Starting phenix.real_space_refine on Wed Mar 4 20:36:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526.map" model { file = "/net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xz6_33526/03_2026/7xz6_33526_trim.cif" } resolution = 2.8 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= -0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians S 57 5.16 5 C 5238 2.51 5 N 1437 2.21 5 O 1533 1.98 5 F 1 1.80 5 H 8192 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16458 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3910 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4609 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'I7J': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.91, per 1000 atoms: 0.18 Number of scatterers: 16458 At special positions: 0 Unit cell: (100.32, 98.23, 115.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 F 1 9.00 O 1533 8.00 N 1437 7.00 C 5238 6.00 H 8192 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.05 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: 1.52 Conformation dependent library (CDL) restraints added in 581.5 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 45.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.559A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.592A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.238A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.469A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.313A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.271A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 2 through 36 Processing helix chain 'R' and resid 39 through 66 removed outlier: 3.690A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 74 through 109 Processing helix chain 'R' and resid 109 through 117 removed outlier: 3.623A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 143 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 172 removed outlier: 3.966A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 210 Processing helix chain 'R' and resid 220 through 251 removed outlier: 4.065A pdb=" N LEU R 224 " --> pdb=" O ASP R 220 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 256 through 263 Processing helix chain 'R' and resid 263 through 280 removed outlier: 3.823A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.239A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.736A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.833A 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: 6.983A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.443A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.749A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.929A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.689A 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: 3.730A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.565A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1311 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: 3.88 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8169 1.04 - 1.25: 1337 1.25 - 1.46: 2546 1.46 - 1.66: 4487 1.66 - 1.87: 83 Bond restraints: 16622 Sorted by residual: bond pdb=" C18 I7J R 401 " pdb=" S1 I7J R 401 " ideal model delta sigma weight residual 1.781 1.867 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C12 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.353 1.422 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 I7J R 401 " pdb=" N1 I7J R 401 " ideal model delta sigma weight residual 1.357 1.425 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 I7J R 401 " pdb=" O3 I7J R 401 " ideal model delta sigma weight residual 1.313 1.372 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" C15 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.402 1.458 -0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 16617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 29752 1.95 - 3.90: 123 3.90 - 5.85: 27 5.85 - 7.80: 3 7.80 - 9.75: 7 Bond angle restraints: 29912 Sorted by residual: angle pdb=" CA CYS R 254 " pdb=" CB CYS R 254 " pdb=" SG CYS R 254 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.29 108.54 3.75 9.40e-01 1.13e+00 1.59e+01 angle pdb=" CA CYS R 251 " pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " ideal model delta sigma weight residual 114.40 122.30 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.44 114.13 -3.69 1.20e+00 6.94e-01 9.47e+00 angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 112.96 109.90 3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 29907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7231 17.51 - 35.01: 437 35.01 - 52.52: 121 52.52 - 70.02: 45 70.02 - 87.53: 14 Dihedral angle restraints: 7848 sinusoidal: 4236 harmonic: 3612 Sorted by residual: dihedral pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " pdb=" SG CYS R 254 " pdb=" CB CYS R 254 " ideal model delta sinusoidal sigma weight residual -86.00 0.40 -86.40 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA GLU R 253 " pdb=" C GLU R 253 " pdb=" N CYS R 254 " pdb=" CA CYS R 254 " ideal model delta harmonic sigma weight residual -180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU G 19 " pdb=" C LEU G 19 " pdb=" N LYS G 20 " pdb=" CA LYS G 20 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 880 0.030 - 0.060: 263 0.060 - 0.089: 87 0.089 - 0.119: 50 0.119 - 0.149: 9 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CG LEU G 19 " pdb=" CB LEU G 19 " pdb=" CD1 LEU G 19 " pdb=" CD2 LEU G 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE R 143 " pdb=" N ILE R 143 " pdb=" C ILE R 143 " pdb=" CB ILE R 143 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1286 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 162 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO R 163 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 163 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO G 60 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 175 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 176 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 176 " 0.015 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 456 2.13 - 2.74: 30563 2.74 - 3.36: 49540 3.36 - 3.98: 63574 3.98 - 4.60: 99183 Nonbonded interactions: 243316 Sorted by model distance: nonbonded pdb="HD21 ASN B 340 " pdb="HD22 ASN G 59 " model vdw 1.507 2.100 nonbonded pdb=" OE1 GLN R 109 " pdb="HH21 ARG R 112 " model vdw 1.534 2.450 nonbonded pdb=" O ALA R 91 " pdb=" HG1 THR R 95 " model vdw 1.538 2.450 nonbonded pdb=" OD1 ASP B 290 " pdb=" HE ARG B 314 " model vdw 1.592 2.450 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.592 2.450 ... (remaining 243311 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: 0.730 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 0.086 8434 Z= 0.183 Angle : 0.560 9.747 11421 Z= 0.310 Chirality : 0.038 0.149 1289 Planarity : 0.002 0.032 1451 Dihedral : 12.807 87.527 3065 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.27), residues: 1036 helix: 2.81 (0.26), residues: 407 sheet: 0.07 (0.36), residues: 216 loop : 0.47 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 19 TYR 0.008 0.001 TYR R 185 PHE 0.013 0.001 PHE B 234 TRP 0.009 0.001 TRP A 281 HIS 0.008 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8430) covalent geometry : angle 0.55911 (11413) SS BOND : bond 0.00878 ( 4) SS BOND : angle 1.13889 ( 8) hydrogen bonds : bond 0.16892 ( 458) hydrogen bonds : angle 6.66026 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7277 (m-30) cc_final: 0.7048 (m-30) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 1.1688 time to fit residues: 239.9298 Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN G 18 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112550 restraints weight = 26040.711| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.59 r_work: 0.3063 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8434 Z= 0.245 Angle : 0.607 8.691 11421 Z= 0.329 Chirality : 0.042 0.152 1289 Planarity : 0.005 0.047 1451 Dihedral : 5.327 29.530 1174 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.91 % Allowed : 10.21 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 1036 helix: 2.24 (0.26), residues: 411 sheet: -0.39 (0.35), residues: 221 loop : 0.18 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 314 TYR 0.021 0.002 TYR B 59 PHE 0.018 0.002 PHE G 61 TRP 0.016 0.003 TRP A 277 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8430) covalent geometry : angle 0.60582 (11413) SS BOND : bond 0.00993 ( 4) SS BOND : angle 1.42547 ( 8) hydrogen bonds : bond 0.04704 ( 458) hydrogen bonds : angle 5.20094 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 32 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: B 155 ASN cc_start: 0.8344 (t0) cc_final: 0.7897 (t0) REVERT: B 219 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7511 (mtt-85) REVERT: G 16 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6674 (t) REVERT: N 5 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: N 33 LYS cc_start: 0.8815 (tttt) cc_final: 0.8578 (tttp) REVERT: N 109 ASP cc_start: 0.7959 (p0) cc_final: 0.7584 (p0) REVERT: N 120 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7490 (mm-40) REVERT: R 175 PHE cc_start: 0.7872 (m-10) cc_final: 0.7638 (m-10) outliers start: 17 outliers final: 8 residues processed: 166 average time/residue: 1.3371 time to fit residues: 235.1655 Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 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 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.144689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111877 restraints weight = 26353.035| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.62 r_work: 0.3061 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8434 Z= 0.192 Angle : 0.546 8.183 11421 Z= 0.295 Chirality : 0.040 0.146 1289 Planarity : 0.004 0.040 1451 Dihedral : 5.231 35.530 1172 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 12.79 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.27), residues: 1036 helix: 2.23 (0.26), residues: 409 sheet: -0.52 (0.34), residues: 210 loop : 0.12 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 232 TYR 0.012 0.002 TYR R 185 PHE 0.019 0.002 PHE N 108 TRP 0.010 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8430) covalent geometry : angle 0.54243 (11413) SS BOND : bond 0.00922 ( 4) SS BOND : angle 2.35237 ( 8) hydrogen bonds : bond 0.04352 ( 458) hydrogen bonds : angle 5.00216 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6186 (pp20) cc_final: 0.4956 (mp0) REVERT: A 347 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7481 (mtm110) REVERT: B 32 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6925 (pt0) REVERT: B 155 ASN cc_start: 0.8329 (t0) cc_final: 0.8011 (t0) REVERT: B 219 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7605 (mtt-85) REVERT: N 5 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: N 120 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7473 (mm-40) REVERT: R 175 PHE cc_start: 0.7903 (m-10) cc_final: 0.7678 (m-10) outliers start: 17 outliers final: 9 residues processed: 151 average time/residue: 1.3505 time to fit residues: 215.5850 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114512 restraints weight = 26162.835| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8434 Z= 0.124 Angle : 0.500 7.909 11421 Z= 0.267 Chirality : 0.039 0.157 1289 Planarity : 0.004 0.037 1451 Dihedral : 4.858 34.473 1172 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.46 % Allowed : 14.14 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1036 helix: 2.40 (0.25), residues: 409 sheet: -0.50 (0.35), residues: 204 loop : 0.01 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.009 0.001 TYR R 185 PHE 0.015 0.001 PHE N 108 TRP 0.010 0.002 TRP B 82 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8430) covalent geometry : angle 0.49561 (11413) SS BOND : bond 0.00864 ( 4) SS BOND : angle 2.44286 ( 8) hydrogen bonds : bond 0.03868 ( 458) hydrogen bonds : angle 4.72632 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.5731 (pp20) cc_final: 0.4777 (mp0) REVERT: A 299 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 347 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7399 (mtm110) REVERT: B 155 ASN cc_start: 0.8187 (t0) cc_final: 0.7880 (t0) REVERT: N 5 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: N 35 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7804 (p0) REVERT: N 120 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7489 (mm-40) REVERT: R 175 PHE cc_start: 0.7804 (m-10) cc_final: 0.7589 (m-10) outliers start: 13 outliers final: 6 residues processed: 146 average time/residue: 1.3572 time to fit residues: 209.3798 Evaluate side-chains 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112987 restraints weight = 26219.432| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.59 r_work: 0.3065 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8434 Z= 0.149 Angle : 0.504 7.592 11421 Z= 0.271 Chirality : 0.039 0.152 1289 Planarity : 0.004 0.050 1451 Dihedral : 4.899 32.214 1172 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.80 % Allowed : 14.81 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.26), residues: 1036 helix: 2.40 (0.25), residues: 409 sheet: -0.66 (0.34), residues: 210 loop : 0.02 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.010 0.001 TYR A 253 PHE 0.015 0.001 PHE N 108 TRP 0.010 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8430) covalent geometry : angle 0.50069 (11413) SS BOND : bond 0.00866 ( 4) SS BOND : angle 2.21401 ( 8) hydrogen bonds : bond 0.03896 ( 458) hydrogen bonds : angle 4.68252 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7222 (mt-10) REVERT: A 299 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 347 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7479 (mtm110) REVERT: B 155 ASN cc_start: 0.8190 (t0) cc_final: 0.7766 (t0) REVERT: N 5 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: N 35 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7747 (p0) REVERT: N 120 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7426 (mm-40) REVERT: R 118 SER cc_start: 0.6367 (t) cc_final: 0.6135 (p) outliers start: 16 outliers final: 12 residues processed: 141 average time/residue: 1.3301 time to fit residues: 198.4446 Evaluate side-chains 142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 10.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109511 restraints weight = 26004.947| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.60 r_work: 0.3029 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8434 Z= 0.211 Angle : 0.544 7.332 11421 Z= 0.294 Chirality : 0.040 0.157 1289 Planarity : 0.004 0.052 1451 Dihedral : 5.175 30.177 1172 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.47 % Allowed : 15.49 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1036 helix: 2.19 (0.25), residues: 409 sheet: -0.85 (0.33), residues: 215 loop : -0.07 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.012 0.002 TYR R 185 PHE 0.015 0.002 PHE N 108 TRP 0.012 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8430) covalent geometry : angle 0.53971 (11413) SS BOND : bond 0.00902 ( 4) SS BOND : angle 2.63912 ( 8) hydrogen bonds : bond 0.04143 ( 458) hydrogen bonds : angle 4.81731 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7312 (mt-10) REVERT: A 50 GLU cc_start: 0.5985 (pp20) cc_final: 0.5183 (mt-10) REVERT: A 299 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6986 (mt-10) REVERT: A 347 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7616 (mtm110) REVERT: B 155 ASN cc_start: 0.8248 (t0) cc_final: 0.7937 (t0) REVERT: G 14 LYS cc_start: 0.7369 (mtmt) cc_final: 0.6540 (mttp) REVERT: N 5 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: N 120 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7452 (mm-40) REVERT: R 13 VAL cc_start: 0.8573 (p) cc_final: 0.8303 (m) REVERT: R 175 PHE cc_start: 0.7733 (m-10) cc_final: 0.7526 (m-10) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 1.3495 time to fit residues: 203.8203 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110375 restraints weight = 25994.182| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.59 r_work: 0.3032 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8434 Z= 0.170 Angle : 0.520 6.974 11421 Z= 0.279 Chirality : 0.040 0.144 1289 Planarity : 0.004 0.059 1451 Dihedral : 5.019 28.429 1172 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.13 % Allowed : 16.05 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1036 helix: 2.23 (0.25), residues: 409 sheet: -0.74 (0.33), residues: 207 loop : -0.16 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.012 0.001 TYR A 253 PHE 0.015 0.002 PHE N 108 TRP 0.010 0.002 TRP A 281 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8430) covalent geometry : angle 0.51676 (11413) SS BOND : bond 0.00850 ( 4) SS BOND : angle 2.25782 ( 8) hydrogen bonds : bond 0.03969 ( 458) hydrogen bonds : angle 4.72250 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7247 (mt-10) REVERT: A 50 GLU cc_start: 0.5922 (pp20) cc_final: 0.5152 (mt-10) REVERT: A 299 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6945 (mt-10) REVERT: A 347 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7571 (mtm110) REVERT: B 155 ASN cc_start: 0.8208 (t0) cc_final: 0.7776 (t0) REVERT: B 219 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7797 (mtt-85) REVERT: G 14 LYS cc_start: 0.7335 (mtmt) cc_final: 0.6508 (mttp) REVERT: N 5 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: N 35 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7836 (p0) REVERT: N 120 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7462 (mm-40) REVERT: R 154 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6802 (tt0) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 1.3938 time to fit residues: 207.5762 Evaluate side-chains 143 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112840 restraints weight = 26148.724| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.58 r_work: 0.3121 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8434 Z= 0.129 Angle : 0.502 7.638 11421 Z= 0.266 Chirality : 0.039 0.145 1289 Planarity : 0.004 0.068 1451 Dihedral : 4.806 27.412 1172 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.36 % Allowed : 16.05 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1036 helix: 2.39 (0.25), residues: 409 sheet: -0.76 (0.34), residues: 207 loop : -0.15 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 96 TYR 0.012 0.001 TYR A 253 PHE 0.014 0.001 PHE N 108 TRP 0.010 0.002 TRP A 281 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8430) covalent geometry : angle 0.50018 (11413) SS BOND : bond 0.00812 ( 4) SS BOND : angle 1.88078 ( 8) hydrogen bonds : bond 0.03761 ( 458) hydrogen bonds : angle 4.59841 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7251 (mt-10) REVERT: A 50 GLU cc_start: 0.5860 (pp20) cc_final: 0.5116 (mt-10) REVERT: A 299 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 347 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7540 (mtm110) REVERT: B 155 ASN cc_start: 0.8162 (t0) cc_final: 0.7740 (t0) REVERT: B 219 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7728 (mtt-85) REVERT: G 14 LYS cc_start: 0.7438 (mtmt) cc_final: 0.6614 (mttp) REVERT: N 5 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: N 120 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7448 (mm-40) REVERT: R 13 VAL cc_start: 0.8589 (p) cc_final: 0.8335 (m) REVERT: R 154 GLN cc_start: 0.7225 (tp-100) cc_final: 0.6770 (tt0) outliers start: 21 outliers final: 12 residues processed: 146 average time/residue: 1.3770 time to fit residues: 212.5302 Evaluate side-chains 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108914 restraints weight = 26187.646| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.60 r_work: 0.3067 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8434 Z= 0.213 Angle : 0.549 6.627 11421 Z= 0.296 Chirality : 0.040 0.156 1289 Planarity : 0.005 0.081 1451 Dihedral : 5.155 26.536 1172 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.13 % Allowed : 16.61 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1036 helix: 2.21 (0.25), residues: 409 sheet: -1.01 (0.32), residues: 221 loop : -0.10 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 96 TYR 0.013 0.002 TYR R 185 PHE 0.014 0.002 PHE N 108 TRP 0.012 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 8430) covalent geometry : angle 0.54489 (11413) SS BOND : bond 0.00857 ( 4) SS BOND : angle 2.48780 ( 8) hydrogen bonds : bond 0.04121 ( 458) hydrogen bonds : angle 4.76543 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7280 (mt-10) REVERT: A 50 GLU cc_start: 0.6029 (pp20) cc_final: 0.5246 (mt-10) REVERT: A 347 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7622 (mtm110) REVERT: B 155 ASN cc_start: 0.8244 (t0) cc_final: 0.7917 (t0) REVERT: B 219 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7781 (mtt-85) REVERT: G 14 LYS cc_start: 0.7515 (mtmt) cc_final: 0.6683 (mttp) REVERT: N 5 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: N 120 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7366 (mm-40) REVERT: R 13 VAL cc_start: 0.8586 (p) cc_final: 0.8312 (m) REVERT: R 154 GLN cc_start: 0.7260 (tp-100) cc_final: 0.6780 (tt0) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 1.4184 time to fit residues: 208.1503 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109960 restraints weight = 26171.704| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.59 r_work: 0.3065 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8434 Z= 0.177 Angle : 0.529 7.302 11421 Z= 0.284 Chirality : 0.040 0.142 1289 Planarity : 0.004 0.085 1451 Dihedral : 5.069 26.417 1172 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.80 % Allowed : 16.95 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1036 helix: 2.31 (0.25), residues: 402 sheet: -0.91 (0.33), residues: 215 loop : -0.17 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 96 TYR 0.011 0.001 TYR A 253 PHE 0.015 0.002 PHE N 108 TRP 0.011 0.002 TRP B 99 HIS 0.005 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8430) covalent geometry : angle 0.52634 (11413) SS BOND : bond 0.00802 ( 4) SS BOND : angle 2.21048 ( 8) hydrogen bonds : bond 0.03993 ( 458) hydrogen bonds : angle 4.71517 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7278 (mt-10) REVERT: A 50 GLU cc_start: 0.6056 (pp20) cc_final: 0.5277 (mt-10) REVERT: A 347 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7595 (mtm110) REVERT: B 155 ASN cc_start: 0.8218 (t0) cc_final: 0.7906 (t0) REVERT: G 14 LYS cc_start: 0.7517 (mtmt) cc_final: 0.6685 (mttp) REVERT: N 5 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: N 120 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7352 (mm-40) REVERT: R 13 VAL cc_start: 0.8577 (p) cc_final: 0.8312 (m) REVERT: R 154 GLN cc_start: 0.7198 (tp-100) cc_final: 0.6756 (tt0) outliers start: 16 outliers final: 14 residues processed: 137 average time/residue: 1.3520 time to fit residues: 195.8367 Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110220 restraints weight = 25993.388| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.59 r_work: 0.3060 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8434 Z= 0.165 Angle : 0.521 6.842 11421 Z= 0.278 Chirality : 0.040 0.144 1289 Planarity : 0.004 0.081 1451 Dihedral : 4.998 26.332 1172 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1036 helix: 2.34 (0.25), residues: 402 sheet: -0.91 (0.33), residues: 215 loop : -0.19 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 96 TYR 0.010 0.001 TYR A 253 PHE 0.014 0.002 PHE N 108 TRP 0.011 0.002 TRP A 281 HIS 0.006 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8430) covalent geometry : angle 0.51765 (11413) SS BOND : bond 0.00811 ( 4) SS BOND : angle 2.12405 ( 8) hydrogen bonds : bond 0.03921 ( 458) hydrogen bonds : angle 4.67576 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.53 seconds wall clock time: 106 minutes 20.13 seconds (6380.13 seconds total)