Starting phenix.real_space_refine on Thu Jun 4 00:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n05_48775/06_2026/9n05_48775.map" } resolution = 2.2 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= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5796 2.51 5 N 1577 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9112 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2615 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2956 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 234 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.40, per 1000 atoms: 0.26 Number of scatterers: 9112 At special positions: 0 Unit cell: (77.19, 99.6, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1685 8.00 N 1577 7.00 C 5796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 352.0 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 42.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.638A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.820A 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 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.100A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.803A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.674A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (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 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 31 through 50 removed outlier: 3.638A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.548A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 222 removed outlier: 3.806A pdb=" N TYR R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.749A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.571A pdb=" N PHE R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.745A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.532A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 402 removed outlier: 3.813A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 2 through 28 removed outlier: 4.084A pdb=" N ILE P 23 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU P 24 " --> pdb=" O GLN P 20 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.268A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.449A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.504A 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: 4.107A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.705A 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: 6.730A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.532A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.879A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.285A 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: 3.546A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.029A 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: 3.749A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.173A 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 11 through 12 removed outlier: 6.083A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 4.078A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 79 through 84 removed outlier: 3.598A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2944 1.34 - 1.46: 2203 1.46 - 1.58: 4080 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9299 Sorted by residual: bond pdb=" C ILE B 273 " pdb=" N THR B 274 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.36e-02 5.41e+03 1.87e+01 bond pdb=" C MET B 45 " pdb=" N ARG B 46 " ideal model delta sigma weight residual 1.331 1.384 -0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" N ILE N 58 " pdb=" CA ILE N 58 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 8.91e+00 bond pdb=" N SER N 59 " pdb=" CA SER N 59 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.27e-02 6.20e+03 7.82e+00 bond pdb=" C ARG B 46 " pdb=" N THR B 47 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.45e-02 4.76e+03 7.72e+00 ... (remaining 9294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12084 1.57 - 3.14: 458 3.14 - 4.71: 57 4.71 - 6.27: 9 6.27 - 7.84: 3 Bond angle restraints: 12611 Sorted by residual: angle pdb=" CA THR B 274 " pdb=" CB THR B 274 " pdb=" OG1 THR B 274 " ideal model delta sigma weight residual 109.60 101.76 7.84 1.50e+00 4.44e-01 2.73e+01 angle pdb=" N ARG N 67 " pdb=" CA ARG N 67 " pdb=" C ARG N 67 " ideal model delta sigma weight residual 114.75 110.01 4.74 1.26e+00 6.30e-01 1.42e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 115.00 109.82 5.18 1.44e+00 4.82e-01 1.29e+01 angle pdb=" C ARG N 67 " pdb=" CA ARG N 67 " pdb=" CB ARG N 67 " ideal model delta sigma weight residual 109.16 113.76 -4.60 1.29e+00 6.01e-01 1.27e+01 angle pdb=" N GLN A 31 " pdb=" CA GLN A 31 " pdb=" C GLN A 31 " ideal model delta sigma weight residual 111.36 107.56 3.80 1.09e+00 8.42e-01 1.21e+01 ... (remaining 12606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5032 17.51 - 35.01: 375 35.01 - 52.52: 70 52.52 - 70.02: 13 70.02 - 87.53: 5 Dihedral angle restraints: 5495 sinusoidal: 2135 harmonic: 3360 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 145.44 -52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 5492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1155 0.059 - 0.118: 210 0.118 - 0.177: 23 0.177 - 0.236: 4 0.236 - 0.295: 3 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL N 64 " pdb=" CA VAL N 64 " pdb=" CG1 VAL N 64 " pdb=" CG2 VAL N 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL N 64 " pdb=" N VAL N 64 " pdb=" C VAL N 64 " pdb=" CB VAL N 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1392 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " -0.030 2.00e-02 2.50e+03 2.49e-02 9.27e+00 pdb=" CG HIS B 142 " 0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " -0.019 2.00e-02 2.50e+03 2.02e-02 6.14e+00 pdb=" CG HIS A 357 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO N 14 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.033 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1528 2.76 - 3.30: 8890 3.30 - 3.83: 15818 3.83 - 4.37: 19672 4.37 - 4.90: 32357 Nonbonded interactions: 78265 Sorted by model distance: nonbonded pdb=" OG SER R 155 " pdb=" O SER R 392 " model vdw 2.228 3.040 nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP R 372 " pdb=" NH2 ARG R 380 " model vdw 2.273 3.120 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.305 3.040 ... (remaining 78260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.570 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: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.004 0.059 9305 Z= 0.238 Angle : 0.687 7.842 12623 Z= 0.415 Chirality : 0.048 0.295 1395 Planarity : 0.006 0.068 1606 Dihedral : 12.917 87.529 3305 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.48 (0.24), residues: 1129 helix: 0.77 (0.22), residues: 441 sheet: 0.44 (0.32), residues: 235 loop : -0.03 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.027 0.002 TYR B 105 PHE 0.023 0.002 PHE B 151 TRP 0.017 0.002 TRP A 234 HIS 0.022 0.003 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.24 ( 9299) covalent geometry : angle 0.68559 / 0.42 (12611) SS BOND : bond 0.00235 / 0.12 ( 6) SS BOND : angle 1.58997 / 0.90 ( 12) hydrogen bonds : bond 0.21238 / 13.51 ( 478) hydrogen bonds : angle 6.88967 / 4.78 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.433 Fit side-chains REVERT: R 138 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5851 (mt-10) REVERT: R 414 ARG cc_start: 0.5254 (mmt-90) cc_final: 0.4865 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.7755 time to fit residues: 123.2051 Evaluate side-chains 116 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 35 GLN B 88 ASN B 142 HIS B 237 ASN B 239 ASN B 259 GLN B 266 HIS R 177 ASN R 180 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.220340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168013 restraints weight = 7526.072| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.52 r_work: 0.3719 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9305 Z= 0.139 Angle : 0.578 5.775 12623 Z= 0.319 Chirality : 0.043 0.144 1395 Planarity : 0.005 0.054 1606 Dihedral : 4.852 24.378 1260 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 6.81 % Favored : 91.52 % 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: 1.48 (0.24), residues: 1129 helix: 2.21 (0.23), residues: 444 sheet: 0.71 (0.33), residues: 223 loop : -0.04 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 376 TYR 0.030 0.002 TYR R 148 PHE 0.019 0.002 PHE R 230 TRP 0.015 0.002 TRP A 234 HIS 0.012 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9299) covalent geometry : angle 0.57653 / 0.32 (12611) SS BOND : bond 0.00155 / 0.08 ( 6) SS BOND : angle 1.44041 / 0.80 ( 12) hydrogen bonds : bond 0.05473 / 3.47 ( 478) hydrogen bonds : angle 4.77352 / 3.39 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.296 Fit side-chains REVERT: A 265 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6165 (mmt-90) REVERT: B 61 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7846 (tmm) REVERT: B 96 ARG cc_start: 0.7465 (mmp-170) cc_final: 0.7180 (mmp-170) REVERT: R 411 LEU cc_start: 0.6847 (mt) cc_final: 0.6467 (mm) REVERT: R 414 ARG cc_start: 0.5284 (mmt-90) cc_final: 0.4721 (mpt-90) outliers start: 16 outliers final: 8 residues processed: 134 average time/residue: 0.7424 time to fit residues: 104.8388 Evaluate side-chains 128 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 39 optimal weight: 0.0370 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 387 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.219284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.176140 restraints weight = 7463.705| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.40 r_work: 0.3689 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9305 Z= 0.110 Angle : 0.494 5.357 12623 Z= 0.274 Chirality : 0.041 0.142 1395 Planarity : 0.004 0.049 1606 Dihedral : 4.433 25.344 1260 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.88 % Allowed : 8.59 % Favored : 89.53 % 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: 1.80 (0.25), residues: 1129 helix: 2.66 (0.24), residues: 440 sheet: 0.67 (0.32), residues: 223 loop : 0.08 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 376 TYR 0.026 0.001 TYR R 148 PHE 0.016 0.001 PHE R 230 TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 9299) covalent geometry : angle 0.49290 / 0.27 (12611) SS BOND : bond 0.00161 / 0.09 ( 6) SS BOND : angle 1.14232 / 0.63 ( 12) hydrogen bonds : bond 0.04701 / 3.03 ( 478) hydrogen bonds : angle 4.37601 / 3.12 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.362 Fit side-chains REVERT: A 265 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6093 (mmt-90) REVERT: B 59 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7607 (t80) REVERT: B 96 ARG cc_start: 0.7571 (mmp-170) cc_final: 0.7288 (mmp-170) REVERT: B 172 GLU cc_start: 0.7450 (tp30) cc_final: 0.7242 (pt0) REVERT: B 259 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: R 139 GLU cc_start: 0.4713 (OUTLIER) cc_final: 0.4220 (tp30) REVERT: R 411 LEU cc_start: 0.6853 (mt) cc_final: 0.6496 (mm) REVERT: R 414 ARG cc_start: 0.5491 (mmt-90) cc_final: 0.4874 (mpt-90) outliers start: 18 outliers final: 7 residues processed: 131 average time/residue: 0.7875 time to fit residues: 108.5583 Evaluate side-chains 125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 142 HIS B 259 GLN B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.216707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165313 restraints weight = 7531.624| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.87 r_work: 0.3642 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9305 Z= 0.139 Angle : 0.542 5.723 12623 Z= 0.300 Chirality : 0.043 0.139 1395 Planarity : 0.004 0.049 1606 Dihedral : 4.674 26.343 1260 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.09 % Allowed : 9.63 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.25), residues: 1129 helix: 2.68 (0.24), residues: 444 sheet: 0.56 (0.32), residues: 225 loop : 0.06 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.026 0.002 TYR R 148 PHE 0.018 0.002 PHE B 151 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9299) covalent geometry : angle 0.54157 / 0.30 (12611) SS BOND : bond 0.00233 / 0.12 ( 6) SS BOND : angle 1.11521 / 0.65 ( 12) hydrogen bonds : bond 0.04874 / 3.13 ( 478) hydrogen bonds : angle 4.45071 / 3.17 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.369 Fit side-chains REVERT: A 265 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6076 (mmt-90) REVERT: B 59 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 76 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6204 (p0) REVERT: B 96 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7328 (mmp-170) REVERT: R 139 GLU cc_start: 0.4752 (OUTLIER) cc_final: 0.4233 (tp30) REVERT: R 411 LEU cc_start: 0.6808 (mt) cc_final: 0.6466 (mm) REVERT: R 414 ARG cc_start: 0.5451 (mmt-90) cc_final: 0.4838 (mpt-90) REVERT: R 417 TRP cc_start: 0.5955 (t60) cc_final: 0.5744 (t-100) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.7724 time to fit residues: 106.4264 Evaluate side-chains 125 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 54 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 142 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.218004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171209 restraints weight = 7548.900| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.77 r_work: 0.3664 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9305 Z= 0.115 Angle : 0.500 5.329 12623 Z= 0.276 Chirality : 0.041 0.138 1395 Planarity : 0.004 0.046 1606 Dihedral : 4.460 26.241 1260 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.88 % Allowed : 10.58 % Favored : 87.54 % 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: 1.90 (0.25), residues: 1129 helix: 2.79 (0.24), residues: 440 sheet: 0.64 (0.32), residues: 223 loop : 0.12 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 376 TYR 0.021 0.001 TYR R 148 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 9299) covalent geometry : angle 0.49963 / 0.28 (12611) SS BOND : bond 0.00209 / 0.11 ( 6) SS BOND : angle 0.96891 / 0.56 ( 12) hydrogen bonds : bond 0.04484 / 2.89 ( 478) hydrogen bonds : angle 4.31848 / 3.09 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.345 Fit side-chains REVERT: A 209 GLU cc_start: 0.7953 (pt0) cc_final: 0.7619 (mt-10) REVERT: A 265 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6083 (mmt-90) REVERT: B 59 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 76 ASP cc_start: 0.6226 (OUTLIER) cc_final: 0.5968 (p0) REVERT: B 96 ARG cc_start: 0.7604 (mmp-170) cc_final: 0.7298 (mmp-170) REVERT: N 5 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7282 (mp-120) REVERT: R 139 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4217 (tp30) REVERT: R 411 LEU cc_start: 0.6853 (mt) cc_final: 0.6484 (mm) REVERT: R 414 ARG cc_start: 0.5561 (mmt-90) cc_final: 0.4971 (mpt-90) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.7737 time to fit residues: 103.3700 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 20 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 142 HIS B 175 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.163880 restraints weight = 7524.397| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.62 r_work: 0.3681 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9305 Z= 0.133 Angle : 0.528 5.400 12623 Z= 0.293 Chirality : 0.042 0.139 1395 Planarity : 0.004 0.046 1606 Dihedral : 4.616 26.331 1260 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.30 % Allowed : 10.68 % Favored : 87.02 % 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: 1.85 (0.25), residues: 1129 helix: 2.74 (0.24), residues: 445 sheet: 0.56 (0.32), residues: 225 loop : 0.10 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 376 TYR 0.021 0.002 TYR R 148 PHE 0.017 0.002 PHE B 151 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 9299) covalent geometry : angle 0.52751 / 0.29 (12611) SS BOND : bond 0.00229 / 0.12 ( 6) SS BOND : angle 0.95606 / 0.58 ( 12) hydrogen bonds : bond 0.04713 / 3.03 ( 478) hydrogen bonds : angle 4.38048 / 3.13 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.401 Fit side-chains REVERT: A 265 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6077 (mmt-90) REVERT: B 59 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 76 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.6035 (p0) REVERT: B 96 ARG cc_start: 0.7515 (mmp-170) cc_final: 0.7216 (mmp-170) REVERT: B 142 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.5911 (t-90) REVERT: B 217 MET cc_start: 0.8310 (ppp) cc_final: 0.8047 (pmm) REVERT: R 138 GLU cc_start: 0.5766 (mt-10) cc_final: 0.5194 (tp30) REVERT: R 264 TRP cc_start: 0.5499 (t60) cc_final: 0.4542 (t-100) REVERT: R 411 LEU cc_start: 0.6841 (mt) cc_final: 0.6498 (mm) REVERT: R 414 ARG cc_start: 0.5533 (mmt-90) cc_final: 0.4921 (mpt-90) outliers start: 22 outliers final: 9 residues processed: 136 average time/residue: 0.7366 time to fit residues: 105.7221 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 259 GLN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.217144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168804 restraints weight = 7546.260| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.00 r_work: 0.3648 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9305 Z= 0.121 Angle : 0.513 5.432 12623 Z= 0.284 Chirality : 0.042 0.141 1395 Planarity : 0.004 0.045 1606 Dihedral : 4.523 26.409 1260 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.09 % Allowed : 11.10 % Favored : 86.81 % 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: 1.89 (0.25), residues: 1129 helix: 2.79 (0.24), residues: 445 sheet: 0.56 (0.32), residues: 225 loop : 0.12 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 376 TYR 0.021 0.001 TYR R 148 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.014 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 9299) covalent geometry : angle 0.51238 / 0.28 (12611) SS BOND : bond 0.00197 / 0.10 ( 6) SS BOND : angle 0.89853 / 0.53 ( 12) hydrogen bonds : bond 0.04531 / 2.91 ( 478) hydrogen bonds : angle 4.33150 / 3.11 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.401 Fit side-chains REVERT: A 209 GLU cc_start: 0.7992 (pt0) cc_final: 0.7650 (mt-10) REVERT: B 59 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 76 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.6030 (p0) REVERT: B 96 ARG cc_start: 0.7595 (mmp-170) cc_final: 0.7291 (mmp-170) REVERT: B 142 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6678 (t-170) REVERT: N 89 GLU cc_start: 0.7403 (pm20) cc_final: 0.7053 (pp20) REVERT: R 139 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.4424 (tp30) REVERT: R 264 TRP cc_start: 0.5417 (t60) cc_final: 0.4418 (t-100) REVERT: R 411 LEU cc_start: 0.6727 (mt) cc_final: 0.6384 (mm) REVERT: R 414 ARG cc_start: 0.5515 (mmt-90) cc_final: 0.4809 (mpt-90) outliers start: 20 outliers final: 13 residues processed: 128 average time/residue: 0.7618 time to fit residues: 102.6618 Evaluate side-chains 128 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 142 HIS B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.217270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.169617 restraints weight = 7440.501| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.81 r_work: 0.3637 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9305 Z= 0.121 Angle : 0.512 5.476 12623 Z= 0.284 Chirality : 0.042 0.137 1395 Planarity : 0.004 0.045 1606 Dihedral : 4.528 26.443 1260 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.99 % Allowed : 11.41 % Favored : 86.60 % 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: 1.82 (0.25), residues: 1129 helix: 2.68 (0.24), residues: 451 sheet: 0.57 (0.32), residues: 225 loop : 0.08 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 376 TYR 0.021 0.001 TYR R 148 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9299) covalent geometry : angle 0.51182 / 0.28 (12611) SS BOND : bond 0.00202 / 0.11 ( 6) SS BOND : angle 0.86557 / 0.52 ( 12) hydrogen bonds : bond 0.04500 / 2.90 ( 478) hydrogen bonds : angle 4.32173 / 3.11 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.362 Fit side-chains REVERT: A 209 GLU cc_start: 0.8017 (pt0) cc_final: 0.7683 (mt-10) REVERT: B 59 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 76 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.6042 (p0) REVERT: B 96 ARG cc_start: 0.7620 (mmp-170) cc_final: 0.7319 (mmp-170) REVERT: N 89 GLU cc_start: 0.7458 (pm20) cc_final: 0.7097 (pp20) REVERT: R 264 TRP cc_start: 0.5344 (t60) cc_final: 0.4376 (t-100) REVERT: R 411 LEU cc_start: 0.6782 (mt) cc_final: 0.6436 (mm) REVERT: R 414 ARG cc_start: 0.5578 (mmt-90) cc_final: 0.4878 (mpt-90) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.7281 time to fit residues: 98.4981 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 175 GLN B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.214168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161059 restraints weight = 7455.360| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.72 r_work: 0.3634 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9305 Z= 0.169 Angle : 0.585 5.637 12623 Z= 0.323 Chirality : 0.045 0.156 1395 Planarity : 0.005 0.046 1606 Dihedral : 4.862 26.301 1260 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % Favored : 86.81 % 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: 1.70 (0.25), residues: 1129 helix: 2.52 (0.24), residues: 452 sheet: 0.57 (0.32), residues: 226 loop : 0.04 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 376 TYR 0.022 0.002 TYR R 148 PHE 0.020 0.002 PHE B 151 TRP 0.015 0.002 TRP A 234 HIS 0.007 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 9299) covalent geometry : angle 0.58460 / 0.32 (12611) SS BOND : bond 0.00307 / 0.16 ( 6) SS BOND : angle 0.94062 / 0.62 ( 12) hydrogen bonds : bond 0.05091 / 3.26 ( 478) hydrogen bonds : angle 4.48871 / 3.21 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.376 Fit side-chains REVERT: A 265 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.5947 (mmt-90) REVERT: B 76 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6251 (p0) REVERT: B 96 ARG cc_start: 0.7629 (mmp-170) cc_final: 0.7313 (mmp-170) REVERT: N 89 GLU cc_start: 0.7419 (pm20) cc_final: 0.7047 (pp20) REVERT: R 264 TRP cc_start: 0.5443 (t60) cc_final: 0.4407 (t-100) REVERT: R 411 LEU cc_start: 0.6819 (mt) cc_final: 0.6493 (mm) REVERT: R 414 ARG cc_start: 0.5635 (mmt-90) cc_final: 0.5214 (ttm170) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.7631 time to fit residues: 107.7365 Evaluate side-chains 133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 142 HIS B 175 GLN B 266 HIS N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.218100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165998 restraints weight = 7517.594| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.89 r_work: 0.3665 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9305 Z= 0.109 Angle : 0.497 5.515 12623 Z= 0.275 Chirality : 0.041 0.140 1395 Planarity : 0.004 0.044 1606 Dihedral : 4.424 26.455 1260 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % Favored : 86.60 % 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: 1.85 (0.25), residues: 1129 helix: 2.72 (0.24), residues: 446 sheet: 0.65 (0.32), residues: 223 loop : 0.07 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 376 TYR 0.021 0.001 TYR R 148 PHE 0.017 0.001 PHE R 230 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 9299) covalent geometry : angle 0.49662 / 0.28 (12611) SS BOND : bond 0.00180 / 0.09 ( 6) SS BOND : angle 0.80168 / 0.48 ( 12) hydrogen bonds : bond 0.04297 / 2.77 ( 478) hydrogen bonds : angle 4.25571 / 3.07 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.253 Fit side-chains REVERT: A 209 GLU cc_start: 0.7967 (pt0) cc_final: 0.7622 (mt-10) REVERT: B 59 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7549 (t80) REVERT: B 96 ARG cc_start: 0.7602 (mmp-170) cc_final: 0.7305 (mmp-170) REVERT: B 304 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6925 (ttp-110) REVERT: N 89 GLU cc_start: 0.7406 (pm20) cc_final: 0.7041 (pp20) REVERT: R 264 TRP cc_start: 0.5324 (t60) cc_final: 0.4324 (t-100) REVERT: R 411 LEU cc_start: 0.6756 (mt) cc_final: 0.6410 (mm) REVERT: R 414 ARG cc_start: 0.5666 (mmt-90) cc_final: 0.5158 (ttm170) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 0.7278 time to fit residues: 98.1437 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.215910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162131 restraints weight = 7438.587| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.71 r_work: 0.3649 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9305 Z= 0.133 Angle : 0.535 5.724 12623 Z= 0.296 Chirality : 0.042 0.137 1395 Planarity : 0.004 0.045 1606 Dihedral : 4.602 27.325 1260 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 11.62 % Favored : 86.70 % 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: 1.82 (0.25), residues: 1129 helix: 2.66 (0.24), residues: 451 sheet: 0.62 (0.32), residues: 225 loop : 0.06 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 376 TYR 0.021 0.002 TYR R 148 PHE 0.017 0.002 PHE R 230 TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9299) covalent geometry : angle 0.53434 / 0.30 (12611) SS BOND : bond 0.00229 / 0.12 ( 6) SS BOND : angle 0.82658 / 0.53 ( 12) hydrogen bonds : bond 0.04631 / 2.97 ( 478) hydrogen bonds : angle 4.34089 / 3.12 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5224.27 seconds wall clock time: 89 minutes 22.25 seconds (5362.25 seconds total)