Starting phenix.real_space_refine on Wed Mar 4 00:22:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyi_26180/03_2026/7tyi_26180.cif" } resolution = 3.3 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= -0.001 sd= 0.087 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 67 5.16 5 C 6032 2.51 5 N 1603 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9413 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: "P" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3039 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 208 Unusual residues: {'NAG': 2, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.25, per 1000 atoms: 0.24 Number of scatterers: 9413 At special positions: 0 Unit cell: (82.176, 99.296, 154.936, 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 67 16.00 O 1711 8.00 N 1603 7.00 C 6032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.04 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 350.4 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 39.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.517A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.576A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.870A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.688A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.707A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.642A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.851A pdb=" N LEU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.969A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.770A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.027A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 7 No H-bonds generated for 'chain 'P' and resid 5 through 7' Processing helix chain 'P' and resid 8 through 21 Processing helix chain 'R' and resid 39 through 59 removed outlier: 3.506A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.518A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 removed outlier: 3.523A pdb=" N GLY R 177 " --> pdb=" O ARG R 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 174 through 177' Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.645A pdb=" N THR R 182 " --> pdb=" O CYS R 178 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.949A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.591A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix removed outlier: 3.616A pdb=" N GLU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 347 removed outlier: 3.518A pdb=" N ILE R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 381 Processing helix chain 'R' and resid 383 through 392 Processing helix chain 'R' and resid 395 through 408 removed outlier: 3.561A pdb=" N GLN R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.775A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.775A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.855A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.851A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.907A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.618A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.700A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.537A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.696A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 423 hydrogen bonds defined for protein. 1212 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: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2487 1.33 - 1.45: 1848 1.45 - 1.58: 5184 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9615 Sorted by residual: bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.64e-02 3.72e+03 1.04e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.49e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.77e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.33e-02 5.65e+03 7.71e+00 bond pdb=" N VAL P 17 " pdb=" CA VAL P 17 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.67e+00 ... (remaining 9610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12585 1.50 - 2.99: 310 2.99 - 4.49: 59 4.49 - 5.99: 11 5.99 - 7.48: 2 Bond angle restraints: 12967 Sorted by residual: angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 111.07 115.98 -4.91 1.07e+00 8.73e-01 2.11e+01 angle pdb=" CA ALA R 136 " pdb=" C ALA R 136 " pdb=" O ALA R 136 " ideal model delta sigma weight residual 121.94 117.03 4.91 1.15e+00 7.56e-01 1.82e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N PHE R 137 " pdb=" CA PHE R 137 " pdb=" C PHE R 137 " ideal model delta sigma weight residual 113.40 107.86 5.54 1.47e+00 4.63e-01 1.42e+01 angle pdb=" CA THR R 138 " pdb=" C THR R 138 " pdb=" N PRO R 139 " ideal model delta sigma weight residual 117.44 121.65 -4.21 1.13e+00 7.83e-01 1.39e+01 ... (remaining 12962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5300 17.92 - 35.85: 387 35.85 - 53.77: 69 53.77 - 71.70: 18 71.70 - 89.62: 7 Dihedral angle restraints: 5781 sinusoidal: 2415 harmonic: 3366 Sorted by residual: dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -153.21 67.21 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 38.43 54.57 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1128 0.046 - 0.091: 210 0.091 - 0.137: 74 0.137 - 0.183: 3 0.183 - 0.229: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PHE R 102 " pdb=" N PHE R 102 " pdb=" C PHE R 102 " pdb=" CB PHE R 102 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1415 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 98 " 0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C TYR R 98 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR R 98 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 99 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 13 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C ALA P 13 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA P 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN P 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1087 2.75 - 3.29: 9102 3.29 - 3.83: 14961 3.83 - 4.36: 18405 4.36 - 4.90: 31689 Nonbonded interactions: 75244 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.248 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.252 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.284 3.040 nonbonded pdb=" NE2 GLN A 384 " pdb=" O ILE R 248 " model vdw 2.306 3.120 ... (remaining 75239 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=0.00 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.740 Find NCS groups from input model: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.106 9625 Z= 0.261 Angle : 0.570 7.483 12987 Z= 0.368 Chirality : 0.041 0.229 1418 Planarity : 0.003 0.031 1638 Dihedral : 12.810 89.619 3586 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.50 % Allowed : 4.10 % Favored : 94.40 % 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: -2.88 (0.21), residues: 1136 helix: -2.47 (0.17), residues: 426 sheet: -0.89 (0.34), residues: 230 loop : -1.70 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.015 0.001 TYR R 56 PHE 0.010 0.001 PHE R 102 TRP 0.009 0.001 TRP R 76 HIS 0.002 0.000 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9615) covalent geometry : angle 0.56786 (12967) SS BOND : bond 0.00244 ( 7) SS BOND : angle 1.49043 ( 14) hydrogen bonds : bond 0.25572 ( 420) hydrogen bonds : angle 8.64986 ( 1212) Misc. bond : bond 0.10570 ( 1) link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 0.73846 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.239 Fit side-chains REVERT: P 16 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (mt) REVERT: R 113 ASP cc_start: 0.2558 (OUTLIER) cc_final: 0.2205 (p0) REVERT: R 215 ASP cc_start: 0.6546 (p0) cc_final: 0.5963 (p0) REVERT: R 229 MET cc_start: 0.8055 (tpp) cc_final: 0.7766 (mmt) REVERT: R 359 PHE cc_start: 0.7587 (m-80) cc_final: 0.7344 (m-80) REVERT: R 396 ASN cc_start: 0.7795 (t0) cc_final: 0.7582 (t0) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.1177 time to fit residues: 24.5117 Evaluate side-chains 113 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 239 ASN A 371 ASN B 16 ASN B 62 HIS B 155 ASN B 266 HIS B 340 ASN N 35 ASN N 53 GLN N 123 GLN P 3 ASN P 14 ASN R 93 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 GLN R 257 GLN R 288 ASN R 296 HIS R 377 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.185664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.149929 restraints weight = 10342.385| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.34 r_work: 0.3391 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9625 Z= 0.198 Angle : 0.604 8.807 12987 Z= 0.318 Chirality : 0.044 0.165 1418 Planarity : 0.004 0.043 1638 Dihedral : 6.430 59.231 1453 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.50 % Allowed : 9.70 % Favored : 87.80 % 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: -1.01 (0.24), residues: 1136 helix: 0.09 (0.24), residues: 424 sheet: -0.68 (0.34), residues: 212 loop : -1.25 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 385 TYR 0.024 0.002 TYR A 358 PHE 0.026 0.002 PHE N 108 TRP 0.017 0.002 TRP B 211 HIS 0.009 0.002 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9615) covalent geometry : angle 0.59971 (12967) SS BOND : bond 0.00119 ( 7) SS BOND : angle 2.27168 ( 14) hydrogen bonds : bond 0.04399 ( 420) hydrogen bonds : angle 4.85500 ( 1212) Misc. bond : bond 0.00036 ( 1) link_NAG-ASN : bond 0.00525 ( 2) link_NAG-ASN : angle 0.81314 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8145 (tt0) cc_final: 0.7903 (tt0) REVERT: A 265 ARG cc_start: 0.8490 (mtt90) cc_final: 0.7790 (mtm110) REVERT: B 45 MET cc_start: 0.7386 (mtm) cc_final: 0.6860 (mtp) REVERT: B 219 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: G 32 LYS cc_start: 0.7913 (tmtt) cc_final: 0.7656 (tmtt) REVERT: N 120 GLN cc_start: 0.8066 (pm20) cc_final: 0.7670 (pm20) REVERT: P 16 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7855 (mm) REVERT: R 113 ASP cc_start: 0.3204 (OUTLIER) cc_final: 0.2108 (p0) REVERT: R 172 PHE cc_start: 0.7031 (t80) cc_final: 0.6239 (m-10) REVERT: R 213 ARG cc_start: 0.7325 (ttm110) cc_final: 0.7103 (ttp80) REVERT: R 230 MET cc_start: 0.8372 (ppp) cc_final: 0.8149 (ppp) REVERT: R 373 ASP cc_start: 0.8558 (m-30) cc_final: 0.7605 (m-30) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.1028 time to fit residues: 19.2960 Evaluate side-chains 125 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 155 ASN B 268 ASN P 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.186873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144918 restraints weight = 10211.962| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.77 r_work: 0.3386 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9625 Z= 0.119 Angle : 0.503 8.446 12987 Z= 0.267 Chirality : 0.041 0.179 1418 Planarity : 0.003 0.034 1638 Dihedral : 6.024 59.931 1452 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.70 % Allowed : 11.60 % Favored : 85.70 % 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: -0.33 (0.25), residues: 1136 helix: 1.00 (0.25), residues: 424 sheet: -0.42 (0.35), residues: 205 loop : -1.15 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 362 TYR 0.016 0.001 TYR B 59 PHE 0.013 0.001 PHE N 108 TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 336 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9615) covalent geometry : angle 0.50064 (12967) SS BOND : bond 0.00144 ( 7) SS BOND : angle 1.61633 ( 14) hydrogen bonds : bond 0.03696 ( 420) hydrogen bonds : angle 4.43279 ( 1212) Misc. bond : bond 0.00013 ( 1) link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 0.80916 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.278 Fit side-chains REVERT: A 265 ARG cc_start: 0.8530 (mtt90) cc_final: 0.7780 (mtm110) REVERT: B 45 MET cc_start: 0.7354 (mtm) cc_final: 0.6985 (mtp) REVERT: B 70 LEU cc_start: 0.8145 (pp) cc_final: 0.7885 (pp) REVERT: B 219 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: G 32 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7561 (tmtt) REVERT: N 120 GLN cc_start: 0.8059 (pm20) cc_final: 0.7717 (pm20) REVERT: P 16 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7807 (mm) REVERT: P 37 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.3696 (p90) REVERT: R 113 ASP cc_start: 0.3354 (OUTLIER) cc_final: 0.2098 (p0) REVERT: R 172 PHE cc_start: 0.6999 (t80) cc_final: 0.6166 (m-10) REVERT: R 359 PHE cc_start: 0.8279 (m-10) cc_final: 0.8073 (m-80) outliers start: 27 outliers final: 19 residues processed: 127 average time/residue: 0.1062 time to fit residues: 18.5671 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.183615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.142264 restraints weight = 10349.526| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.64 r_work: 0.3345 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9625 Z= 0.153 Angle : 0.522 7.794 12987 Z= 0.278 Chirality : 0.041 0.149 1418 Planarity : 0.004 0.037 1638 Dihedral : 6.171 59.634 1452 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.10 % Allowed : 12.20 % Favored : 84.70 % 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: -0.12 (0.25), residues: 1136 helix: 1.18 (0.26), residues: 423 sheet: -0.44 (0.35), residues: 212 loop : -0.97 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 362 TYR 0.018 0.001 TYR B 59 PHE 0.017 0.002 PHE N 108 TRP 0.014 0.001 TRP R 236 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9615) covalent geometry : angle 0.51929 (12967) SS BOND : bond 0.00120 ( 7) SS BOND : angle 1.74554 ( 14) hydrogen bonds : bond 0.03587 ( 420) hydrogen bonds : angle 4.26809 ( 1212) Misc. bond : bond 0.00012 ( 1) link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 0.77696 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.351 Fit side-chains REVERT: A 215 ASP cc_start: 0.8131 (t0) cc_final: 0.7931 (t0) REVERT: A 265 ARG cc_start: 0.8570 (mtt90) cc_final: 0.7793 (mtm110) REVERT: B 45 MET cc_start: 0.7693 (mtm) cc_final: 0.7263 (mtp) REVERT: B 158 VAL cc_start: 0.9020 (t) cc_final: 0.8767 (p) REVERT: B 219 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: G 32 LYS cc_start: 0.7778 (tmtt) cc_final: 0.7501 (tmtt) REVERT: N 65 LYS cc_start: 0.8307 (tptt) cc_final: 0.8017 (tttm) REVERT: P 16 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (mm) REVERT: P 37 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.3909 (p90) REVERT: R 113 ASP cc_start: 0.3456 (OUTLIER) cc_final: 0.2339 (p0) REVERT: R 172 PHE cc_start: 0.7017 (t80) cc_final: 0.6081 (m-10) REVERT: R 284 TYR cc_start: 0.7841 (m-10) cc_final: 0.7623 (m-10) REVERT: R 346 MET cc_start: 0.7667 (mtm) cc_final: 0.7393 (mtt) outliers start: 31 outliers final: 27 residues processed: 125 average time/residue: 0.0998 time to fit residues: 17.6020 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.192972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142539 restraints weight = 10451.660| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.16 r_work: 0.3423 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9625 Z= 0.114 Angle : 0.475 5.809 12987 Z= 0.255 Chirality : 0.040 0.145 1418 Planarity : 0.003 0.039 1638 Dihedral : 5.918 59.745 1452 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.20 % Allowed : 12.50 % Favored : 84.30 % 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: 0.07 (0.25), residues: 1136 helix: 1.41 (0.26), residues: 424 sheet: -0.46 (0.34), residues: 211 loop : -0.88 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.012 0.001 TYR B 59 PHE 0.011 0.001 PHE N 108 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9615) covalent geometry : angle 0.47257 (12967) SS BOND : bond 0.00143 ( 7) SS BOND : angle 1.48506 ( 14) hydrogen bonds : bond 0.03181 ( 420) hydrogen bonds : angle 4.07499 ( 1212) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 0.72421 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.344 Fit side-chains REVERT: A 29 GLN cc_start: 0.7394 (tp40) cc_final: 0.7110 (mm-40) REVERT: A 215 ASP cc_start: 0.8205 (t0) cc_final: 0.7997 (t0) REVERT: A 265 ARG cc_start: 0.8704 (mtt90) cc_final: 0.7662 (mtm110) REVERT: B 45 MET cc_start: 0.7838 (mtm) cc_final: 0.7418 (mtp) REVERT: B 59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B 158 VAL cc_start: 0.9041 (t) cc_final: 0.8725 (p) REVERT: B 219 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7321 (ttm-80) REVERT: N 65 LYS cc_start: 0.8253 (tptt) cc_final: 0.7988 (tttm) REVERT: P 37 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.3734 (p90) REVERT: R 113 ASP cc_start: 0.3630 (OUTLIER) cc_final: 0.2439 (p0) REVERT: R 172 PHE cc_start: 0.6828 (t80) cc_final: 0.5731 (m-10) REVERT: R 227 GLN cc_start: 0.7978 (tp40) cc_final: 0.7735 (mm-40) REVERT: R 284 TYR cc_start: 0.7964 (m-10) cc_final: 0.7750 (m-10) REVERT: R 346 MET cc_start: 0.7689 (mtm) cc_final: 0.7420 (mtt) outliers start: 32 outliers final: 20 residues processed: 131 average time/residue: 0.1069 time to fit residues: 19.0618 Evaluate side-chains 121 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.189797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142057 restraints weight = 10358.943| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.95 r_work: 0.3418 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9625 Z= 0.129 Angle : 0.503 9.683 12987 Z= 0.264 Chirality : 0.041 0.178 1418 Planarity : 0.003 0.051 1638 Dihedral : 5.870 58.568 1450 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.70 % Allowed : 13.20 % Favored : 83.10 % 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: 0.11 (0.25), residues: 1136 helix: 1.46 (0.26), residues: 424 sheet: -0.50 (0.34), residues: 204 loop : -0.84 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 362 TYR 0.010 0.001 TYR N 94 PHE 0.015 0.001 PHE N 108 TRP 0.013 0.001 TRP R 236 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9615) covalent geometry : angle 0.50081 (12967) SS BOND : bond 0.00159 ( 7) SS BOND : angle 1.51803 ( 14) hydrogen bonds : bond 0.03197 ( 420) hydrogen bonds : angle 4.04594 ( 1212) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 0.72516 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.362 Fit side-chains REVERT: A 215 ASP cc_start: 0.8238 (t0) cc_final: 0.8037 (t0) REVERT: A 265 ARG cc_start: 0.8709 (mtt90) cc_final: 0.7726 (mtm110) REVERT: B 45 MET cc_start: 0.7954 (mtm) cc_final: 0.7551 (mtp) REVERT: B 59 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8210 (t80) REVERT: B 158 VAL cc_start: 0.9058 (t) cc_final: 0.8744 (p) REVERT: B 219 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7353 (ttm-80) REVERT: N 65 LYS cc_start: 0.8289 (tptt) cc_final: 0.8021 (tttm) REVERT: P 16 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7462 (mm) REVERT: P 37 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.3724 (p90) REVERT: R 48 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6969 (mtm) REVERT: R 113 ASP cc_start: 0.3647 (OUTLIER) cc_final: 0.2349 (p0) REVERT: R 172 PHE cc_start: 0.6859 (t80) cc_final: 0.5737 (m-10) REVERT: R 284 TYR cc_start: 0.7968 (m-10) cc_final: 0.7752 (m-10) REVERT: R 346 MET cc_start: 0.7709 (mtm) cc_final: 0.7457 (mtt) outliers start: 37 outliers final: 25 residues processed: 128 average time/residue: 0.1016 time to fit residues: 17.8791 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.192594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142062 restraints weight = 10530.491| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.16 r_work: 0.3411 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9625 Z= 0.115 Angle : 0.481 7.489 12987 Z= 0.255 Chirality : 0.040 0.160 1418 Planarity : 0.003 0.041 1638 Dihedral : 5.777 58.416 1450 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.20 % Allowed : 13.60 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.25), residues: 1136 helix: 1.58 (0.26), residues: 424 sheet: -0.46 (0.34), residues: 204 loop : -0.80 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 362 TYR 0.009 0.001 TYR B 59 PHE 0.012 0.001 PHE N 108 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9615) covalent geometry : angle 0.47859 (12967) SS BOND : bond 0.00208 ( 7) SS BOND : angle 1.36199 ( 14) hydrogen bonds : bond 0.03053 ( 420) hydrogen bonds : angle 3.98994 ( 1212) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00239 ( 2) link_NAG-ASN : angle 0.71805 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8547 (mtt90) cc_final: 0.7604 (mtm110) REVERT: B 45 MET cc_start: 0.7897 (mtm) cc_final: 0.7516 (mtp) REVERT: B 59 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 158 VAL cc_start: 0.8965 (t) cc_final: 0.8696 (p) REVERT: B 219 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: G 27 ARG cc_start: 0.7673 (ptp-170) cc_final: 0.7402 (ptp-170) REVERT: P 16 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7311 (mm) REVERT: R 48 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (mtm) REVERT: R 113 ASP cc_start: 0.3686 (OUTLIER) cc_final: 0.2346 (p0) REVERT: R 172 PHE cc_start: 0.6702 (t80) cc_final: 0.5794 (m-10) REVERT: R 284 TYR cc_start: 0.7926 (m-10) cc_final: 0.7684 (m-10) REVERT: R 346 MET cc_start: 0.7531 (mtm) cc_final: 0.7272 (mtt) outliers start: 32 outliers final: 24 residues processed: 125 average time/residue: 0.1045 time to fit residues: 17.9814 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 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 384 GLN ** 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 = 0.4078 r_free = 0.4078 target = 0.192042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141348 restraints weight = 10439.932| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.16 r_work: 0.3405 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9625 Z= 0.120 Angle : 0.494 10.307 12987 Z= 0.258 Chirality : 0.040 0.147 1418 Planarity : 0.003 0.041 1638 Dihedral : 5.719 57.763 1448 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.20 % Allowed : 13.50 % Favored : 83.30 % 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: 0.23 (0.25), residues: 1136 helix: 1.62 (0.26), residues: 424 sheet: -0.54 (0.34), residues: 204 loop : -0.78 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 362 TYR 0.009 0.001 TYR R 391 PHE 0.013 0.001 PHE A 222 TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9615) covalent geometry : angle 0.49211 (12967) SS BOND : bond 0.00157 ( 7) SS BOND : angle 1.36084 ( 14) hydrogen bonds : bond 0.03054 ( 420) hydrogen bonds : angle 3.98608 ( 1212) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00237 ( 2) link_NAG-ASN : angle 0.70643 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7965 (t0) cc_final: 0.7746 (t0) REVERT: A 265 ARG cc_start: 0.8521 (mtt90) cc_final: 0.7578 (mtm110) REVERT: B 45 MET cc_start: 0.7999 (mtm) cc_final: 0.7647 (mtp) REVERT: B 59 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 219 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7251 (ttm-80) REVERT: G 27 ARG cc_start: 0.7636 (ptp-170) cc_final: 0.7324 (ptp-170) REVERT: P 16 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7327 (mm) REVERT: P 37 TYR cc_start: 0.5729 (OUTLIER) cc_final: 0.3881 (p90) REVERT: R 48 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7133 (mtm) REVERT: R 113 ASP cc_start: 0.3770 (OUTLIER) cc_final: 0.2373 (p0) REVERT: R 172 PHE cc_start: 0.6702 (t80) cc_final: 0.5788 (m-10) REVERT: R 346 MET cc_start: 0.7545 (mtm) cc_final: 0.7283 (mtt) outliers start: 32 outliers final: 25 residues processed: 122 average time/residue: 0.1052 time to fit residues: 17.5865 Evaluate side-chains 124 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** 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 = 0.4089 r_free = 0.4089 target = 0.193322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143052 restraints weight = 10447.174| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.15 r_work: 0.3426 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9625 Z= 0.103 Angle : 0.468 7.208 12987 Z= 0.247 Chirality : 0.040 0.143 1418 Planarity : 0.003 0.041 1638 Dihedral : 5.588 58.097 1448 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.00 % Allowed : 13.60 % Favored : 83.40 % 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: 0.32 (0.25), residues: 1136 helix: 1.73 (0.26), residues: 424 sheet: -0.48 (0.34), residues: 204 loop : -0.77 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 362 TYR 0.010 0.001 TYR R 338 PHE 0.014 0.001 PHE A 222 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9615) covalent geometry : angle 0.46662 (12967) SS BOND : bond 0.00160 ( 7) SS BOND : angle 1.22446 ( 14) hydrogen bonds : bond 0.02920 ( 420) hydrogen bonds : angle 3.93262 ( 1212) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00237 ( 2) link_NAG-ASN : angle 0.68607 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8029 (t0) cc_final: 0.7800 (t0) REVERT: A 265 ARG cc_start: 0.8514 (mtt90) cc_final: 0.7582 (mtm110) REVERT: B 45 MET cc_start: 0.7923 (mtm) cc_final: 0.7582 (mtp) REVERT: B 59 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 219 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7250 (ttm-80) REVERT: P 16 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7375 (mm) REVERT: P 37 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4083 (p90) REVERT: R 48 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: R 113 ASP cc_start: 0.3789 (OUTLIER) cc_final: 0.2385 (p0) REVERT: R 172 PHE cc_start: 0.6685 (t80) cc_final: 0.5798 (m-10) REVERT: R 346 MET cc_start: 0.7565 (mtm) cc_final: 0.7327 (mtt) outliers start: 30 outliers final: 24 residues processed: 121 average time/residue: 0.1081 time to fit residues: 17.9627 Evaluate side-chains 123 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** 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 = 0.4079 r_free = 0.4079 target = 0.192220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141697 restraints weight = 10463.003| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.14 r_work: 0.3409 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9625 Z= 0.118 Angle : 0.492 10.680 12987 Z= 0.256 Chirality : 0.040 0.143 1418 Planarity : 0.003 0.053 1638 Dihedral : 5.623 57.446 1446 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.90 % Allowed : 14.00 % Favored : 83.10 % 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: 0.33 (0.25), residues: 1136 helix: 1.73 (0.26), residues: 424 sheet: -0.46 (0.34), residues: 204 loop : -0.77 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 362 TYR 0.010 0.001 TYR R 391 PHE 0.015 0.001 PHE A 222 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9615) covalent geometry : angle 0.49046 (12967) SS BOND : bond 0.00158 ( 7) SS BOND : angle 1.29013 ( 14) hydrogen bonds : bond 0.03006 ( 420) hydrogen bonds : angle 3.95685 ( 1212) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 0.71200 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8054 (t0) cc_final: 0.7832 (t0) REVERT: A 265 ARG cc_start: 0.8513 (mtt90) cc_final: 0.7590 (mtm110) REVERT: B 45 MET cc_start: 0.7969 (mtm) cc_final: 0.7625 (mtp) REVERT: B 59 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8015 (t80) REVERT: B 219 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: P 16 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7306 (mm) REVERT: P 37 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.4095 (p90) REVERT: R 48 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7147 (mtm) REVERT: R 113 ASP cc_start: 0.3776 (OUTLIER) cc_final: 0.2391 (p0) REVERT: R 172 PHE cc_start: 0.6678 (t80) cc_final: 0.5802 (m-10) REVERT: R 346 MET cc_start: 0.7564 (mtm) cc_final: 0.7325 (mtt) outliers start: 29 outliers final: 24 residues processed: 119 average time/residue: 0.1045 time to fit residues: 17.1160 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 0.0060 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.190038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.139182 restraints weight = 10411.597| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.14 r_work: 0.3380 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9625 Z= 0.148 Angle : 0.515 7.054 12987 Z= 0.271 Chirality : 0.041 0.144 1418 Planarity : 0.004 0.057 1638 Dihedral : 6.002 55.457 1446 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.10 % Allowed : 13.80 % Favored : 83.10 % 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: 0.24 (0.25), residues: 1136 helix: 1.55 (0.26), residues: 429 sheet: -0.53 (0.34), residues: 199 loop : -0.72 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 362 TYR 0.011 0.001 TYR R 391 PHE 0.020 0.002 PHE A 222 TRP 0.013 0.001 TRP R 236 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9615) covalent geometry : angle 0.51303 (12967) SS BOND : bond 0.00174 ( 7) SS BOND : angle 1.45140 ( 14) hydrogen bonds : bond 0.03267 ( 420) hydrogen bonds : angle 4.08089 ( 1212) Misc. bond : bond 0.00006 ( 1) link_NAG-ASN : bond 0.00229 ( 2) link_NAG-ASN : angle 0.75107 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.09 seconds wall clock time: 42 minutes 4.11 seconds (2524.11 seconds total)