Starting phenix.real_space_refine on Thu Jul 2 11:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jvp_22509/07_2026/7jvp_22509.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 5462 2.51 5 N 1440 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2227 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 3 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1966 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 280 Unusual residues: {'CLR': 6, 'PLM': 5, 'SK9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 1.86, per 1000 atoms: 0.22 Number of scatterers: 8486 At special positions: 0 Unit cell: (97.185, 106.59, 122.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 53 16.00 O 1530 8.00 N 1440 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 444.4 milliseconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 45.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 51 through 57 removed outlier: 3.519A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 4.392A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.661A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.380A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.141A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 239 Processing helix chain 'R' and resid 265 through 299 Proline residue: R 287 - end of helix Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.598A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.877A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.244A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.671A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 312 through 317 removed outlier: 4.033A pdb=" N ALA A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 331 through 353 Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) 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 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.924A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.744A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.880A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.704A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.864A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.855A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.051A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2656 1.34 - 1.46: 1951 1.46 - 1.58: 3987 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8667 Sorted by residual: bond pdb=" N LEU R 291 " pdb=" CA LEU R 291 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.23e-02 6.61e+03 5.36e+00 bond pdb=" N PHE R 313 " pdb=" CA PHE R 313 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" C05 SK9 R 501 " pdb=" C07 SK9 R 501 " ideal model delta sigma weight residual 1.520 1.561 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.11e+00 bond pdb=" C18 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sigma weight residual 1.448 1.409 0.039 2.00e-02 2.50e+03 3.83e+00 ... (remaining 8662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11122 2.01 - 4.01: 535 4.01 - 6.02: 63 6.02 - 8.03: 18 8.03 - 10.03: 3 Bond angle restraints: 11741 Sorted by residual: angle pdb=" C CYS A 365 " pdb=" N SER A 366 " pdb=" CA SER A 366 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 113.16 118.65 -5.49 1.42e+00 4.96e-01 1.49e+01 angle pdb=" C CYS B 250 " pdb=" N ARG B 251 " pdb=" CA ARG B 251 " ideal model delta sigma weight residual 122.99 117.69 5.30 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C CYS B 166 " pdb=" N ALA B 167 " pdb=" CA ALA B 167 " ideal model delta sigma weight residual 122.62 117.27 5.35 1.56e+00 4.11e-01 1.18e+01 angle pdb=" C07 SK9 R 501 " pdb=" C09 SK9 R 501 " pdb=" N01 SK9 R 501 " ideal model delta sigma weight residual 114.07 124.10 -10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 11736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4910 15.07 - 30.14: 193 30.14 - 45.22: 30 45.22 - 60.29: 6 60.29 - 75.36: 2 Dihedral angle restraints: 5141 sinusoidal: 2112 harmonic: 3029 Sorted by residual: dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual -86.00 -115.08 29.08 1 1.00e+01 1.00e-02 1.21e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1133 0.087 - 0.174: 163 0.174 - 0.261: 22 0.261 - 0.348: 6 0.348 - 0.435: 6 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1327 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG A 380 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG A 380 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP A 381 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 375 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C VAL A 375 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 375 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 376 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO A 361 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.041 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.28: 8315 3.28 - 3.82: 14214 3.82 - 4.36: 16907 4.36 - 4.90: 29451 Nonbonded interactions: 69361 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.254 3.040 nonbonded pdb=" O SER R 198 " pdb=" OG SER R 202 " model vdw 2.264 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.268 3.040 ... (remaining 69356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 : 0.005 0.059 8670 Z= 0.260 Angle : 0.966 10.032 11747 Z= 0.535 Chirality : 0.070 0.435 1330 Planarity : 0.007 0.075 1447 Dihedral : 8.784 75.358 3164 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.24), residues: 1021 helix: 3.52 (0.21), residues: 423 sheet: 2.92 (0.34), residues: 196 loop : -1.16 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 266 TYR 0.023 0.003 TYR A 311 PHE 0.041 0.004 PHE B 234 TRP 0.030 0.004 TRP A 281 HIS 0.019 0.004 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.26 ( 8667) covalent geometry : angle 0.96507 / 0.53 (11741) SS BOND : bond 0.00381 / 0.18 ( 3) SS BOND : angle 1.97513 / 1.37 ( 6) hydrogen bonds : bond 0.13726 / 9.11 ( 462) hydrogen bonds : angle 6.22628 / 4.84 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 278 MET cc_start: 0.7523 (mmm) cc_final: 0.7252 (mmp) REVERT: A 17 LYS cc_start: 0.7640 (tttt) cc_final: 0.7074 (mmmt) REVERT: A 378 ASP cc_start: 0.7661 (m-30) cc_final: 0.7416 (m-30) REVERT: B 161 SER cc_start: 0.8590 (t) cc_final: 0.8082 (m) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.5039 time to fit residues: 132.4924 Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 53 HIS ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 294 GLN B 6 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 110 ASN B 156 GLN B 259 GLN N 31 ASN N 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.163978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131190 restraints weight = 9823.566| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.84 r_work: 0.3308 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8670 Z= 0.160 Angle : 0.556 7.798 11747 Z= 0.300 Chirality : 0.043 0.150 1330 Planarity : 0.005 0.052 1447 Dihedral : 6.009 58.933 1272 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.91 % Allowed : 11.87 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.25), residues: 1021 helix: 3.19 (0.23), residues: 423 sheet: 1.78 (0.33), residues: 210 loop : -0.56 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 347 TYR 0.015 0.002 TYR A 339 PHE 0.016 0.002 PHE R 288 TRP 0.027 0.002 TRP A 281 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8667) covalent geometry : angle 0.55607 / 0.30 (11741) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 1.07580 / 0.69 ( 6) hydrogen bonds : bond 0.04858 / 3.38 ( 462) hydrogen bonds : angle 4.79094 / 3.76 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.221 Fit side-chains REVERT: R 50 ARG cc_start: 0.6634 (mmt90) cc_final: 0.5676 (tpp-160) REVERT: R 59 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8672 (p) REVERT: R 213 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8533 (m) REVERT: R 216 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7792 (mtt180) REVERT: R 219 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7490 (mtt-85) REVERT: R 278 MET cc_start: 0.8153 (mmm) cc_final: 0.7860 (mmp) REVERT: A 17 LYS cc_start: 0.7368 (tttt) cc_final: 0.6597 (mmmt) REVERT: A 53 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6357 (ttpt) REVERT: A 209 GLU cc_start: 0.7538 (tt0) cc_final: 0.7338 (tp30) REVERT: A 344 GLU cc_start: 0.7911 (tp30) cc_final: 0.7697 (tp30) REVERT: A 378 ASP cc_start: 0.8350 (m-30) cc_final: 0.8145 (m-30) REVERT: A 386 MET cc_start: 0.8918 (ttm) cc_final: 0.8629 (ttp) REVERT: B 96 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7872 (mtp85) REVERT: B 325 MET cc_start: 0.8767 (tpp) cc_final: 0.8564 (tpp) REVERT: N 5 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7195 (tm-30) outliers start: 26 outliers final: 7 residues processed: 201 average time/residue: 0.5000 time to fit residues: 106.7392 Evaluate side-chains 163 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain N residue 65 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127298 restraints weight = 9625.243| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.89 r_work: 0.3250 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8670 Z= 0.153 Angle : 0.521 7.606 11747 Z= 0.279 Chirality : 0.041 0.138 1330 Planarity : 0.004 0.038 1447 Dihedral : 5.927 59.543 1272 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.81 % Allowed : 15.34 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.25), residues: 1021 helix: 2.97 (0.23), residues: 423 sheet: 1.08 (0.31), residues: 210 loop : -0.30 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.012 0.001 TYR R 194 PHE 0.023 0.002 PHE R 297 TRP 0.017 0.002 TRP A 281 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8667) covalent geometry : angle 0.52099 / 0.28 (11741) SS BOND : bond 0.00976 / 0.47 ( 3) SS BOND : angle 0.98238 / 0.58 ( 6) hydrogen bonds : bond 0.04575 / 3.14 ( 462) hydrogen bonds : angle 4.67992 / 3.68 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.235 Fit side-chains REVERT: R 50 ARG cc_start: 0.6744 (mmt90) cc_final: 0.5764 (tpp-160) REVERT: R 213 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8702 (m) REVERT: R 219 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7441 (mtt-85) REVERT: R 278 MET cc_start: 0.8277 (mmm) cc_final: 0.8025 (mmp) REVERT: A 17 LYS cc_start: 0.7310 (tttt) cc_final: 0.6531 (mmmt) REVERT: A 53 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6546 (ttpt) REVERT: A 265 ARG cc_start: 0.7797 (ptt180) cc_final: 0.7427 (ppt-90) REVERT: A 296 LEU cc_start: 0.7403 (tp) cc_final: 0.7015 (tp) REVERT: A 307 LYS cc_start: 0.4938 (mmtt) cc_final: 0.4619 (mtpm) REVERT: A 330 GLU cc_start: 0.5948 (tt0) cc_final: 0.5152 (tp30) REVERT: A 344 GLU cc_start: 0.8010 (tp30) cc_final: 0.7766 (tp30) REVERT: A 370 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: A 378 ASP cc_start: 0.8299 (m-30) cc_final: 0.8097 (m-30) REVERT: A 386 MET cc_start: 0.8910 (ttm) cc_final: 0.8611 (ttp) REVERT: B 42 ARG cc_start: 0.6930 (tpt170) cc_final: 0.6698 (tpt170) REVERT: B 96 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7938 (mtp85) REVERT: B 262 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (ttm) REVERT: B 325 MET cc_start: 0.8813 (tpp) cc_final: 0.8605 (tpp) REVERT: G 46 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7480 (mppt) REVERT: N 5 GLN cc_start: 0.7912 (mm-40) cc_final: 0.6965 (tm-30) REVERT: N 38 ARG cc_start: 0.8582 (ptt-90) cc_final: 0.8330 (ptp90) outliers start: 34 outliers final: 16 residues processed: 174 average time/residue: 0.5809 time to fit residues: 107.3383 Evaluate side-chains 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121826 restraints weight = 9810.547| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.92 r_work: 0.3247 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8670 Z= 0.128 Angle : 0.490 7.534 11747 Z= 0.261 Chirality : 0.040 0.136 1330 Planarity : 0.004 0.039 1447 Dihedral : 5.383 59.621 1272 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.14 % Allowed : 15.68 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1021 helix: 2.89 (0.24), residues: 422 sheet: 0.71 (0.31), residues: 216 loop : -0.21 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 356 TYR 0.011 0.001 TYR R 194 PHE 0.015 0.001 PHE R 288 TRP 0.014 0.002 TRP A 281 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8667) covalent geometry : angle 0.48963 / 0.26 (11741) SS BOND : bond 0.00354 / 0.17 ( 3) SS BOND : angle 1.06183 / 0.65 ( 6) hydrogen bonds : bond 0.04240 / 2.92 ( 462) hydrogen bonds : angle 4.60654 / 3.63 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.325 Fit side-chains REVERT: R 50 ARG cc_start: 0.6737 (mmt90) cc_final: 0.5762 (tpp-160) REVERT: R 213 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (m) REVERT: R 219 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7449 (mtt-85) REVERT: R 278 MET cc_start: 0.8386 (mmm) cc_final: 0.8125 (mmp) REVERT: A 17 LYS cc_start: 0.7298 (tttt) cc_final: 0.6571 (mmmt) REVERT: A 265 ARG cc_start: 0.7787 (ptt180) cc_final: 0.7464 (ppt-90) REVERT: A 330 GLU cc_start: 0.5953 (tt0) cc_final: 0.5256 (tp30) REVERT: A 344 GLU cc_start: 0.7958 (tp30) cc_final: 0.7714 (tp30) REVERT: A 378 ASP cc_start: 0.8274 (m-30) cc_final: 0.7966 (m-30) REVERT: A 386 MET cc_start: 0.8897 (ttm) cc_final: 0.8601 (ttp) REVERT: A 392 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7575 (tt0) REVERT: B 96 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7932 (mtp85) REVERT: B 325 MET cc_start: 0.8796 (tpp) cc_final: 0.8565 (tpp) REVERT: G 46 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7487 (mppt) REVERT: N 3 GLN cc_start: 0.8169 (pt0) cc_final: 0.7295 (tp-100) REVERT: N 5 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7213 (tm-30) outliers start: 37 outliers final: 21 residues processed: 168 average time/residue: 0.5823 time to fit residues: 103.7432 Evaluate side-chains 161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 259 GLN N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108373 restraints weight = 9762.357| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.93 r_work: 0.3041 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8670 Z= 0.250 Angle : 0.587 7.161 11747 Z= 0.314 Chirality : 0.043 0.140 1330 Planarity : 0.005 0.050 1447 Dihedral : 6.288 55.411 1272 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.70 % Allowed : 16.01 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1021 helix: 2.21 (0.24), residues: 430 sheet: 0.18 (0.31), residues: 217 loop : -0.29 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 356 TYR 0.016 0.002 TYR N 95 PHE 0.026 0.002 PHE R 288 TRP 0.017 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 ( 8667) covalent geometry : angle 0.58614 / 0.31 (11741) SS BOND : bond 0.00228 / 0.11 ( 3) SS BOND : angle 1.43743 / 0.88 ( 6) hydrogen bonds : bond 0.04947 / 3.37 ( 462) hydrogen bonds : angle 5.06716 / 3.98 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.336 Fit side-chains REVERT: R 50 ARG cc_start: 0.6881 (mmt90) cc_final: 0.5968 (tpm170) REVERT: R 57 LYS cc_start: 0.7259 (mttt) cc_final: 0.6815 (mtmm) REVERT: R 92 PHE cc_start: 0.4134 (m-80) cc_final: 0.3451 (m-80) REVERT: R 154 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7885 (tt) REVERT: R 202 SER cc_start: 0.8919 (t) cc_final: 0.8437 (m) REVERT: R 213 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8364 (p) REVERT: R 219 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7552 (mtt-85) REVERT: R 223 LYS cc_start: 0.8091 (mttt) cc_final: 0.7875 (mtpt) REVERT: R 265 LYS cc_start: 0.7601 (tttt) cc_final: 0.7274 (tmtm) REVERT: A 17 LYS cc_start: 0.7328 (tttt) cc_final: 0.6571 (mmmt) REVERT: A 53 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7052 (ttpt) REVERT: A 265 ARG cc_start: 0.7782 (ptt180) cc_final: 0.7479 (ppt-90) REVERT: A 266 LEU cc_start: 0.8846 (tp) cc_final: 0.8604 (tm) REVERT: A 307 LYS cc_start: 0.4900 (mtpm) cc_final: 0.4495 (mtmm) REVERT: A 356 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7087 (mtm110) REVERT: A 378 ASP cc_start: 0.8416 (m-30) cc_final: 0.8096 (m-30) REVERT: A 386 MET cc_start: 0.8935 (ttm) cc_final: 0.8653 (ttp) REVERT: B 32 GLN cc_start: 0.8553 (mt0) cc_final: 0.8288 (mt0) REVERT: B 96 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7994 (mtp85) REVERT: G 46 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7508 (mppt) REVERT: N 3 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: N 110 VAL cc_start: 0.9006 (t) cc_final: 0.8648 (m) outliers start: 42 outliers final: 21 residues processed: 185 average time/residue: 0.5485 time to fit residues: 107.4474 Evaluate side-chains 164 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113658 restraints weight = 9637.040| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.90 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8670 Z= 0.146 Angle : 0.516 6.612 11747 Z= 0.276 Chirality : 0.040 0.136 1330 Planarity : 0.004 0.041 1447 Dihedral : 5.844 57.865 1272 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.14 % Allowed : 18.48 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1021 helix: 2.40 (0.24), residues: 431 sheet: -0.01 (0.31), residues: 217 loop : -0.24 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.020 0.001 TYR N 95 PHE 0.020 0.001 PHE R 288 TRP 0.016 0.002 TRP R 80 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8667) covalent geometry : angle 0.51616 / 0.28 (11741) SS BOND : bond 0.00128 / 0.06 ( 3) SS BOND : angle 0.94960 / 0.60 ( 6) hydrogen bonds : bond 0.04363 / 2.98 ( 462) hydrogen bonds : angle 4.84666 / 3.80 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.333 Fit side-chains REVERT: R 50 ARG cc_start: 0.6757 (mmt90) cc_final: 0.5925 (tpm170) REVERT: R 57 LYS cc_start: 0.7359 (mttt) cc_final: 0.6960 (mtmm) REVERT: R 92 PHE cc_start: 0.3900 (m-80) cc_final: 0.3331 (m-80) REVERT: R 213 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8379 (p) REVERT: R 219 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7466 (mtt-85) REVERT: R 223 LYS cc_start: 0.8154 (mttt) cc_final: 0.7886 (mtpt) REVERT: R 265 LYS cc_start: 0.7595 (tttt) cc_final: 0.7266 (tmtm) REVERT: A 17 LYS cc_start: 0.7356 (tttt) cc_final: 0.6603 (mmmt) REVERT: A 265 ARG cc_start: 0.7781 (ptt180) cc_final: 0.7566 (ppt-90) REVERT: A 299 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: A 307 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.4169 (mtmm) REVERT: A 314 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: A 356 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7228 (mtm110) REVERT: A 370 GLU cc_start: 0.7742 (pm20) cc_final: 0.7006 (mm-30) REVERT: A 378 ASP cc_start: 0.8401 (m-30) cc_final: 0.8035 (m-30) REVERT: A 386 MET cc_start: 0.8912 (ttm) cc_final: 0.8616 (ttp) REVERT: B 32 GLN cc_start: 0.8497 (mt0) cc_final: 0.8271 (mt0) REVERT: N 3 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: N 5 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7317 (tm-30) REVERT: N 110 VAL cc_start: 0.9014 (t) cc_final: 0.8695 (m) outliers start: 37 outliers final: 21 residues processed: 169 average time/residue: 0.6185 time to fit residues: 110.7573 Evaluate side-chains 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 164 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113900 restraints weight = 9816.281| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.98 r_work: 0.3115 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8670 Z= 0.141 Angle : 0.510 6.113 11747 Z= 0.273 Chirality : 0.040 0.136 1330 Planarity : 0.004 0.039 1447 Dihedral : 5.538 58.436 1272 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.81 % Allowed : 19.04 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1021 helix: 2.45 (0.24), residues: 431 sheet: -0.05 (0.31), residues: 216 loop : -0.24 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 356 TYR 0.015 0.001 TYR N 95 PHE 0.021 0.001 PHE R 288 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8667) covalent geometry : angle 0.50993 / 0.27 (11741) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.90175 / 0.57 ( 6) hydrogen bonds : bond 0.04273 / 2.91 ( 462) hydrogen bonds : angle 4.80219 / 3.75 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.326 Fit side-chains REVERT: R 50 ARG cc_start: 0.6710 (mmt90) cc_final: 0.5940 (tpm170) REVERT: R 57 LYS cc_start: 0.7396 (mttt) cc_final: 0.7059 (mtmm) REVERT: R 92 PHE cc_start: 0.3967 (m-80) cc_final: 0.3360 (m-80) REVERT: R 134 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8092 (mmmm) REVERT: R 213 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8426 (p) REVERT: R 219 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7517 (mtt-85) REVERT: R 223 LYS cc_start: 0.8233 (mttt) cc_final: 0.7970 (mtpt) REVERT: R 265 LYS cc_start: 0.7611 (tttt) cc_final: 0.7279 (tmtm) REVERT: A 17 LYS cc_start: 0.7389 (tttt) cc_final: 0.6645 (mmmt) REVERT: A 265 ARG cc_start: 0.7806 (ptt180) cc_final: 0.7599 (ppt-90) REVERT: A 307 LYS cc_start: 0.4594 (OUTLIER) cc_final: 0.4156 (mtmm) REVERT: A 314 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 356 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7278 (mtm110) REVERT: A 370 GLU cc_start: 0.7771 (pm20) cc_final: 0.7009 (mm-30) REVERT: A 378 ASP cc_start: 0.8439 (m-30) cc_final: 0.8108 (m-30) REVERT: A 386 MET cc_start: 0.8948 (ttm) cc_final: 0.8660 (ttp) REVERT: N 3 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: N 5 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7244 (tm-30) REVERT: N 110 VAL cc_start: 0.9070 (t) cc_final: 0.8783 (m) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 0.6285 time to fit residues: 105.9398 Evaluate side-chains 156 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.148265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112898 restraints weight = 9700.992| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.97 r_work: 0.3099 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8670 Z= 0.144 Angle : 0.512 6.223 11747 Z= 0.273 Chirality : 0.040 0.135 1330 Planarity : 0.004 0.046 1447 Dihedral : 5.507 58.680 1272 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.92 % Allowed : 19.26 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1021 helix: 2.33 (0.24), residues: 437 sheet: -0.11 (0.32), residues: 216 loop : -0.30 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 19 TYR 0.013 0.001 TYR N 95 PHE 0.020 0.001 PHE R 288 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8667) covalent geometry : angle 0.51140 / 0.27 (11741) SS BOND : bond 0.00060 / 0.03 ( 3) SS BOND : angle 0.94830 / 0.60 ( 6) hydrogen bonds : bond 0.04253 / 2.89 ( 462) hydrogen bonds : angle 4.81345 / 3.76 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.325 Fit side-chains REVERT: R 36 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8416 (m) REVERT: R 50 ARG cc_start: 0.6754 (mmt90) cc_final: 0.5944 (tpm170) REVERT: R 57 LYS cc_start: 0.7450 (mttt) cc_final: 0.7049 (mtmm) REVERT: R 92 PHE cc_start: 0.3979 (m-80) cc_final: 0.3372 (m-80) REVERT: R 213 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8641 (m) REVERT: R 219 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7515 (mtt-85) REVERT: R 223 LYS cc_start: 0.8231 (mttt) cc_final: 0.7972 (mtpt) REVERT: R 265 LYS cc_start: 0.7604 (tttt) cc_final: 0.7266 (tmtm) REVERT: R 278 MET cc_start: 0.8719 (mmm) cc_final: 0.8512 (mmm) REVERT: A 17 LYS cc_start: 0.7480 (tttt) cc_final: 0.6688 (mmmt) REVERT: A 299 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: A 307 LYS cc_start: 0.4607 (OUTLIER) cc_final: 0.4322 (mtmm) REVERT: A 314 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: A 356 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7357 (mtm110) REVERT: A 378 ASP cc_start: 0.8429 (m-30) cc_final: 0.8098 (m-30) REVERT: A 386 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (ttp) REVERT: B 19 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7804 (ttm-80) REVERT: N 3 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: N 5 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7200 (tm-30) REVERT: N 110 VAL cc_start: 0.9065 (t) cc_final: 0.8790 (m) outliers start: 35 outliers final: 24 residues processed: 162 average time/residue: 0.5927 time to fit residues: 102.0211 Evaluate side-chains 163 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111548 restraints weight = 9744.753| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.97 r_work: 0.3111 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8670 Z= 0.160 Angle : 0.526 6.689 11747 Z= 0.281 Chirality : 0.040 0.146 1330 Planarity : 0.004 0.046 1447 Dihedral : 5.532 58.291 1272 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.47 % Allowed : 20.16 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.26), residues: 1021 helix: 2.25 (0.24), residues: 439 sheet: -0.20 (0.31), residues: 227 loop : -0.22 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.014 0.001 TYR N 95 PHE 0.021 0.002 PHE R 288 TRP 0.014 0.002 TRP R 80 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 8667) covalent geometry : angle 0.52574 / 0.28 (11741) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 1.10866 / 0.70 ( 6) hydrogen bonds : bond 0.04332 / 2.94 ( 462) hydrogen bonds : angle 4.84841 / 3.79 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.347 Fit side-chains REVERT: R 36 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8427 (m) REVERT: R 50 ARG cc_start: 0.6738 (mmt90) cc_final: 0.5920 (tpm170) REVERT: R 57 LYS cc_start: 0.7480 (mttt) cc_final: 0.7112 (mtmm) REVERT: R 92 PHE cc_start: 0.4033 (m-80) cc_final: 0.3460 (m-80) REVERT: R 134 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8037 (mmmm) REVERT: R 213 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8439 (p) REVERT: R 219 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7583 (mtt-85) REVERT: R 223 LYS cc_start: 0.8232 (mttt) cc_final: 0.7985 (mtpt) REVERT: R 265 LYS cc_start: 0.7603 (tttt) cc_final: 0.7259 (tmtm) REVERT: R 269 LYS cc_start: 0.8160 (tttt) cc_final: 0.7901 (tttp) REVERT: R 278 MET cc_start: 0.8729 (mmm) cc_final: 0.8470 (mmm) REVERT: A 17 LYS cc_start: 0.7459 (tttt) cc_final: 0.6654 (mmmt) REVERT: A 299 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: A 307 LYS cc_start: 0.4713 (OUTLIER) cc_final: 0.4428 (mtmm) REVERT: A 314 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: A 356 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7493 (mtm110) REVERT: A 378 ASP cc_start: 0.8451 (m-30) cc_final: 0.8082 (m-30) REVERT: A 386 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8648 (ttp) REVERT: B 32 GLN cc_start: 0.8489 (mt0) cc_final: 0.8259 (mt0) REVERT: N 3 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: N 5 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7172 (tm-30) REVERT: N 110 VAL cc_start: 0.9057 (t) cc_final: 0.8793 (m) outliers start: 31 outliers final: 23 residues processed: 154 average time/residue: 0.6188 time to fit residues: 100.9436 Evaluate side-chains 161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111852 restraints weight = 9700.076| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.97 r_work: 0.3092 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8670 Z= 0.157 Angle : 0.525 7.070 11747 Z= 0.280 Chirality : 0.040 0.145 1330 Planarity : 0.004 0.043 1447 Dihedral : 5.560 58.373 1272 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.47 % Allowed : 20.49 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1021 helix: 2.21 (0.24), residues: 440 sheet: -0.29 (0.31), residues: 227 loop : -0.21 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.014 0.001 TYR N 95 PHE 0.021 0.002 PHE R 288 TRP 0.016 0.002 TRP R 80 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8667) covalent geometry : angle 0.52443 / 0.28 (11741) SS BOND : bond 0.00043 / 0.02 ( 3) SS BOND : angle 1.08397 / 0.69 ( 6) hydrogen bonds : bond 0.04319 / 2.93 ( 462) hydrogen bonds : angle 4.87647 / 3.81 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.333 Fit side-chains REVERT: R 36 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8446 (m) REVERT: R 50 ARG cc_start: 0.6738 (mmt90) cc_final: 0.5885 (tpm170) REVERT: R 57 LYS cc_start: 0.7556 (mttt) cc_final: 0.7106 (mtmm) REVERT: R 92 PHE cc_start: 0.4056 (m-80) cc_final: 0.3475 (m-80) REVERT: R 213 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8427 (p) REVERT: R 219 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7536 (mtt-85) REVERT: R 223 LYS cc_start: 0.8236 (mttt) cc_final: 0.7992 (mtpt) REVERT: R 265 LYS cc_start: 0.7653 (tttt) cc_final: 0.7292 (tmtm) REVERT: R 269 LYS cc_start: 0.8196 (tttt) cc_final: 0.7923 (tttp) REVERT: R 278 MET cc_start: 0.8732 (mmm) cc_final: 0.8514 (mmm) REVERT: A 17 LYS cc_start: 0.7455 (tttt) cc_final: 0.6656 (mmmt) REVERT: A 299 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: A 307 LYS cc_start: 0.4718 (mtpm) cc_final: 0.4392 (mtmm) REVERT: A 314 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: A 356 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7566 (mtm110) REVERT: A 378 ASP cc_start: 0.8527 (m-30) cc_final: 0.8160 (m-30) REVERT: A 386 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8648 (ttp) REVERT: B 32 GLN cc_start: 0.8501 (mt0) cc_final: 0.8265 (mt0) REVERT: N 3 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: N 5 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7200 (tm-30) REVERT: N 110 VAL cc_start: 0.9041 (t) cc_final: 0.8781 (m) outliers start: 31 outliers final: 23 residues processed: 152 average time/residue: 0.6473 time to fit residues: 104.0740 Evaluate side-chains 160 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.149058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114100 restraints weight = 9735.127| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3127 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8670 Z= 0.135 Angle : 0.518 7.044 11747 Z= 0.275 Chirality : 0.039 0.140 1330 Planarity : 0.004 0.039 1447 Dihedral : 5.341 59.157 1272 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.47 % Allowed : 20.38 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1021 helix: 2.42 (0.24), residues: 433 sheet: -0.31 (0.32), residues: 221 loop : -0.18 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.013 0.001 TYR N 95 PHE 0.019 0.001 PHE R 288 TRP 0.015 0.002 TRP R 80 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8667) covalent geometry : angle 0.51781 / 0.27 (11741) SS BOND : bond 0.00040 / 0.02 ( 3) SS BOND : angle 0.98054 / 0.63 ( 6) hydrogen bonds : bond 0.04170 / 2.83 ( 462) hydrogen bonds : angle 4.80313 / 3.74 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.28 seconds wall clock time: 57 minutes 58.08 seconds (3478.08 seconds total)