Starting phenix.real_space_refine on Thu Jul 2 06:10:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.map" model { file = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2z_30973/07_2026/7e2z_30973.cif" } resolution = 3.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 53 5.16 5 Cl 2 4.86 5 C 4494 2.51 5 N 1172 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 6997 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2516 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 171 Unusual residues: {'9SC': 1, 'CLR': 3, 'J40': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.47, per 1000 atoms: 0.21 Number of scatterers: 6997 At special positions: 0 Unit cell: (77.064, 115.596, 112.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 53 16.00 P 2 15.00 O 1274 8.00 N 1172 7.00 C 4494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 0.59 Conformation dependent library (CDL) restraints added in 330.9 milliseconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 49.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.734A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.296A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.229A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 232' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.712A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.815A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.803A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.953A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.220A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 3.772A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.697A 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 19 through 23 removed outlier: 3.828A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 19 through 23' Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.941A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 removed outlier: 3.726A pdb=" N LEU R 74 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.682A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 146 Processing helix chain 'R' and resid 149 through 175 removed outlier: 3.926A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.660A pdb=" N PHE R 354 " --> pdb=" O ILE R 350 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 369 through 375 removed outlier: 4.672A pdb=" N GLU R 372 " --> pdb=" O PRO R 369 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER R 373 " --> pdb=" O PHE R 370 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 374 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS R 375 " --> pdb=" O GLU R 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 369 through 375' Processing helix chain 'R' and resid 378 through 391 Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.669A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.544A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.010A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.548A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.907A 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: 4.392A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.746A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.693A 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: 3.780A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.843A 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: 3.962A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1104 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: 0.71 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1116 1.31 - 1.44: 1890 1.44 - 1.56: 4042 1.56 - 1.69: 18 1.69 - 1.82: 76 Bond restraints: 7142 Sorted by residual: bond pdb=" C19 9SC R 501 " pdb=" N3 9SC R 501 " ideal model delta sigma weight residual 1.395 1.650 -0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C18 J40 R 505 " pdb=" C19 J40 R 505 " ideal model delta sigma weight residual 1.330 1.528 -0.198 2.00e-02 2.50e+03 9.76e+01 bond pdb=" C15 J40 R 505 " pdb=" C16 J40 R 505 " ideal model delta sigma weight residual 1.329 1.527 -0.198 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C24 J40 R 505 " pdb=" C25 J40 R 505 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C21 J40 R 505 " pdb=" C22 J40 R 505 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 7137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 9582 3.53 - 7.05: 75 7.05 - 10.58: 11 10.58 - 14.10: 10 14.10 - 17.63: 4 Bond angle restraints: 9682 Sorted by residual: angle pdb=" O11 J40 R 505 " pdb=" P1 J40 R 505 " pdb=" O12 J40 R 505 " ideal model delta sigma weight residual 119.00 101.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" O1 J40 R 505 " pdb=" P1 J40 R 505 " pdb=" O13 J40 R 505 " ideal model delta sigma weight residual 92.86 109.69 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C24 J40 R 505 " pdb=" C25 J40 R 505 " pdb=" C26 J40 R 505 " ideal model delta sigma weight residual 127.60 113.29 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C23 J40 R 505 " pdb=" C24 J40 R 505 " pdb=" C25 J40 R 505 " ideal model delta sigma weight residual 127.40 113.24 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C21 J40 R 505 " pdb=" C22 J40 R 505 " pdb=" C23 J40 R 505 " ideal model delta sigma weight residual 126.99 113.07 13.92 3.00e+00 1.11e-01 2.15e+01 ... (remaining 9677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 4041 23.97 - 47.93: 198 47.93 - 71.90: 25 71.90 - 95.87: 6 95.87 - 119.83: 1 Dihedral angle restraints: 4271 sinusoidal: 1740 harmonic: 2531 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 133.58 -40.58 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C12 9SC R 501 " pdb=" C11 9SC R 501 " pdb=" N2 9SC R 501 " pdb=" C8 9SC R 501 " ideal model delta sinusoidal sigma weight residual -165.81 -45.98 -119.83 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CB LYS A 46 " pdb=" CG LYS A 46 " pdb=" CD LYS A 46 " pdb=" CE LYS A 46 " ideal model delta sinusoidal sigma weight residual -180.00 -126.35 -53.65 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 848 0.044 - 0.088: 192 0.088 - 0.132: 64 0.132 - 0.176: 5 0.176 - 0.220: 7 Chirality restraints: 1116 Sorted by residual: 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 -2.54 0.22 2.00e-01 2.50e+01 1.21e+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 -2.53 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C14 CLR R 502 " pdb=" C13 CLR R 502 " pdb=" C15 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1113 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 505 " 0.138 2.00e-02 2.50e+03 2.37e-01 5.63e+02 pdb=" C21 J40 R 505 " -0.306 2.00e-02 2.50e+03 pdb=" C22 J40 R 505 " 0.306 2.00e-02 2.50e+03 pdb=" C23 J40 R 505 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 505 " -0.136 2.00e-02 2.50e+03 2.32e-01 5.39e+02 pdb=" C24 J40 R 505 " 0.299 2.00e-02 2.50e+03 pdb=" C25 J40 R 505 " -0.299 2.00e-02 2.50e+03 pdb=" C26 J40 R 505 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 J40 R 505 " -0.146 2.00e-02 2.50e+03 1.46e-01 2.14e+02 pdb=" C18 J40 R 505 " 0.146 2.00e-02 2.50e+03 pdb=" C19 J40 R 505 " 0.147 2.00e-02 2.50e+03 pdb=" C20 J40 R 505 " -0.146 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 154 2.71 - 3.26: 6772 3.26 - 3.80: 10881 3.80 - 4.35: 13669 4.35 - 4.90: 23560 Nonbonded interactions: 55036 Sorted by model distance: nonbonded pdb=" O PHE R 403 " pdb=" O2 J40 R 505 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN B 119 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.314 3.040 nonbonded pdb=" NH1 ARG B 22 " pdb=" O ASP B 258 " model vdw 2.324 3.120 ... (remaining 55031 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.530 Find NCS groups from input model: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.009 0.255 7144 Z= 0.459 Angle : 0.876 17.627 9686 Z= 0.375 Chirality : 0.043 0.220 1116 Planarity : 0.011 0.237 1192 Dihedral : 13.906 119.832 2623 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: 2.35 (0.30), residues: 854 helix: 3.25 (0.27), residues: 384 sheet: 1.29 (0.41), residues: 154 loop : -0.52 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 333 TYR 0.018 0.001 TYR A 230 PHE 0.009 0.001 PHE R 48 TRP 0.020 0.001 TRP B 211 HIS 0.001 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00912 / 0.46 ( 7142) covalent geometry : angle 0.87559 / 0.38 ( 9682) SS BOND : bond 0.00436 / 0.22 ( 2) SS BOND : angle 0.77316 / 0.42 ( 4) hydrogen bonds : bond 0.11627 / 7.56 ( 382) hydrogen bonds : angle 4.98357 / 3.52 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.278 Fit side-chains REVERT: A 14 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5270 (mm-30) REVERT: A 21 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7080 (ttm110) REVERT: B 67 SER cc_start: 0.8260 (m) cc_final: 0.7901 (t) REVERT: B 161 SER cc_start: 0.8781 (t) cc_final: 0.8285 (m) REVERT: B 331 SER cc_start: 0.8426 (t) cc_final: 0.8147 (t) REVERT: R 387 TRP cc_start: 0.6930 (m100) cc_final: 0.6443 (m100) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1094 time to fit residues: 15.8079 Evaluate side-chains 91 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149543 restraints weight = 7689.447| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.19 r_work: 0.3683 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7144 Z= 0.122 Angle : 0.529 9.056 9686 Z= 0.269 Chirality : 0.041 0.137 1116 Planarity : 0.003 0.031 1192 Dihedral : 9.186 127.777 1052 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.81 % Allowed : 7.56 % Favored : 91.63 % 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: 2.30 (0.30), residues: 854 helix: 3.29 (0.27), residues: 378 sheet: 1.07 (0.40), residues: 165 loop : -0.53 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.011 0.001 TYR R 195 PHE 0.012 0.002 PHE B 292 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7142) covalent geometry : angle 0.52845 / 0.27 ( 9682) SS BOND : bond 0.01040 / 0.54 ( 2) SS BOND : angle 1.14496 / 0.66 ( 4) hydrogen bonds : bond 0.03599 / 2.42 ( 382) hydrogen bonds : angle 4.04529 / 2.84 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.292 Fit side-chains REVERT: A 269 ASN cc_start: 0.8785 (m110) cc_final: 0.8466 (m110) REVERT: B 67 SER cc_start: 0.8624 (m) cc_final: 0.8298 (t) REVERT: B 119 ASN cc_start: 0.6846 (m110) cc_final: 0.6488 (m-40) REVERT: B 217 MET cc_start: 0.6594 (ppp) cc_final: 0.6262 (ppp) REVERT: B 322 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: G 46 LYS cc_start: 0.7750 (ptpp) cc_final: 0.7542 (ptmt) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.0935 time to fit residues: 12.9465 Evaluate side-chains 94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 269 ASN A 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.165946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125725 restraints weight = 7842.236| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.21 r_work: 0.3487 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7144 Z= 0.170 Angle : 0.596 10.013 9686 Z= 0.303 Chirality : 0.042 0.164 1116 Planarity : 0.004 0.035 1192 Dihedral : 9.225 136.901 1052 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.83 % Allowed : 9.45 % Favored : 87.72 % 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: 1.96 (0.29), residues: 854 helix: 2.91 (0.27), residues: 377 sheet: 1.05 (0.40), residues: 167 loop : -0.65 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.013 0.002 TYR A 230 PHE 0.017 0.002 PHE R 407 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7142) covalent geometry : angle 0.59571 / 0.30 ( 9682) SS BOND : bond 0.01378 / 0.72 ( 2) SS BOND : angle 1.29889 / 0.80 ( 4) hydrogen bonds : bond 0.04452 / 3.03 ( 382) hydrogen bonds : angle 4.31009 / 3.05 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8965 (ttm) cc_final: 0.8707 (ttp) REVERT: A 269 ASN cc_start: 0.8817 (m-40) cc_final: 0.8609 (m110) REVERT: A 306 GLN cc_start: 0.8281 (mm-40) cc_final: 0.8063 (mm-40) REVERT: B 67 SER cc_start: 0.8688 (m) cc_final: 0.8392 (t) REVERT: B 111 TYR cc_start: 0.8447 (m-10) cc_final: 0.8192 (m-80) REVERT: B 234 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: B 322 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: G 46 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7429 (ptmt) REVERT: R 95 LEU cc_start: 0.7848 (tt) cc_final: 0.7553 (tp) outliers start: 21 outliers final: 7 residues processed: 116 average time/residue: 0.0890 time to fit residues: 13.8327 Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146599 restraints weight = 7532.014| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.98 r_work: 0.3640 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7144 Z= 0.104 Angle : 0.495 8.041 9686 Z= 0.255 Chirality : 0.039 0.143 1116 Planarity : 0.003 0.035 1192 Dihedral : 9.021 136.021 1052 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.29 % Allowed : 12.42 % Favored : 85.29 % 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: 2.01 (0.29), residues: 854 helix: 3.02 (0.27), residues: 378 sheet: 0.78 (0.39), residues: 170 loop : -0.56 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.012 0.001 TYR A 230 PHE 0.009 0.001 PHE R 362 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 7142) covalent geometry : angle 0.49522 / 0.25 ( 9682) SS BOND : bond 0.00847 / 0.44 ( 2) SS BOND : angle 0.84758 / 0.48 ( 4) hydrogen bonds : bond 0.03428 / 2.33 ( 382) hydrogen bonds : angle 4.01701 / 2.84 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8925 (ttm) cc_final: 0.8644 (ttp) REVERT: B 58 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8332 (pt) REVERT: B 234 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: R 95 LEU cc_start: 0.7897 (tt) cc_final: 0.7622 (tp) REVERT: R 147 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8216 (mmtt) outliers start: 17 outliers final: 8 residues processed: 110 average time/residue: 0.0889 time to fit residues: 13.1391 Evaluate side-chains 98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 223 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123624 restraints weight = 8014.874| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.22 r_work: 0.3330 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7144 Z= 0.180 Angle : 0.589 10.176 9686 Z= 0.298 Chirality : 0.042 0.164 1116 Planarity : 0.003 0.037 1192 Dihedral : 8.922 140.383 1052 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.10 % Allowed : 13.09 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.29), residues: 854 helix: 2.81 (0.27), residues: 377 sheet: 0.71 (0.38), residues: 175 loop : -0.72 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 27 TYR 0.013 0.001 TYR R 195 PHE 0.013 0.002 PHE B 278 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 7142) covalent geometry : angle 0.58890 / 0.30 ( 9682) SS BOND : bond 0.01502 / 0.79 ( 2) SS BOND : angle 1.25086 / 0.76 ( 4) hydrogen bonds : bond 0.04315 / 2.92 ( 382) hydrogen bonds : angle 4.26166 / 3.00 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8950 (ttm) cc_final: 0.8632 (ttp) REVERT: B 58 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8280 (pt) REVERT: B 234 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: B 322 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: R 95 LEU cc_start: 0.7662 (tt) cc_final: 0.7399 (tp) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.0925 time to fit residues: 13.1871 Evaluate side-chains 110 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 overall best weight: 0.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.181963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142448 restraints weight = 7814.356| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.18 r_work: 0.3606 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7144 Z= 0.105 Angle : 0.506 8.121 9686 Z= 0.258 Chirality : 0.039 0.139 1116 Planarity : 0.003 0.036 1192 Dihedral : 8.588 137.030 1052 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.83 % Allowed : 13.90 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.29), residues: 854 helix: 2.89 (0.27), residues: 384 sheet: 0.78 (0.39), residues: 169 loop : -0.71 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.011 0.001 TYR A 230 PHE 0.009 0.001 PHE R 362 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7142) covalent geometry : angle 0.50569 / 0.26 ( 9682) SS BOND : bond 0.00801 / 0.42 ( 2) SS BOND : angle 0.58135 / 0.33 ( 4) hydrogen bonds : bond 0.03445 / 2.35 ( 382) hydrogen bonds : angle 4.00224 / 2.83 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8965 (ttm) cc_final: 0.8667 (ttp) REVERT: A 346 ASN cc_start: 0.8334 (m-40) cc_final: 0.8035 (m110) REVERT: B 58 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8348 (pt) REVERT: B 234 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: R 95 LEU cc_start: 0.7943 (tt) cc_final: 0.7675 (tp) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.0820 time to fit residues: 11.5794 Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143524 restraints weight = 7748.483| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.16 r_work: 0.3620 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7144 Z= 0.098 Angle : 0.502 8.634 9686 Z= 0.254 Chirality : 0.039 0.136 1116 Planarity : 0.003 0.035 1192 Dihedral : 8.393 135.553 1052 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.51 % Allowed : 13.63 % Favored : 82.86 % 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: 2.01 (0.30), residues: 854 helix: 3.07 (0.27), residues: 378 sheet: 0.67 (0.40), residues: 169 loop : -0.56 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.013 0.001 TYR A 230 PHE 0.008 0.001 PHE R 354 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7142) covalent geometry : angle 0.50190 / 0.25 ( 9682) SS BOND : bond 0.00773 / 0.41 ( 2) SS BOND : angle 0.42761 / 0.25 ( 4) hydrogen bonds : bond 0.03240 / 2.21 ( 382) hydrogen bonds : angle 3.91273 / 2.77 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8975 (ttm) cc_final: 0.8685 (ttp) REVERT: A 231 ASP cc_start: 0.7694 (p0) cc_final: 0.7420 (p0) REVERT: A 346 ASN cc_start: 0.8312 (m-40) cc_final: 0.7972 (m110) REVERT: B 58 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8298 (pt) REVERT: B 234 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: R 95 LEU cc_start: 0.7878 (tt) cc_final: 0.7610 (tp) outliers start: 26 outliers final: 19 residues processed: 112 average time/residue: 0.0712 time to fit residues: 10.6551 Evaluate side-chains 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.183068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143767 restraints weight = 7758.413| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.15 r_work: 0.3622 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7144 Z= 0.099 Angle : 0.506 8.180 9686 Z= 0.254 Chirality : 0.039 0.137 1116 Planarity : 0.003 0.034 1192 Dihedral : 8.299 135.574 1052 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.24 % Allowed : 14.71 % Favored : 82.05 % 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: 2.02 (0.30), residues: 854 helix: 3.06 (0.27), residues: 381 sheet: 0.83 (0.40), residues: 163 loop : -0.63 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.012 0.001 TYR A 230 PHE 0.007 0.001 PHE R 362 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 7142) covalent geometry : angle 0.50547 / 0.25 ( 9682) SS BOND : bond 0.00642 / 0.34 ( 2) SS BOND : angle 0.64064 / 0.33 ( 4) hydrogen bonds : bond 0.03233 / 2.20 ( 382) hydrogen bonds : angle 3.90029 / 2.75 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.250 Fit side-chains REVERT: A 198 MET cc_start: 0.8999 (ttm) cc_final: 0.8713 (ttp) REVERT: A 346 ASN cc_start: 0.8285 (m-40) cc_final: 0.7915 (m110) REVERT: B 58 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8287 (pt) REVERT: B 234 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: R 95 LEU cc_start: 0.7849 (tt) cc_final: 0.7569 (tp) outliers start: 24 outliers final: 20 residues processed: 109 average time/residue: 0.0765 time to fit residues: 11.2522 Evaluate side-chains 115 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.182362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142939 restraints weight = 7788.835| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.17 r_work: 0.3612 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7144 Z= 0.107 Angle : 0.520 10.731 9686 Z= 0.260 Chirality : 0.039 0.145 1116 Planarity : 0.003 0.033 1192 Dihedral : 8.268 135.749 1052 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.24 % Allowed : 14.30 % Favored : 82.46 % 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: 2.04 (0.29), residues: 854 helix: 3.14 (0.27), residues: 376 sheet: 0.88 (0.40), residues: 162 loop : -0.67 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.013 0.001 TYR A 230 PHE 0.008 0.001 PHE R 362 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7142) covalent geometry : angle 0.51947 / 0.26 ( 9682) SS BOND : bond 0.00907 / 0.48 ( 2) SS BOND : angle 0.76760 / 0.40 ( 4) hydrogen bonds : bond 0.03351 / 2.28 ( 382) hydrogen bonds : angle 3.91207 / 2.76 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8987 (ttm) cc_final: 0.8688 (ttp) REVERT: B 58 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8327 (pt) REVERT: B 234 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: G 38 MET cc_start: 0.5838 (mtp) cc_final: 0.5597 (mtt) REVERT: R 95 LEU cc_start: 0.7856 (tt) cc_final: 0.7573 (tp) outliers start: 24 outliers final: 21 residues processed: 107 average time/residue: 0.0761 time to fit residues: 11.1139 Evaluate side-chains 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141399 restraints weight = 7717.825| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.14 r_work: 0.3615 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7144 Z= 0.106 Angle : 0.515 8.113 9686 Z= 0.259 Chirality : 0.039 0.142 1116 Planarity : 0.003 0.033 1192 Dihedral : 8.235 135.317 1052 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.10 % Allowed : 14.30 % Favored : 82.59 % 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: 2.02 (0.29), residues: 854 helix: 3.11 (0.27), residues: 376 sheet: 0.80 (0.40), residues: 164 loop : -0.63 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.014 0.001 TYR A 230 PHE 0.007 0.001 PHE R 362 TRP 0.010 0.001 TRP R 387 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7142) covalent geometry : angle 0.51484 / 0.26 ( 9682) SS BOND : bond 0.00872 / 0.46 ( 2) SS BOND : angle 1.09217 / 0.61 ( 4) hydrogen bonds : bond 0.03345 / 2.27 ( 382) hydrogen bonds : angle 3.90981 / 2.75 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7126 (ttm110) REVERT: A 198 MET cc_start: 0.8990 (ttm) cc_final: 0.8704 (ttp) REVERT: B 58 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8329 (pt) REVERT: B 234 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: G 38 MET cc_start: 0.5743 (mtp) cc_final: 0.5490 (mtt) REVERT: R 95 LEU cc_start: 0.7860 (tt) cc_final: 0.7573 (tp) outliers start: 23 outliers final: 20 residues processed: 105 average time/residue: 0.0736 time to fit residues: 10.4853 Evaluate side-chains 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 100 ASN Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.183029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143954 restraints weight = 7633.797| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.13 r_work: 0.3625 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7144 Z= 0.100 Angle : 0.510 7.919 9686 Z= 0.256 Chirality : 0.039 0.140 1116 Planarity : 0.003 0.033 1192 Dihedral : 8.175 134.941 1052 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.24 % Allowed : 14.04 % Favored : 82.73 % 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: 2.09 (0.29), residues: 854 helix: 3.26 (0.27), residues: 370 sheet: 0.78 (0.40), residues: 165 loop : -0.61 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 27 TYR 0.014 0.001 TYR A 230 PHE 0.008 0.001 PHE R 362 TRP 0.010 0.001 TRP R 387 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7142) covalent geometry : angle 0.50976 / 0.26 ( 9682) SS BOND : bond 0.00817 / 0.43 ( 2) SS BOND : angle 1.01373 / 0.55 ( 4) hydrogen bonds : bond 0.03244 / 2.20 ( 382) hydrogen bonds : angle 3.87789 / 2.73 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.63 seconds wall clock time: 33 minutes 15.66 seconds (1995.66 seconds total)