 (ppp) cc_final: 0.7806 (ppp) REVERT: B 259 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: E 93 MET cc_start: 0.8511 (tpp) cc_final: 0.8078 (mmm) REVERT: E 115 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7858 (t) REVERT: E 162 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8460 (tp) REVERT: R 47 ARG cc_start: 0.8721 (mmt-90) cc_final: 0.8175 (mmt-90) REVERT: R 61 ASP cc_start: 0.7838 (m-30) cc_final: 0.7487 (m-30) REVERT: R 370 LEU cc_start: 0.8470 (mt) cc_final: 0.8202 (mp) outliers start: 41 outliers final: 22 residues processed: 167 average time/residue: 0.6053 time to fit residues: 107.4805 Evaluate side-chains 161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 353 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 75 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN B 239 ASN B 259 GLN E 182 ASN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.174988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.139801 restraints weight = 9770.697| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.64 r_work: 0.3178 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9046 Z= 0.175 Angle : 0.579 6.534 12255 Z= 0.309 Chirality : 0.043 0.152 1376 Planarity : 0.004 0.055 1538 Dihedral : 5.469 49.346 1212 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.25 % Allowed : 15.23 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.25), residues: 1098 helix: 1.94 (0.25), residues: 409 sheet: -0.16 (0.29), residues: 285 loop : -0.82 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.016 0.002 TYR R 358 PHE 0.015 0.002 PHE B 151 TRP 0.019 0.002 TRP B 99 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9043) covalent geometry : angle 0.57811 (12249) SS BOND : bond 0.00544 ( 3) SS BOND : angle 1.12824 ( 6) hydrogen bonds : bond 0.04724 ( 461) hydrogen bonds : angle 4.91669 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7857 (tt0) cc_final: 0.7121 (tp30) REVERT: A 249 LEU cc_start: 0.8210 (tp) cc_final: 0.7948 (tt) REVERT: A 252 SER cc_start: 0.8645 (t) cc_final: 0.8290 (m) REVERT: A 308 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 350 ASP cc_start: 0.8027 (m-30) cc_final: 0.7558 (m-30) REVERT: B 66 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (t70) REVERT: E 93 MET cc_start: 0.8465 (tpp) cc_final: 0.8187 (mmm) REVERT: E 115 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7929 (t) REVERT: E 162 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8470 (tp) REVERT: R 61 ASP cc_start: 0.7811 (m-30) cc_final: 0.7527 (m-30) REVERT: R 71 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7298 (mp) REVERT: R 150 MET cc_start: 0.7028 (mmt) cc_final: 0.6779 (mmm) REVERT: R 360 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (tp) REVERT: R 370 LEU cc_start: 0.8452 (mt) cc_final: 0.8165 (mp) outliers start: 41 outliers final: 14 residues processed: 164 average time/residue: 0.6223 time to fit residues: 108.2615 Evaluate side-chains 147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 0.0060 chunk 46 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 204 GLN B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 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 = 0.3950 r_free = 0.3950 target = 0.180157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146789 restraints weight = 9883.699| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.76 r_work: 0.3241 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9046 Z= 0.107 Angle : 0.495 5.521 12255 Z= 0.267 Chirality : 0.041 0.143 1376 Planarity : 0.004 0.042 1538 Dihedral : 4.860 48.993 1212 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.21 % Allowed : 16.48 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1098 helix: 2.29 (0.26), residues: 408 sheet: 0.20 (0.30), residues: 278 loop : -0.63 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.012 0.001 TYR E 178 PHE 0.012 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9043) covalent geometry : angle 0.49455 (12249) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.82563 ( 6) hydrogen bonds : bond 0.03754 ( 461) hydrogen bonds : angle 4.52232 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7463 (ttp-110) REVERT: A 28 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7379 (pt0) REVERT: A 249 LEU cc_start: 0.8103 (tp) cc_final: 0.7858 (tt) REVERT: A 252 SER cc_start: 0.8525 (t) cc_final: 0.8195 (m) REVERT: A 277 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6940 (mtmt) REVERT: A 308 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 350 ASP cc_start: 0.7778 (m-30) cc_final: 0.7426 (m-30) REVERT: B 217 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: E 115 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7914 (t) REVERT: G 38 MET cc_start: 0.7580 (ttp) cc_final: 0.7354 (mtp) REVERT: R 27 PHE cc_start: 0.6670 (m-10) cc_final: 0.6448 (m-80) REVERT: R 61 ASP cc_start: 0.7435 (m-30) cc_final: 0.7163 (m-30) REVERT: R 360 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8091 (tp) REVERT: R 370 LEU cc_start: 0.8485 (mt) cc_final: 0.8200 (mp) outliers start: 31 outliers final: 8 residues processed: 154 average time/residue: 0.5766 time to fit residues: 94.4850 Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.174226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139506 restraints weight = 9795.855| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.87 r_work: 0.3145 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9046 Z= 0.221 Angle : 0.612 9.064 12255 Z= 0.324 Chirality : 0.045 0.169 1376 Planarity : 0.004 0.056 1538 Dihedral : 5.475 48.497 1212 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.25 % Allowed : 16.99 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.25), residues: 1098 helix: 1.97 (0.25), residues: 409 sheet: 0.06 (0.28), residues: 297 loop : -0.71 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 134 TYR 0.017 0.002 TYR R 358 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.006 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9043) covalent geometry : angle 0.61043 (12249) SS BOND : bond 0.00515 ( 3) SS BOND : angle 1.87790 ( 6) hydrogen bonds : bond 0.04843 ( 461) hydrogen bonds : angle 4.80404 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7870 (ttp-110) cc_final: 0.7469 (ttp-110) REVERT: A 28 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7469 (pt0) REVERT: A 249 LEU cc_start: 0.8236 (tp) cc_final: 0.7990 (tt) REVERT: A 252 SER cc_start: 0.8627 (t) cc_final: 0.8264 (m) REVERT: A 308 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 350 ASP cc_start: 0.7932 (m-30) cc_final: 0.7548 (m-30) REVERT: B 217 MET cc_start: 0.8414 (pmt) cc_final: 0.8188 (pmm) REVERT: E 162 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8426 (tp) REVERT: G 38 MET cc_start: 0.7824 (ttp) cc_final: 0.7561 (mtp) REVERT: R 61 ASP cc_start: 0.7623 (m-30) cc_final: 0.7295 (m-30) REVERT: R 71 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7196 (mp) REVERT: R 360 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8140 (tp) REVERT: R 370 LEU cc_start: 0.8502 (mt) cc_final: 0.8198 (mp) outliers start: 41 outliers final: 22 residues processed: 146 average time/residue: 0.5677 time to fit residues: 88.5039 Evaluate side-chains 143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 337 SER Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.176638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141811 restraints weight = 9787.999| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.89 r_work: 0.3209 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9046 Z= 0.122 Angle : 0.517 8.676 12255 Z= 0.276 Chirality : 0.041 0.145 1376 Planarity : 0.004 0.044 1538 Dihedral : 5.008 48.262 1212 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 19.48 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1098 helix: 2.20 (0.26), residues: 408 sheet: 0.19 (0.28), residues: 299 loop : -0.55 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.012 0.001 TYR R 358 PHE 0.014 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9043) covalent geometry : angle 0.51634 (12249) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.33636 ( 6) hydrogen bonds : bond 0.03948 ( 461) hydrogen bonds : angle 4.53028 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7523 (ttp-110) REVERT: A 28 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7443 (pt0) REVERT: A 252 SER cc_start: 0.8585 (t) cc_final: 0.8260 (m) REVERT: A 277 LYS cc_start: 0.7230 (mtpt) cc_final: 0.6984 (mtpt) REVERT: A 308 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7662 (mt-10) REVERT: A 350 ASP cc_start: 0.7895 (m-30) cc_final: 0.7493 (m-30) REVERT: B 217 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8127 (pmm) REVERT: B 259 GLN cc_start: 0.8302 (pt0) cc_final: 0.8006 (pt0) REVERT: E 93 MET cc_start: 0.8169 (tpp) cc_final: 0.7837 (mmm) REVERT: E 162 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8429 (tp) REVERT: G 19 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7089 (mp) REVERT: G 38 MET cc_start: 0.7652 (ttp) cc_final: 0.7418 (mtp) REVERT: R 61 ASP cc_start: 0.7500 (m-30) cc_final: 0.7194 (m-30) REVERT: R 370 LEU cc_start: 0.8512 (mt) cc_final: 0.8201 (mp) outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.6336 time to fit residues: 93.4728 Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.178228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143769 restraints weight = 9828.600| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.83 r_work: 0.3208 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9046 Z= 0.128 Angle : 0.520 8.404 12255 Z= 0.277 Chirality : 0.041 0.144 1376 Planarity : 0.004 0.042 1538 Dihedral : 4.947 47.353 1212 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.80 % Allowed : 19.27 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.25), residues: 1098 helix: 2.26 (0.26), residues: 408 sheet: 0.29 (0.28), residues: 292 loop : -0.62 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.011 0.001 TYR R 358 PHE 0.013 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9043) covalent geometry : angle 0.51928 (12249) SS BOND : bond 0.00395 ( 3) SS BOND : angle 1.25716 ( 6) hydrogen bonds : bond 0.03943 ( 461) hydrogen bonds : angle 4.48632 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7911 (ttp-110) cc_final: 0.7421 (ttp-110) REVERT: A 252 SER cc_start: 0.8585 (t) cc_final: 0.8278 (m) REVERT: A 308 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 350 ASP cc_start: 0.7906 (m-30) cc_final: 0.7546 (m-30) REVERT: B 134 ARG cc_start: 0.8616 (ptp-170) cc_final: 0.7992 (ptt-90) REVERT: B 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8154 (pmm) REVERT: B 259 GLN cc_start: 0.8340 (pt0) cc_final: 0.8068 (pt0) REVERT: E 162 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8408 (tp) REVERT: G 19 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7217 (mp) REVERT: G 38 MET cc_start: 0.7639 (ttp) cc_final: 0.7436 (mtp) REVERT: R 61 ASP cc_start: 0.7454 (m-30) cc_final: 0.7150 (m-30) REVERT: R 150 MET cc_start: 0.6768 (mmt) cc_final: 0.6563 (mmm) REVERT: R 360 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8068 (tp) REVERT: R 370 LEU cc_start: 0.8516 (mt) cc_final: 0.8226 (mp) outliers start: 27 outliers final: 14 residues processed: 144 average time/residue: 0.6095 time to fit residues: 93.4507 Evaluate side-chains 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.180201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.145362 restraints weight = 9740.411| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.76 r_work: 0.3232 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9046 Z= 0.110 Angle : 0.501 7.892 12255 Z= 0.268 Chirality : 0.041 0.145 1376 Planarity : 0.004 0.044 1538 Dihedral : 4.781 46.119 1212 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 19.90 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1098 helix: 2.33 (0.26), residues: 408 sheet: 0.28 (0.29), residues: 294 loop : -0.47 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.012 0.001 TYR A 230 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9043) covalent geometry : angle 0.50011 (12249) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.03540 ( 6) hydrogen bonds : bond 0.03711 ( 461) hydrogen bonds : angle 4.38804 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7647 (ttp-110) REVERT: A 26 ASP cc_start: 0.8498 (m-30) cc_final: 0.8236 (m-30) REVERT: A 252 SER cc_start: 0.8585 (t) cc_final: 0.8292 (m) REVERT: A 277 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6867 (mtmt) REVERT: A 308 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 350 ASP cc_start: 0.7875 (m-30) cc_final: 0.7528 (m-30) REVERT: B 134 ARG cc_start: 0.8596 (ptp-170) cc_final: 0.7966 (ptt-90) REVERT: B 214 ARG cc_start: 0.7617 (mmt-90) cc_final: 0.7416 (mmt-90) REVERT: B 217 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: B 234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: B 259 GLN cc_start: 0.8303 (pt0) cc_final: 0.8022 (pt0) REVERT: E 25 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7853 (p) REVERT: E 162 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8447 (tp) REVERT: G 19 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7180 (mp) REVERT: G 38 MET cc_start: 0.7584 (ttp) cc_final: 0.7320 (mtp) REVERT: R 61 ASP cc_start: 0.7427 (m-30) cc_final: 0.7102 (m-30) REVERT: R 177 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7896 (mp) REVERT: R 360 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8071 (tp) REVERT: R 370 LEU cc_start: 0.8534 (mt) cc_final: 0.8240 (mp) outliers start: 28 outliers final: 14 residues processed: 142 average time/residue: 0.5875 time to fit residues: 88.7847 Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.178701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144113 restraints weight = 9734.762| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.80 r_work: 0.3194 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9046 Z= 0.138 Angle : 0.537 7.626 12255 Z= 0.284 Chirality : 0.042 0.142 1376 Planarity : 0.004 0.044 1538 Dihedral : 4.967 45.580 1212 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.80 % Allowed : 20.00 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.25), residues: 1098 helix: 2.30 (0.26), residues: 407 sheet: 0.22 (0.29), residues: 296 loop : -0.45 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.016 0.001 TYR A 302 PHE 0.014 0.001 PHE E 80 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9043) covalent geometry : angle 0.53591 (12249) SS BOND : bond 0.00459 ( 3) SS BOND : angle 1.38946 ( 6) hydrogen bonds : bond 0.04027 ( 461) hydrogen bonds : angle 4.48837 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7578 (mtm-85) REVERT: A 252 SER cc_start: 0.8590 (t) cc_final: 0.8283 (m) REVERT: A 277 LYS cc_start: 0.7268 (mtpt) cc_final: 0.6797 (mtmt) REVERT: A 350 ASP cc_start: 0.7950 (m-30) cc_final: 0.7597 (m-30) REVERT: B 134 ARG cc_start: 0.8634 (ptp-170) cc_final: 0.7973 (ptt-90) REVERT: B 217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8195 (pmm) REVERT: B 259 GLN cc_start: 0.8286 (pt0) cc_final: 0.7996 (pt0) REVERT: E 25 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7893 (p) REVERT: E 162 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8428 (tp) REVERT: G 19 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7176 (mp) REVERT: G 38 MET cc_start: 0.7608 (ttp) cc_final: 0.7402 (mtp) REVERT: R 61 ASP cc_start: 0.7492 (m-30) cc_final: 0.7163 (m-30) REVERT: R 177 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7901 (mp) REVERT: R 360 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8060 (tp) REVERT: R 370 LEU cc_start: 0.8538 (mt) cc_final: 0.8243 (mp) outliers start: 27 outliers final: 14 residues processed: 139 average time/residue: 0.5778 time to fit residues: 85.7231 Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.180312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145399 restraints weight = 9700.983| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.79 r_work: 0.3236 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9046 Z= 0.113 Angle : 0.516 7.704 12255 Z= 0.272 Chirality : 0.041 0.142 1376 Planarity : 0.004 0.046 1538 Dihedral : 4.774 45.108 1212 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.49 % Allowed : 19.79 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1098 helix: 2.35 (0.26), residues: 408 sheet: 0.23 (0.29), residues: 298 loop : -0.40 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.012 0.001 TYR A 230 PHE 0.018 0.001 PHE R 82 TRP 0.020 0.001 TRP R 316 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9043) covalent geometry : angle 0.51433 (12249) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.65379 ( 6) hydrogen bonds : bond 0.03706 ( 461) hydrogen bonds : angle 4.37403 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7681 (ttp-110) REVERT: A 252 SER cc_start: 0.8570 (t) cc_final: 0.8300 (m) REVERT: A 277 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6896 (mtmt) REVERT: A 308 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 330 LYS cc_start: 0.7612 (tttt) cc_final: 0.7349 (tptt) REVERT: A 350 ASP cc_start: 0.7881 (m-30) cc_final: 0.7548 (m-30) REVERT: B 134 ARG cc_start: 0.8567 (ptp-170) cc_final: 0.7926 (ptt-90) REVERT: B 259 GLN cc_start: 0.8252 (pt0) cc_final: 0.7999 (pt0) REVERT: E 25 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7843 (p) REVERT: E 162 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 180 MET cc_start: 0.8439 (ttp) cc_final: 0.8220 (ppp) REVERT: G 19 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7202 (mp) REVERT: G 38 MET cc_start: 0.7563 (ttp) cc_final: 0.7312 (mtp) REVERT: R 61 ASP cc_start: 0.7426 (m-30) cc_final: 0.7102 (m-30) REVERT: R 177 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7886 (mp) REVERT: R 360 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8010 (tp) REVERT: R 370 LEU cc_start: 0.8532 (mt) cc_final: 0.8238 (mp) outliers start: 24 outliers final: 16 residues processed: 133 average time/residue: 0.6433 time to fit residues: 91.0615 Evaluate side-chains 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN B 220 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.180442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.146186 restraints weight = 9612.841| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.73 r_work: 0.3244 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9046 Z= 0.113 Angle : 0.519 7.579 12255 Z= 0.276 Chirality : 0.041 0.140 1376 Planarity : 0.004 0.051 1538 Dihedral : 4.753 44.658 1212 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 20.10 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.26), residues: 1098 helix: 2.39 (0.25), residues: 408 sheet: 0.34 (0.29), residues: 294 loop : -0.44 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.012 0.001 TYR A 230 PHE 0.014 0.001 PHE E 80 TRP 0.016 0.001 TRP R 316 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9043) covalent geometry : angle 0.51811 (12249) SS BOND : bond 0.00424 ( 3) SS BOND : angle 1.29804 ( 6) hydrogen bonds : bond 0.03664 ( 461) hydrogen bonds : angle 4.34647 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3141.18 seconds wall clock time: 54 minutes 28.18 seconds (3268.18 seconds total)