Starting phenix.real_space_refine on Sat Jul 26 18:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lre_63327/07_2025/9lre_63327_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lre_63327/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lre_63327/07_2025/9lre_63327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lre_63327/07_2025/9lre_63327.map" model { file = "/net/cci-nas-00/data/ceres_data/9lre_63327/07_2025/9lre_63327_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lre_63327/07_2025/9lre_63327_neut.cif" } resolution = 2.84 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= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.20, per 1000 atoms: 0.81 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: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.15 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: 3.63 Time building geometry restraints manager: 3.65 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.060 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:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.150 ------------------------------------------------------------------------------- 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 (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: 0.15 (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 TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR R 358 ARG 0.002 0.000 ARG R 364 Details of bonding type rmsd hydrogen bonds : bond 0.19014 ( 461) hydrogen bonds : angle 6.81906 ( 1308) SS BOND : bond 0.00434 ( 3) SS BOND : angle 1.13975 ( 6) covalent geometry : bond 0.00281 ( 9043) covalent geometry : angle 0.52020 (12249) *********************** 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 : 0.949 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: 1.3060 time to fit residues: 279.0190 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 : 0.958 ------------------------------------------------------------------------------- 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 92 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0070 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 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 59 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.141173 restraints weight = 9790.748| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.67 r_work: 0.3201 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9046 Z= 0.186 Angle : 0.611 7.780 12255 Z= 0.326 Chirality : 0.044 0.158 1376 Planarity : 0.005 0.050 1538 Dihedral : 5.649 50.503 1217 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.52 % Allowed : 13.58 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.44 (0.25), residues: 1098 helix: 1.84 (0.26), residues: 409 sheet: -0.20 (0.29), residues: 285 loop : -0.90 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.006 0.002 HIS B 54 PHE 0.015 0.002 PHE B 151 TYR 0.017 0.002 TYR R 358 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 461) hydrogen bonds : angle 5.04124 ( 1308) SS BOND : bond 0.00556 ( 3) SS BOND : angle 1.38484 ( 6) covalent geometry : bond 0.00434 ( 9043) covalent geometry : angle 0.61065 (12249) *********************** 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 181 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7413 (ptp90) REVERT: A 26 ASP cc_start: 0.8568 (m-30) cc_final: 0.8317 (m-30) REVERT: A 207 GLU cc_start: 0.7806 (tt0) cc_final: 0.7201 (tp30) REVERT: A 249 LEU cc_start: 0.8198 (tp) cc_final: 0.7936 (tt) REVERT: A 252 SER cc_start: 0.8487 (t) cc_final: 0.8087 (m) REVERT: A 302 TYR cc_start: 0.7351 (t80) cc_final: 0.7087 (t80) REVERT: A 308 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 350 ASP cc_start: 0.7995 (m-30) cc_final: 0.7520 (m-30) REVERT: B 66 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6988 (t70) REVERT: B 259 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: E 162 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (tp) REVERT: R 61 ASP cc_start: 0.7717 (m-30) cc_final: 0.7393 (m-30) REVERT: R 136 MET cc_start: 0.8003 (mtp) cc_final: 0.7794 (mtp) REVERT: R 370 LEU cc_start: 0.8418 (mt) cc_final: 0.8151 (mp) outliers start: 34 outliers final: 14 residues processed: 166 average time/residue: 1.2364 time to fit residues: 218.8855 Evaluate side-chains 155 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 175 GLN B 220 GLN B 259 GLN E 182 ASN G 59 ASN ** R 33 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 = 0.3932 r_free = 0.3932 target = 0.178853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.143212 restraints weight = 9837.135| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.72 r_work: 0.3210 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9046 Z= 0.125 Angle : 0.524 5.939 12255 Z= 0.282 Chirality : 0.041 0.143 1376 Planarity : 0.004 0.042 1538 Dihedral : 5.018 47.730 1212 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 16.17 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1098 helix: 2.13 (0.26), residues: 409 sheet: -0.05 (0.29), residues: 284 loop : -0.72 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 461) hydrogen bonds : angle 4.71553 ( 1308) SS BOND : bond 0.00455 ( 3) SS BOND : angle 0.93590 ( 6) covalent geometry : bond 0.00273 ( 9043) covalent geometry : angle 0.52397 (12249) *********************** 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 169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (ttm170) REVERT: A 24 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7322 (ptp90) REVERT: A 28 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7309 (pt0) REVERT: A 207 GLU cc_start: 0.7663 (tt0) cc_final: 0.7005 (tp30) REVERT: A 249 LEU cc_start: 0.8108 (tp) cc_final: 0.7868 (tt) REVERT: A 308 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 350 ASP cc_start: 0.7778 (m-30) cc_final: 0.7371 (m-30) REVERT: E 162 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8375 (tp) REVERT: R 27 PHE cc_start: 0.6574 (m-80) cc_final: 0.6361 (m-80) REVERT: R 61 ASP cc_start: 0.7497 (m-30) cc_final: 0.7206 (m-30) REVERT: R 370 LEU cc_start: 0.8415 (mt) cc_final: 0.8120 (mp) outliers start: 28 outliers final: 10 residues processed: 155 average time/residue: 1.3822 time to fit residues: 227.5522 Evaluate side-chains 142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 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 317 CYS 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 121 SER Chi-restraints excluded: chain R residue 125 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 175 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 = 0.3920 r_free = 0.3920 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141602 restraints weight = 9782.452| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.73 r_work: 0.3220 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9046 Z= 0.135 Angle : 0.526 5.830 12255 Z= 0.282 Chirality : 0.042 0.137 1376 Planarity : 0.004 0.043 1538 Dihedral : 5.004 47.527 1212 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.94 % Allowed : 16.27 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.93 (0.26), residues: 1098 helix: 2.15 (0.25), residues: 408 sheet: 0.06 (0.29), residues: 297 loop : -0.52 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 358 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 461) hydrogen bonds : angle 4.59758 ( 1308) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.04925 ( 6) covalent geometry : bond 0.00305 ( 9043) covalent geometry : angle 0.52543 (12249) *********************** 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 173 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.8003 (ttm170) REVERT: A 24 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7605 (mtm-85) REVERT: A 28 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7641 (pt0) REVERT: A 207 GLU cc_start: 0.7780 (tt0) cc_final: 0.7097 (tp30) REVERT: A 249 LEU cc_start: 0.8157 (tp) cc_final: 0.7913 (tt) REVERT: A 252 SER cc_start: 0.8604 (t) cc_final: 0.8253 (m) REVERT: A 277 LYS cc_start: 0.7256 (mtpt) cc_final: 0.6938 (mtmt) REVERT: A 308 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 350 ASP cc_start: 0.8002 (m-30) cc_final: 0.7577 (m-30) REVERT: E 162 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8431 (tp) REVERT: R 27 PHE cc_start: 0.6743 (m-10) cc_final: 0.6523 (m-80) REVERT: R 61 ASP cc_start: 0.7698 (m-30) cc_final: 0.7414 (m-30) REVERT: R 360 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8082 (tp) REVERT: R 370 LEU cc_start: 0.8475 (mt) cc_final: 0.8182 (mp) outliers start: 38 outliers final: 17 residues processed: 159 average time/residue: 1.4198 time to fit residues: 240.3279 Evaluate side-chains 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 21 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 76 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 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 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 353 VAL 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 80 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 175 GLN G 59 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.176653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.141255 restraints weight = 9704.622| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.85 r_work: 0.3199 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2588 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= 0.142 Angle : 0.538 9.451 12255 Z= 0.286 Chirality : 0.042 0.140 1376 Planarity : 0.004 0.043 1538 Dihedral : 5.048 47.321 1212 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.83 % Allowed : 16.58 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.99 (0.26), residues: 1098 helix: 2.19 (0.25), residues: 408 sheet: 0.19 (0.29), residues: 292 loop : -0.57 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 358 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 461) hydrogen bonds : angle 4.54965 ( 1308) SS BOND : bond 0.00497 ( 3) SS BOND : angle 0.96684 ( 6) covalent geometry : bond 0.00325 ( 9043) covalent geometry : angle 0.53735 (12249) *********************** 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: 37 poor density : 125 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7421 (mtm-85) REVERT: A 28 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7554 (pt0) REVERT: A 249 LEU cc_start: 0.8157 (tp) cc_final: 0.7916 (tt) REVERT: A 252 SER cc_start: 0.8560 (t) cc_final: 0.8204 (m) REVERT: A 308 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 350 ASP cc_start: 0.7834 (m-30) cc_final: 0.7489 (m-30) REVERT: B 217 MET cc_start: 0.8364 (pmm) cc_final: 0.8068 (pp-130) REVERT: B 219 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7509 (mmt90) REVERT: B 258 ASP cc_start: 0.6960 (t0) cc_final: 0.6585 (p0) REVERT: E 162 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8413 (tp) REVERT: G 38 MET cc_start: 0.7654 (ttp) cc_final: 0.7420 (mtp) REVERT: R 61 ASP cc_start: 0.7463 (m-30) cc_final: 0.7192 (m-30) REVERT: R 360 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8049 (tp) REVERT: R 370 LEU cc_start: 0.8482 (mt) cc_final: 0.8189 (mp) outliers start: 37 outliers final: 17 residues processed: 149 average time/residue: 1.4381 time to fit residues: 229.1315 Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 253 ILE 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 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 195 ASP 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 121 SER Chi-restraints excluded: chain R residue 125 GLN 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 90 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.179882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145451 restraints weight = 9692.677| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9046 Z= 0.120 Angle : 0.513 8.192 12255 Z= 0.273 Chirality : 0.041 0.151 1376 Planarity : 0.004 0.042 1538 Dihedral : 4.835 46.803 1212 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.32 % Allowed : 17.41 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.26), residues: 1098 helix: 2.26 (0.26), residues: 408 sheet: 0.18 (0.29), residues: 296 loop : -0.46 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.001 TYR A 230 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 461) hydrogen bonds : angle 4.46768 ( 1308) SS BOND : bond 0.00409 ( 3) SS BOND : angle 1.10316 ( 6) covalent geometry : bond 0.00267 ( 9043) covalent geometry : angle 0.51281 (12249) *********************** 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 158 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7475 (mtm-85) REVERT: A 249 LEU cc_start: 0.8169 (tp) cc_final: 0.7920 (tt) REVERT: A 252 SER cc_start: 0.8541 (t) cc_final: 0.8205 (m) REVERT: A 308 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 350 ASP cc_start: 0.7876 (m-30) cc_final: 0.7538 (m-30) REVERT: B 217 MET cc_start: 0.8401 (pmm) cc_final: 0.8143 (pp-130) REVERT: E 162 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8408 (tp) REVERT: E 180 MET cc_start: 0.8435 (ttp) cc_final: 0.8143 (ppp) REVERT: G 19 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7060 (mp) REVERT: G 38 MET cc_start: 0.7611 (ttp) cc_final: 0.7293 (mtp) REVERT: R 61 ASP cc_start: 0.7437 (m-30) cc_final: 0.7173 (m-30) REVERT: R 177 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7790 (mp) REVERT: R 360 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8069 (tp) REVERT: R 370 LEU cc_start: 0.8491 (mt) cc_final: 0.8196 (mp) outliers start: 32 outliers final: 13 residues processed: 148 average time/residue: 1.1531 time to fit residues: 182.8772 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 : 1.028 ------------------------------------------------------------------------------- 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 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 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 121 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 105 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.178952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145677 restraints weight = 9762.184| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.71 r_work: 0.3226 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2826 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= 0.138 Angle : 0.532 7.841 12255 Z= 0.285 Chirality : 0.042 0.148 1376 Planarity : 0.004 0.044 1538 Dihedral : 4.935 46.458 1212 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.32 % Allowed : 17.20 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.26), residues: 1098 helix: 2.26 (0.26), residues: 408 sheet: 0.24 (0.29), residues: 294 loop : -0.48 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE E 80 TYR 0.012 0.001 TYR A 302 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 461) hydrogen bonds : angle 4.50311 ( 1308) SS BOND : bond 0.00419 ( 3) SS BOND : angle 1.63895 ( 6) covalent geometry : bond 0.00315 ( 9043) covalent geometry : angle 0.53108 (12249) *********************** 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 151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7540 (ttp-110) REVERT: A 249 LEU cc_start: 0.8232 (tp) cc_final: 0.7970 (tt) REVERT: A 252 SER cc_start: 0.8636 (t) cc_final: 0.8275 (m) REVERT: A 277 LYS cc_start: 0.7085 (mtpt) cc_final: 0.6866 (ptpt) REVERT: A 308 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7825 (mt-10) REVERT: A 350 ASP cc_start: 0.8128 (m-30) cc_final: 0.7739 (m-30) REVERT: B 217 MET cc_start: 0.8571 (pmm) cc_final: 0.7903 (pp-130) REVERT: E 25 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7912 (p) REVERT: E 162 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (tp) REVERT: E 180 MET cc_start: 0.8541 (ttp) cc_final: 0.8252 (ppp) REVERT: G 19 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7090 (mp) REVERT: G 38 MET cc_start: 0.7707 (ttp) cc_final: 0.7401 (mtp) REVERT: R 61 ASP cc_start: 0.7720 (m-30) cc_final: 0.7374 (m-30) REVERT: R 177 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7850 (mp) REVERT: R 360 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (tp) REVERT: R 370 LEU cc_start: 0.8546 (mt) cc_final: 0.8244 (mp) outliers start: 32 outliers final: 19 residues processed: 140 average time/residue: 1.2041 time to fit residues: 180.9613 Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 21 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 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 156 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 223 THR 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 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 353 VAL 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 99 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.178048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145143 restraints weight = 9877.656| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.79 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9046 Z= 0.154 Angle : 0.552 7.355 12255 Z= 0.293 Chirality : 0.042 0.145 1376 Planarity : 0.004 0.046 1538 Dihedral : 5.059 46.702 1212 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.42 % Allowed : 17.41 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.08 (0.25), residues: 1098 helix: 2.24 (0.25), residues: 409 sheet: 0.25 (0.29), residues: 294 loop : -0.50 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.002 PHE R 82 TYR 0.013 0.001 TYR R 358 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 461) hydrogen bonds : angle 4.57060 ( 1308) SS BOND : bond 0.00485 ( 3) SS BOND : angle 1.95574 ( 6) covalent geometry : bond 0.00356 ( 9043) covalent geometry : angle 0.55032 (12249) *********************** 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 153 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7467 (mtm-85) REVERT: A 249 LEU cc_start: 0.8193 (tp) cc_final: 0.7944 (tt) REVERT: A 252 SER cc_start: 0.8578 (t) cc_final: 0.8230 (m) REVERT: A 308 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 350 ASP cc_start: 0.7958 (m-30) cc_final: 0.7605 (m-30) REVERT: B 215 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7982 (mp0) REVERT: B 217 MET cc_start: 0.8486 (pmm) cc_final: 0.7892 (pp-130) REVERT: E 25 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7777 (p) REVERT: E 162 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8416 (tp) REVERT: G 19 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7122 (mp) REVERT: G 38 MET cc_start: 0.7684 (ttp) cc_final: 0.7390 (mtp) REVERT: R 61 ASP cc_start: 0.7508 (m-30) cc_final: 0.7201 (m-30) REVERT: R 177 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7841 (mp) REVERT: R 360 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8060 (tp) REVERT: R 370 LEU cc_start: 0.8528 (mt) cc_final: 0.8231 (mp) outliers start: 33 outliers final: 16 residues processed: 139 average time/residue: 1.1444 time to fit residues: 170.3927 Evaluate side-chains 140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain B residue 223 THR 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 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 353 VAL 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 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.179623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.145125 restraints weight = 9775.714| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.83 r_work: 0.3229 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2959 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= 0.121 Angle : 0.520 7.410 12255 Z= 0.277 Chirality : 0.041 0.139 1376 Planarity : 0.004 0.046 1538 Dihedral : 4.857 46.002 1212 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.69 % Allowed : 18.13 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.16 (0.26), residues: 1098 helix: 2.31 (0.25), residues: 409 sheet: 0.28 (0.29), residues: 294 loop : -0.44 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 80 TYR 0.017 0.001 TYR A 302 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 461) hydrogen bonds : angle 4.46417 ( 1308) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.50582 ( 6) covalent geometry : bond 0.00271 ( 9043) covalent geometry : angle 0.51946 (12249) *********************** 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 141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7363 (ttp-110) REVERT: A 249 LEU cc_start: 0.8145 (tp) cc_final: 0.7892 (tt) REVERT: A 252 SER cc_start: 0.8555 (t) cc_final: 0.8219 (m) REVERT: A 308 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 350 ASP cc_start: 0.7910 (m-30) cc_final: 0.7575 (m-30) REVERT: B 46 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7410 (ttt180) REVERT: B 217 MET cc_start: 0.8452 (pmm) cc_final: 0.7907 (pp-130) REVERT: B 259 GLN cc_start: 0.8344 (pt0) cc_final: 0.8022 (pt0) REVERT: E 25 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7845 (p) REVERT: E 180 MET cc_start: 0.8457 (ttp) cc_final: 0.8237 (ppp) REVERT: G 19 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7146 (mp) REVERT: G 38 MET cc_start: 0.7605 (ttp) cc_final: 0.7327 (mtp) REVERT: R 61 ASP cc_start: 0.7428 (m-30) cc_final: 0.7118 (m-30) REVERT: R 177 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7794 (mp) REVERT: R 360 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8055 (tp) REVERT: R 370 LEU cc_start: 0.8540 (mt) cc_final: 0.8243 (mp) outliers start: 26 outliers final: 16 residues processed: 134 average time/residue: 1.1273 time to fit residues: 162.2483 Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 223 THR 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 203 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 125 GLN Chi-restraints excluded: chain R residue 177 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 60 optimal weight: 0.0370 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 14 optimal weight: 0.0000 overall best weight: 0.5462 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.180699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147963 restraints weight = 9782.534| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.69 r_work: 0.3260 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9046 Z= 0.112 Angle : 0.511 8.614 12255 Z= 0.272 Chirality : 0.041 0.136 1376 Planarity : 0.004 0.045 1538 Dihedral : 4.698 44.592 1212 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 18.65 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.23 (0.26), residues: 1098 helix: 2.37 (0.25), residues: 409 sheet: 0.30 (0.29), residues: 294 loop : -0.39 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 82 TYR 0.011 0.001 TYR E 178 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 461) hydrogen bonds : angle 4.38196 ( 1308) SS BOND : bond 0.00414 ( 3) SS BOND : angle 1.34195 ( 6) covalent geometry : bond 0.00246 ( 9043) covalent geometry : angle 0.50990 (12249) ********************** 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 139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7360 (ttp-110) REVERT: A 249 LEU cc_start: 0.8141 (tp) cc_final: 0.7874 (tt) REVERT: A 252 SER cc_start: 0.8542 (t) cc_final: 0.8212 (m) REVERT: A 277 LYS cc_start: 0.7577 (ptpt) cc_final: 0.7195 (ptpt) REVERT: A 308 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 330 LYS cc_start: 0.7568 (tttt) cc_final: 0.7339 (tptt) REVERT: A 350 ASP cc_start: 0.7882 (m-30) cc_final: 0.7552 (m-30) REVERT: B 46 ARG cc_start: 0.7584 (ttt180) cc_final: 0.7358 (ttt180) REVERT: B 217 MET cc_start: 0.8406 (pmm) cc_final: 0.7923 (pp-130) REVERT: B 259 GLN cc_start: 0.8227 (pt0) cc_final: 0.7954 (pt0) REVERT: E 25 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7797 (p) REVERT: E 162 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 180 MET cc_start: 0.8382 (ttp) cc_final: 0.8170 (ppp) REVERT: G 19 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7163 (mp) REVERT: G 38 MET cc_start: 0.7531 (ttp) cc_final: 0.7281 (mtp) REVERT: R 61 ASP cc_start: 0.7393 (m-30) cc_final: 0.7073 (m-30) REVERT: R 177 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7788 (mp) REVERT: R 360 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8042 (tp) REVERT: R 370 LEU cc_start: 0.8545 (mt) cc_final: 0.8252 (mp) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 1.1333 time to fit residues: 161.7673 Evaluate side-chains 132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 223 THR 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 121 SER Chi-restraints excluded: chain R residue 177 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.180178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.145441 restraints weight = 9819.169| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.81 r_work: 0.3247 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9046 Z= 0.113 Angle : 0.516 8.891 12255 Z= 0.273 Chirality : 0.041 0.137 1376 Planarity : 0.004 0.046 1538 Dihedral : 4.701 44.357 1212 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.38 % Allowed : 18.96 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.26 (0.26), residues: 1098 helix: 2.41 (0.25), residues: 409 sheet: 0.30 (0.29), residues: 294 loop : -0.37 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE R 82 TYR 0.013 0.001 TYR A 302 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 461) hydrogen bonds : angle 4.37405 ( 1308) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.30492 ( 6) covalent geometry : bond 0.00251 ( 9043) covalent geometry : angle 0.51548 (12249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6930.94 seconds wall clock time: 123 minutes 9.07 seconds (7389.07 seconds total)