Starting phenix.real_space_refine on Tue Dec 31 17:14:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xz6_33526/12_2024/7xz6_33526_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xz6_33526/12_2024/7xz6_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_33526/12_2024/7xz6_33526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xz6_33526/12_2024/7xz6_33526.map" model { file = "/net/cci-nas-00/data/ceres_data/7xz6_33526/12_2024/7xz6_33526_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xz6_33526/12_2024/7xz6_33526_trim.cif" } resolution = 2.8 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.45, per 1000 atoms: 0.45 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: 4.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.13 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: 6.45 Time building geometry restraints manager: 5.16 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: 0.440 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: 0.280 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.610 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- 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 8430 Z= 0.226 Angle : 0.559 9.747 11413 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 : 5.47 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 (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: 1.92 (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 TRP 0.009 0.001 TRP A 281 HIS 0.008 0.001 HIS R 292 PHE 0.013 0.001 PHE B 234 TYR 0.008 0.001 TYR R 185 ARG 0.004 0.001 ARG B 19 *********************** 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 : 1.296 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: 0.7049 (m-30) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 2.4116 time to fit residues: 497.4808 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 : 1.389 ------------------------------------------------------------------------------- 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 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 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 B 259 GLN G 18 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8430 Z= 0.262 Angle : 0.557 8.674 11413 Z= 0.300 Chirality : 0.041 0.151 1289 Planarity : 0.004 0.037 1451 Dihedral : 5.059 27.584 1174 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 10.66 % 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 (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: 1.46 (0.27), residues: 1036 helix: 2.45 (0.26), residues: 411 sheet: -0.30 (0.35), residues: 221 loop : 0.27 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE G 61 TYR 0.016 0.002 TYR B 59 ARG 0.003 0.000 ARG G 13 *********************** 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 167 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.8037 (t0) cc_final: 0.7687 (t0) REVERT: B 186 ASP cc_start: 0.7656 (m-30) cc_final: 0.7359 (m-30) REVERT: B 219 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7200 (mmm160) REVERT: G 16 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7099 (t) REVERT: N 5 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: N 33 LYS cc_start: 0.8601 (tttt) cc_final: 0.8388 (tttp) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 2.6779 time to fit residues: 462.1025 Evaluate side-chains 144 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN 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 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8430 Z= 0.200 Angle : 0.501 8.070 11413 Z= 0.270 Chirality : 0.039 0.178 1289 Planarity : 0.004 0.039 1451 Dihedral : 4.817 23.733 1172 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.35 % Allowed : 12.46 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.27), residues: 1036 helix: 2.42 (0.25), residues: 410 sheet: -0.40 (0.35), residues: 211 loop : 0.18 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.006 0.001 HIS A 41 PHE 0.011 0.001 PHE N 108 TYR 0.011 0.001 TYR B 59 ARG 0.003 0.000 ARG A 265 *********************** 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 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7980 (t0) cc_final: 0.7591 (t0) REVERT: B 258 ASP cc_start: 0.7287 (t0) cc_final: 0.7073 (m-30) REVERT: N 5 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: R 120 PHE cc_start: 0.7051 (t80) cc_final: 0.6831 (t80) outliers start: 12 outliers final: 6 residues processed: 145 average time/residue: 2.8316 time to fit residues: 435.5422 Evaluate side-chains 136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN 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 69 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8430 Z= 0.241 Angle : 0.510 7.831 11413 Z= 0.276 Chirality : 0.039 0.161 1289 Planarity : 0.004 0.042 1451 Dihedral : 4.903 23.780 1172 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.13 % Allowed : 13.69 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.26), residues: 1036 helix: 2.32 (0.25), residues: 409 sheet: -0.45 (0.35), residues: 206 loop : -0.01 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.002 PHE G 61 TYR 0.012 0.001 TYR R 185 ARG 0.008 0.000 ARG B 214 *********************** 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 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7965 (t0) cc_final: 0.7688 (t0) REVERT: N 5 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6646 (tm-30) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 2.6657 time to fit residues: 428.9746 Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 34 THR 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 R residue 16 SER Chi-restraints excluded: chain R residue 228 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 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8430 Z= 0.274 Angle : 0.524 7.518 11413 Z= 0.284 Chirality : 0.040 0.142 1289 Planarity : 0.004 0.038 1451 Dihedral : 5.067 24.456 1172 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 : 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: 1036 helix: 2.17 (0.25), residues: 409 sheet: -0.55 (0.34), residues: 207 loop : -0.13 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 277 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.002 PHE N 29 TYR 0.013 0.001 TYR R 185 ARG 0.004 0.000 ARG B 214 *********************** 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 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6795 (mt-10) REVERT: B 155 ASN cc_start: 0.8016 (t0) cc_final: 0.7612 (t0) REVERT: N 5 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6626 (tm-30) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 2.6645 time to fit residues: 388.5936 Evaluate side-chains 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU 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 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 R residue 16 SER Chi-restraints excluded: chain R residue 228 SER 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 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8430 Z= 0.221 Angle : 0.507 7.540 11413 Z= 0.272 Chirality : 0.039 0.142 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.912 25.180 1172 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.80 % Allowed : 15.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1036 helix: 2.22 (0.25), residues: 409 sheet: -0.68 (0.34), residues: 208 loop : -0.12 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 181 TYR 0.012 0.001 TYR R 185 ARG 0.003 0.000 ARG B 214 *********************** 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 142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6873 (mt-10) REVERT: B 155 ASN cc_start: 0.7940 (t0) cc_final: 0.7544 (t0) REVERT: G 14 LYS cc_start: 0.7504 (mtmt) cc_final: 0.6798 (mttp) REVERT: N 5 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6614 (tm-30) outliers start: 16 outliers final: 13 residues processed: 137 average time/residue: 2.7389 time to fit residues: 399.2870 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU 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 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 R residue 16 SER Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 64 ASP Chi-restraints excluded: chain R residue 228 SER 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 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8430 Z= 0.233 Angle : 0.505 6.869 11413 Z= 0.273 Chirality : 0.039 0.146 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.905 25.184 1172 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 15.94 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.26), residues: 1036 helix: 2.25 (0.25), residues: 409 sheet: -0.72 (0.34), residues: 208 loop : -0.17 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 PHE 0.011 0.002 PHE N 29 TYR 0.012 0.001 TYR R 185 ARG 0.003 0.000 ARG B 214 *********************** 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 145 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6853 (mt-10) REVERT: B 155 ASN cc_start: 0.7934 (t0) cc_final: 0.7679 (t0) REVERT: G 14 LYS cc_start: 0.7492 (mtmt) cc_final: 0.6792 (mttp) REVERT: N 5 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: R 13 VAL cc_start: 0.8662 (p) cc_final: 0.8454 (m) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 2.7003 time to fit residues: 402.0031 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR 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 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 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 254 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8430 Z= 0.192 Angle : 0.492 6.608 11413 Z= 0.264 Chirality : 0.039 0.155 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.763 25.849 1172 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.91 % Allowed : 16.72 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.26), residues: 1036 helix: 2.33 (0.25), residues: 409 sheet: -0.76 (0.34), residues: 214 loop : -0.09 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.004 0.001 HIS A 41 PHE 0.010 0.001 PHE R 181 TYR 0.011 0.001 TYR A 253 ARG 0.003 0.000 ARG B 214 *********************** 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 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6849 (mt-10) REVERT: B 155 ASN cc_start: 0.7916 (t0) cc_final: 0.7682 (t0) REVERT: G 14 LYS cc_start: 0.7574 (mtmt) cc_final: 0.6872 (mttp) REVERT: N 5 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6614 (tm-30) outliers start: 17 outliers final: 12 residues processed: 139 average time/residue: 2.7516 time to fit residues: 407.5575 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 R residue 10 ILE Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 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 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8430 Z= 0.178 Angle : 0.485 7.005 11413 Z= 0.260 Chirality : 0.039 0.143 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.673 25.984 1172 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.57 % Allowed : 17.28 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1036 helix: 2.38 (0.25), residues: 413 sheet: -0.75 (0.34), residues: 214 loop : -0.11 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.004 0.001 HIS A 41 PHE 0.013 0.001 PHE R 175 TYR 0.010 0.001 TYR R 185 ARG 0.003 0.000 ARG B 214 *********************** 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 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6846 (mt-10) REVERT: B 155 ASN cc_start: 0.7872 (t0) cc_final: 0.7633 (t0) REVERT: G 14 LYS cc_start: 0.7604 (mtmt) cc_final: 0.6914 (mttp) REVERT: N 5 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: N 35 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7177 (p0) REVERT: N 109 ASP cc_start: 0.7779 (p0) cc_final: 0.7468 (p0) REVERT: R 13 VAL cc_start: 0.8673 (p) cc_final: 0.8457 (m) outliers start: 14 outliers final: 13 residues processed: 141 average time/residue: 2.6461 time to fit residues: 397.8962 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR 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 B residue 176 GLN Chi-restraints excluded: chain B residue 340 ASN 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 R residue 10 ILE Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 228 SER 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 101 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 8430 Z= 0.262 Angle : 0.873 59.188 11413 Z= 0.522 Chirality : 0.039 0.200 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.676 26.008 1172 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.57 % Allowed : 17.06 % Favored : 81.37 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.26), residues: 1036 helix: 2.38 (0.25), residues: 413 sheet: -0.76 (0.34), residues: 214 loop : -0.11 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.004 0.001 HIS A 41 PHE 0.010 0.001 PHE R 181 TYR 0.010 0.001 TYR R 185 ARG 0.002 0.000 ARG A 265 ********************** 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 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6850 (mt-10) REVERT: B 155 ASN cc_start: 0.7874 (t0) cc_final: 0.7635 (t0) REVERT: G 14 LYS cc_start: 0.7604 (mtmt) cc_final: 0.6915 (mttp) REVERT: N 5 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: N 35 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7198 (p0) REVERT: N 109 ASP cc_start: 0.7784 (p0) cc_final: 0.7473 (p0) REVERT: R 13 VAL cc_start: 0.8676 (p) cc_final: 0.8447 (m) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 2.7258 time to fit residues: 388.8661 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 TYR 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 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 R residue 10 ILE Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 228 SER 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 22 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112251 restraints weight = 26065.740| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.60 r_work: 0.3063 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 8430 Z= 0.262 Angle : 0.873 59.188 11413 Z= 0.522 Chirality : 0.039 0.200 1289 Planarity : 0.004 0.038 1451 Dihedral : 4.676 26.008 1172 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.57 % Allowed : 17.06 % Favored : 81.37 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.26), residues: 1036 helix: 2.38 (0.25), residues: 413 sheet: -0.76 (0.34), residues: 214 loop : -0.11 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.004 0.001 HIS A 41 PHE 0.010 0.001 PHE R 181 TYR 0.010 0.001 TYR R 185 ARG 0.002 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7193.60 seconds wall clock time: 128 minutes 3.55 seconds (7683.55 seconds total)