Starting phenix.real_space_refine on Sun Jun 8 10:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyi_26180/06_2025/7tyi_26180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyi_26180/06_2025/7tyi_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_26180/06_2025/7tyi_26180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyi_26180/06_2025/7tyi_26180.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyi_26180/06_2025/7tyi_26180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyi_26180/06_2025/7tyi_26180.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.59, per 1000 atoms: 0.59 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: 2.19 Conformation dependent library (CDL) restraints added in 984.7 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: 0.94 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: 2.49 Time building geometry restraints manager: 2.63 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- 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 : 6.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP R 76 HIS 0.002 0.000 HIS R 121 PHE 0.010 0.001 PHE R 102 TYR 0.015 0.001 TYR R 56 ARG 0.004 0.000 ARG G 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 0.73846 ( 6) hydrogen bonds : bond 0.25572 ( 420) hydrogen bonds : angle 8.64986 ( 1212) SS BOND : bond 0.00244 ( 7) SS BOND : angle 1.49043 ( 14) covalent geometry : bond 0.00392 ( 9615) covalent geometry : angle 0.56786 (12967) Misc. bond : bond 0.10570 ( 1) *********************** 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 : 1.002 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: 0.2204 (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: 0.7345 (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: 0.2573 time to fit residues: 53.6547 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 : 0.900 ------------------------------------------------------------------------------- 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 93 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.182356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.140544 restraints weight = 10307.781| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.54 r_work: 0.3344 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9625 Z= 0.242 Angle : 0.665 10.271 12987 Z= 0.350 Chirality : 0.046 0.167 1418 Planarity : 0.005 0.051 1638 Dihedral : 6.839 59.628 1453 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.60 % Allowed : 10.00 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1136 helix: -0.10 (0.23), residues: 425 sheet: -0.70 (0.34), residues: 214 loop : -1.24 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 236 HIS 0.009 0.002 HIS R 336 PHE 0.031 0.002 PHE N 108 TYR 0.031 0.002 TYR A 358 ARG 0.008 0.001 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 2) link_NAG-ASN : angle 0.62154 ( 6) hydrogen bonds : bond 0.04570 ( 420) hydrogen bonds : angle 4.95790 ( 1212) SS BOND : bond 0.00254 ( 7) SS BOND : angle 2.51394 ( 14) covalent geometry : bond 0.00575 ( 9615) covalent geometry : angle 0.65975 (12967) Misc. bond : bond 0.00018 ( 1) *********************** 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 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8526 (mtt90) cc_final: 0.7830 (mtm110) REVERT: B 45 MET cc_start: 0.7607 (mtm) cc_final: 0.7098 (mtp) REVERT: B 219 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: G 32 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7720 (tmtt) REVERT: N 65 LYS cc_start: 0.8261 (tptt) cc_final: 0.7938 (tttm) REVERT: N 120 GLN cc_start: 0.8082 (pm20) cc_final: 0.7689 (pm20) REVERT: P 16 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7883 (mm) REVERT: P 18 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7446 (mtm180) REVERT: R 113 ASP cc_start: 0.3237 (OUTLIER) cc_final: 0.2808 (m-30) REVERT: R 172 PHE cc_start: 0.7056 (t80) cc_final: 0.6244 (m-10) REVERT: R 230 MET cc_start: 0.8342 (ppp) cc_final: 0.8094 (ppp) REVERT: R 284 TYR cc_start: 0.7883 (m-10) cc_final: 0.7638 (m-10) REVERT: R 327 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (mtp) REVERT: R 373 ASP cc_start: 0.8599 (m-30) cc_final: 0.7676 (m-30) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.2664 time to fit residues: 48.5436 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 105 TYR 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 Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3921 r_free = 0.3921 target = 0.179909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.136926 restraints weight = 10318.171| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.60 r_work: 0.3280 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9625 Z= 0.188 Angle : 0.573 8.917 12987 Z= 0.304 Chirality : 0.043 0.160 1418 Planarity : 0.004 0.034 1638 Dihedral : 6.684 58.957 1452 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.20 % Allowed : 11.80 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1136 helix: 0.64 (0.25), residues: 426 sheet: -0.63 (0.34), residues: 206 loop : -1.12 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 236 HIS 0.007 0.001 HIS B 54 PHE 0.018 0.002 PHE N 108 TYR 0.017 0.001 TYR B 59 ARG 0.004 0.000 ARG A 385 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 2) link_NAG-ASN : angle 0.83665 ( 6) hydrogen bonds : bond 0.04177 ( 420) hydrogen bonds : angle 4.60952 ( 1212) SS BOND : bond 0.00175 ( 7) SS BOND : angle 2.02683 ( 14) covalent geometry : bond 0.00449 ( 9615) covalent geometry : angle 0.56912 (12967) Misc. bond : bond 0.00004 ( 1) *********************** 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 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.041 Fit side-chains REVERT: A 265 ARG cc_start: 0.8626 (mtt90) cc_final: 0.7737 (mtm110) REVERT: B 45 MET cc_start: 0.7685 (mtm) cc_final: 0.7281 (mtp) REVERT: B 96 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.7168 (tmm-80) REVERT: B 219 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7477 (ttm-80) REVERT: G 32 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7367 (tmtt) REVERT: N 65 LYS cc_start: 0.8213 (tptt) cc_final: 0.7901 (tttm) REVERT: P 16 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7593 (mm) REVERT: P 37 TYR cc_start: 0.5672 (OUTLIER) cc_final: 0.3570 (p90) REVERT: R 113 ASP cc_start: 0.3443 (OUTLIER) cc_final: 0.2197 (p0) REVERT: R 172 PHE cc_start: 0.6830 (t80) cc_final: 0.5883 (m-10) REVERT: R 284 TYR cc_start: 0.8004 (m-10) cc_final: 0.7753 (m-10) REVERT: R 327 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8330 (mtp) outliers start: 32 outliers final: 23 residues processed: 131 average time/residue: 0.2676 time to fit residues: 47.0718 Evaluate side-chains 128 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU 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 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 Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.0010 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN P 14 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.181635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140064 restraints weight = 10150.106| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.69 r_work: 0.3298 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.033 9625 Z= 0.129 Angle : 0.502 5.925 12987 Z= 0.268 Chirality : 0.041 0.148 1418 Planarity : 0.003 0.037 1638 Dihedral : 6.383 59.659 1452 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 12.70 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1136 helix: 1.10 (0.26), residues: 424 sheet: -0.57 (0.35), residues: 204 loop : -0.99 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 137 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 2) link_NAG-ASN : angle 0.75536 ( 6) hydrogen bonds : bond 0.03463 ( 420) hydrogen bonds : angle 4.28973 ( 1212) SS BOND : bond 0.00139 ( 7) SS BOND : angle 1.66203 ( 14) covalent geometry : bond 0.00299 ( 9615) covalent geometry : angle 0.49922 (12967) Misc. bond : bond 0.00009 ( 1) *********************** 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 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.340 Fit side-chains REVERT: A 265 ARG cc_start: 0.8645 (mtt90) cc_final: 0.7636 (mtm110) REVERT: B 45 MET cc_start: 0.7789 (mtm) cc_final: 0.7438 (mtp) REVERT: B 59 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 96 ARG cc_start: 0.7307 (ttp-110) cc_final: 0.7090 (tmm-80) REVERT: B 219 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7420 (ttm-80) REVERT: G 32 LYS cc_start: 0.7582 (tmtt) cc_final: 0.7286 (tmtt) REVERT: N 65 LYS cc_start: 0.8167 (tptt) cc_final: 0.7863 (tttm) REVERT: P 16 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7412 (mm) REVERT: P 37 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.3823 (p90) REVERT: R 113 ASP cc_start: 0.3683 (OUTLIER) cc_final: 0.2431 (p0) REVERT: R 172 PHE cc_start: 0.6745 (t80) cc_final: 0.5799 (m-10) REVERT: R 284 TYR cc_start: 0.8012 (m-10) cc_final: 0.7751 (m-10) REVERT: R 327 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: R 346 MET cc_start: 0.7678 (mtm) cc_final: 0.7368 (mtt) REVERT: R 359 PHE cc_start: 0.8260 (m-10) cc_final: 0.7905 (m-80) outliers start: 33 outliers final: 24 residues processed: 125 average time/residue: 0.2338 time to fit residues: 40.0403 Evaluate side-chains 124 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 35 ASN 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 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN P 14 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.180877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138254 restraints weight = 10261.880| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.73 r_work: 0.3268 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9625 Z= 0.146 Angle : 0.520 10.524 12987 Z= 0.274 Chirality : 0.041 0.148 1418 Planarity : 0.003 0.039 1638 Dihedral : 6.323 57.257 1452 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.90 % Allowed : 12.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1136 helix: 1.22 (0.26), residues: 427 sheet: -0.54 (0.34), residues: 206 loop : -0.91 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.002 PHE N 108 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG R 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 2) link_NAG-ASN : angle 0.73479 ( 6) hydrogen bonds : bond 0.03410 ( 420) hydrogen bonds : angle 4.22297 ( 1212) SS BOND : bond 0.00168 ( 7) SS BOND : angle 1.68054 ( 14) covalent geometry : bond 0.00346 ( 9615) covalent geometry : angle 0.51727 (12967) Misc. bond : bond 0.00006 ( 1) *********************** 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 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.314 Fit side-chains REVERT: A 215 ASP cc_start: 0.8023 (t0) cc_final: 0.7777 (t0) REVERT: A 265 ARG cc_start: 0.8669 (mtt90) cc_final: 0.7698 (mtm110) REVERT: B 45 MET cc_start: 0.7938 (mtm) cc_final: 0.7573 (mtp) REVERT: B 59 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8299 (t80) REVERT: B 96 ARG cc_start: 0.7426 (ttp-110) cc_final: 0.7168 (tmm-80) REVERT: B 219 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.7550 (ttm-80) REVERT: N 65 LYS cc_start: 0.8219 (tptt) cc_final: 0.7915 (tttm) REVERT: P 16 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7406 (mm) REVERT: P 37 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.3808 (p90) REVERT: R 113 ASP cc_start: 0.3454 (OUTLIER) cc_final: 0.2272 (p0) REVERT: R 172 PHE cc_start: 0.6840 (t80) cc_final: 0.5781 (m-10) REVERT: R 327 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (mtp) outliers start: 39 outliers final: 27 residues processed: 132 average time/residue: 0.2734 time to fit residues: 48.8347 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 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 35 ASN 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 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.190786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140483 restraints weight = 10366.501| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.13 r_work: 0.3395 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9625 Z= 0.129 Angle : 0.504 9.317 12987 Z= 0.266 Chirality : 0.041 0.198 1418 Planarity : 0.003 0.040 1638 Dihedral : 6.163 57.132 1452 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.70 % Allowed : 13.60 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1136 helix: 1.44 (0.26), residues: 424 sheet: -0.66 (0.34), residues: 204 loop : -0.87 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE N 108 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 2) link_NAG-ASN : angle 0.71129 ( 6) hydrogen bonds : bond 0.03210 ( 420) hydrogen bonds : angle 4.13213 ( 1212) SS BOND : bond 0.00160 ( 7) SS BOND : angle 1.50770 ( 14) covalent geometry : bond 0.00306 ( 9615) covalent geometry : angle 0.50219 (12967) Misc. bond : bond 0.00008 ( 1) *********************** 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 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8156 (t0) cc_final: 0.7809 (t0) REVERT: A 265 ARG cc_start: 0.8705 (mtt90) cc_final: 0.7663 (mtm110) REVERT: A 384 GLN cc_start: 0.8660 (tt0) cc_final: 0.8362 (tt0) REVERT: B 45 MET cc_start: 0.8040 (mtm) cc_final: 0.7693 (mtp) REVERT: B 59 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8258 (t80) REVERT: B 96 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7208 (tmm-80) REVERT: B 118 ASP cc_start: 0.6827 (p0) cc_final: 0.6605 (p0) REVERT: B 219 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7295 (ttm-80) REVERT: N 65 LYS cc_start: 0.8217 (tptt) cc_final: 0.7930 (tttm) REVERT: P 16 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7400 (mm) REVERT: P 37 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.3753 (p90) REVERT: R 113 ASP cc_start: 0.3528 (OUTLIER) cc_final: 0.2314 (p0) REVERT: R 172 PHE cc_start: 0.6797 (t80) cc_final: 0.5672 (m-10) REVERT: R 327 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: R 346 MET cc_start: 0.7802 (mtm) cc_final: 0.7521 (mtt) outliers start: 37 outliers final: 27 residues processed: 125 average time/residue: 0.4200 time to fit residues: 72.2448 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 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 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 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 35 ASN Chi-restraints excluded: chain N residue 52 SER 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 324 VAL Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 75 optimal weight: 0.1980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.191969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141748 restraints weight = 10424.447| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.13 r_work: 0.3408 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9625 Z= 0.108 Angle : 0.490 10.153 12987 Z= 0.256 Chirality : 0.040 0.168 1418 Planarity : 0.003 0.045 1638 Dihedral : 5.952 57.158 1452 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.90 % Allowed : 14.30 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1136 helix: 1.61 (0.26), residues: 424 sheet: -0.62 (0.33), residues: 205 loop : -0.84 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 245 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR R 149 ARG 0.009 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 0.68456 ( 6) hydrogen bonds : bond 0.03023 ( 420) hydrogen bonds : angle 4.03390 ( 1212) SS BOND : bond 0.00126 ( 7) SS BOND : angle 1.36528 ( 14) covalent geometry : bond 0.00251 ( 9615) covalent geometry : angle 0.48805 (12967) Misc. bond : bond 0.00007 ( 1) *********************** 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 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7980 (t0) cc_final: 0.7714 (t0) REVERT: A 265 ARG cc_start: 0.8556 (mtt90) cc_final: 0.7590 (mtm110) REVERT: B 45 MET cc_start: 0.7933 (mtm) cc_final: 0.7614 (mtp) REVERT: B 59 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7986 (t80) REVERT: B 118 ASP cc_start: 0.6678 (p0) cc_final: 0.6451 (p0) REVERT: B 219 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7267 (ttm-80) REVERT: P 37 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.3863 (p90) REVERT: R 113 ASP cc_start: 0.3692 (OUTLIER) cc_final: 0.2353 (p0) REVERT: R 172 PHE cc_start: 0.6690 (t80) cc_final: 0.5776 (m-10) REVERT: R 327 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8204 (mtp) REVERT: R 346 MET cc_start: 0.7596 (mtm) cc_final: 0.7323 (mtt) outliers start: 29 outliers final: 24 residues processed: 126 average time/residue: 0.3106 time to fit residues: 53.8793 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 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 155 ASN 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 G residue 52 THR Chi-restraints excluded: chain N residue 35 ASN 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 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 Chi-restraints excluded: chain R residue 327 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.0570 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 overall best weight: 0.7902 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.191435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141057 restraints weight = 10660.983| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.14 r_work: 0.3401 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9625 Z= 0.119 Angle : 0.496 7.456 12987 Z= 0.260 Chirality : 0.040 0.163 1418 Planarity : 0.003 0.043 1638 Dihedral : 5.862 56.228 1450 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.50 % Allowed : 14.50 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1136 helix: 1.64 (0.26), residues: 424 sheet: -0.58 (0.33), residues: 205 loop : -0.86 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE N 108 TYR 0.010 0.001 TYR R 149 ARG 0.008 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 2) link_NAG-ASN : angle 0.68936 ( 6) hydrogen bonds : bond 0.03039 ( 420) hydrogen bonds : angle 4.03126 ( 1212) SS BOND : bond 0.00161 ( 7) SS BOND : angle 1.37165 ( 14) covalent geometry : bond 0.00280 ( 9615) covalent geometry : angle 0.49419 (12967) Misc. bond : bond 0.00007 ( 1) *********************** 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 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8061 (t0) cc_final: 0.7794 (t0) REVERT: A 265 ARG cc_start: 0.8541 (mtt90) cc_final: 0.7593 (mtm110) REVERT: B 45 MET cc_start: 0.7970 (mtm) cc_final: 0.7646 (mtp) REVERT: B 59 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8006 (t80) REVERT: B 118 ASP cc_start: 0.6730 (p0) cc_final: 0.6498 (p0) REVERT: B 219 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: R 113 ASP cc_start: 0.3718 (OUTLIER) cc_final: 0.2332 (p0) REVERT: R 172 PHE cc_start: 0.6737 (t80) cc_final: 0.5800 (m-10) REVERT: R 346 MET cc_start: 0.7632 (mtm) cc_final: 0.7349 (mtt) outliers start: 35 outliers final: 29 residues processed: 123 average time/residue: 0.2332 time to fit residues: 39.4470 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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 N residue 35 ASN Chi-restraints excluded: chain N residue 52 SER 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 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 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 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.188261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137402 restraints weight = 10489.295| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.13 r_work: 0.3361 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9625 Z= 0.175 Angle : 0.557 10.952 12987 Z= 0.289 Chirality : 0.042 0.163 1418 Planarity : 0.004 0.048 1638 Dihedral : 6.270 53.565 1448 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.10 % Allowed : 14.80 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1136 helix: 1.41 (0.26), residues: 428 sheet: -0.57 (0.34), residues: 202 loop : -0.87 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.002 PHE N 108 TYR 0.012 0.001 TYR R 391 ARG 0.008 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 0.73947 ( 6) hydrogen bonds : bond 0.03427 ( 420) hydrogen bonds : angle 4.19834 ( 1212) SS BOND : bond 0.00191 ( 7) SS BOND : angle 1.63379 ( 14) covalent geometry : bond 0.00421 ( 9615) covalent geometry : angle 0.55420 (12967) Misc. bond : bond 0.00006 ( 1) *********************** 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 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8210 (t0) cc_final: 0.7926 (t0) REVERT: A 265 ARG cc_start: 0.8686 (mtt90) cc_final: 0.7698 (mtm110) REVERT: B 45 MET cc_start: 0.8131 (mtm) cc_final: 0.7791 (mtp) REVERT: B 59 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8353 (t80) REVERT: B 219 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: N 65 LYS cc_start: 0.8316 (tptt) cc_final: 0.8068 (tttm) REVERT: N 117 TYR cc_start: 0.8636 (m-80) cc_final: 0.8006 (m-80) REVERT: R 113 ASP cc_start: 0.3916 (OUTLIER) cc_final: 0.2421 (p0) REVERT: R 172 PHE cc_start: 0.6835 (t80) cc_final: 0.5707 (m-10) REVERT: R 213 ARG cc_start: 0.7436 (ttp80) cc_final: 0.7046 (ttp80) outliers start: 31 outliers final: 28 residues processed: 123 average time/residue: 0.2416 time to fit residues: 40.6508 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 A residue 386 MET 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 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 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 N residue 35 ASN Chi-restraints excluded: chain N residue 52 SER 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 36 THR 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 102 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.192432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142249 restraints weight = 10536.040| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.13 r_work: 0.3413 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9625 Z= 0.100 Angle : 0.487 7.216 12987 Z= 0.257 Chirality : 0.040 0.144 1418 Planarity : 0.003 0.041 1638 Dihedral : 5.808 57.192 1447 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.70 % Allowed : 15.40 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1136 helix: 1.74 (0.26), residues: 423 sheet: -0.58 (0.34), residues: 200 loop : -0.85 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 234 HIS 0.004 0.001 HIS R 245 PHE 0.011 0.001 PHE A 222 TYR 0.013 0.001 TYR R 191 ARG 0.007 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 2) link_NAG-ASN : angle 0.67773 ( 6) hydrogen bonds : bond 0.02959 ( 420) hydrogen bonds : angle 4.01521 ( 1212) SS BOND : bond 0.00155 ( 7) SS BOND : angle 1.22696 ( 14) covalent geometry : bond 0.00226 ( 9615) covalent geometry : angle 0.48583 (12967) Misc. bond : bond 0.00008 ( 1) ********************** 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 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.8072 (t0) cc_final: 0.7825 (t0) REVERT: A 265 ARG cc_start: 0.8528 (mtt90) cc_final: 0.7573 (mtm110) REVERT: B 45 MET cc_start: 0.8012 (mtm) cc_final: 0.7706 (mtp) REVERT: B 59 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7971 (t80) REVERT: B 118 ASP cc_start: 0.6727 (p0) cc_final: 0.6484 (p0) REVERT: B 219 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7182 (ttm-80) REVERT: R 113 ASP cc_start: 0.3879 (OUTLIER) cc_final: 0.2408 (p0) REVERT: R 172 PHE cc_start: 0.6721 (t80) cc_final: 0.5786 (m-10) REVERT: R 213 ARG cc_start: 0.7407 (ttp80) cc_final: 0.6998 (ttp80) REVERT: R 346 MET cc_start: 0.7636 (mtm) cc_final: 0.7374 (mtt) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.2674 time to fit residues: 42.7786 Evaluate side-chains 123 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 A residue 386 MET 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 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 35 ASN Chi-restraints excluded: chain N residue 52 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 0.0170 chunk 75 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.192206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141963 restraints weight = 10504.890| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.12 r_work: 0.3411 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3502 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= 0.110 Angle : 0.492 10.747 12987 Z= 0.256 Chirality : 0.040 0.145 1418 Planarity : 0.003 0.041 1638 Dihedral : 5.698 55.872 1446 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.70 % Allowed : 15.40 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1136 helix: 1.80 (0.26), residues: 423 sheet: -0.50 (0.34), residues: 200 loop : -0.87 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR R 191 ARG 0.004 0.000 ARG R 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 2) link_NAG-ASN : angle 0.70475 ( 6) hydrogen bonds : bond 0.02978 ( 420) hydrogen bonds : angle 3.97636 ( 1212) SS BOND : bond 0.00155 ( 7) SS BOND : angle 1.26742 ( 14) covalent geometry : bond 0.00256 ( 9615) covalent geometry : angle 0.49044 (12967) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5387.27 seconds wall clock time: 95 minutes 28.58 seconds (5728.58 seconds total)