Starting phenix.real_space_refine on Thu Jul 2 05:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e2y_30972/07_2026/7e2y_30972.map" } resolution = 3.0 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= 0.006 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 P 2 5.49 5 S 53 5.16 5 C 4492 2.51 5 N 1168 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s 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: 6987 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: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2176 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 2 Chain: "R" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 182 Unusual residues: {'CLR': 4, 'J40': 1, 'SRO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 6987 At special positions: 0 Unit cell: (77.064, 112.554, 113.568, 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) S 53 16.00 P 2 15.00 O 1272 8.00 N 1168 7.00 C 4492 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: 0.41 Conformation dependent library (CDL) restraints added in 263.7 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 48.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.761A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.501A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.048A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.565A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 3.954A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 36 removed outlier: 3.938A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.850A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.575A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.748A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 36 through 64 removed outlier: 3.539A pdb=" N LEU R 42 " --> pdb=" O ILE R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 100 removed outlier: 4.260A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 104 through 140 removed outlier: 4.112A pdb=" N THR R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 111 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 174 removed outlier: 3.996A 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 removed outlier: 3.745A pdb=" N LEU R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.677A 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 371 No H-bonds generated for 'chain 'R' and resid 369 through 371' Processing helix chain 'R' and resid 378 through 392 removed outlier: 3.937A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 401 Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.287A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.902A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.021A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.812A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.557A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.133A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.781A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.744A 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: 6.738A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1053 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: 0.91 Time building geometry restraints manager: 0.52 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: 1115 1.31 - 1.44: 1873 1.44 - 1.57: 4054 1.57 - 1.70: 14 1.70 - 1.82: 74 Bond restraints: 7130 Sorted by residual: bond pdb=" C15 J40 R 502 " pdb=" C16 J40 R 502 " ideal model delta sigma weight residual 1.329 1.527 -0.198 2.00e-02 2.50e+03 9.78e+01 bond pdb=" C18 J40 R 502 " pdb=" C19 J40 R 502 " ideal model delta sigma weight residual 1.330 1.528 -0.198 2.00e-02 2.50e+03 9.76e+01 bond pdb=" C21 J40 R 502 " pdb=" C22 J40 R 502 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C24 J40 R 502 " pdb=" C25 J40 R 502 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" CZ2 SRO R 501 " pdb=" CH2 SRO R 501 " ideal model delta sigma weight residual 1.386 1.521 -0.135 2.00e-02 2.50e+03 4.53e+01 ... (remaining 7125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 9581 3.56 - 7.13: 69 7.13 - 10.69: 9 10.69 - 14.26: 7 14.26 - 17.82: 4 Bond angle restraints: 9670 Sorted by residual: angle pdb=" O11 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O12 J40 R 502 " ideal model delta sigma weight residual 119.00 101.18 17.82 3.00e+00 1.11e-01 3.53e+01 angle pdb=" O1 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O13 J40 R 502 " ideal model delta sigma weight residual 92.86 110.57 -17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C24 J40 R 502 " pdb=" C25 J40 R 502 " pdb=" C26 J40 R 502 " ideal model delta sigma weight residual 127.60 112.97 14.63 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C23 J40 R 502 " pdb=" C24 J40 R 502 " pdb=" C25 J40 R 502 " ideal model delta sigma weight residual 127.40 112.95 14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C21 J40 R 502 " pdb=" C22 J40 R 502 " pdb=" C23 J40 R 502 " ideal model delta sigma weight residual 126.99 113.06 13.93 3.00e+00 1.11e-01 2.16e+01 ... (remaining 9665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 4244 20.92 - 41.84: 207 41.84 - 62.76: 19 62.76 - 83.68: 6 83.68 - 104.60: 4 Dihedral angle restraints: 4480 sinusoidal: 1955 harmonic: 2525 Sorted by residual: dihedral pdb=" C40 J40 R 502 " pdb=" C41 J40 R 502 " pdb=" C42 J40 R 502 " pdb=" C43 J40 R 502 " ideal model delta sinusoidal sigma weight residual 178.73 74.13 104.60 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" C21 J40 R 502 " pdb=" C22 J40 R 502 " pdb=" C23 J40 R 502 " pdb=" C24 J40 R 502 " ideal model delta sinusoidal sigma weight residual 103.24 16.92 86.32 1 3.00e+01 1.11e-03 9.98e+00 dihedral pdb=" CB MET B 188 " pdb=" CG MET B 188 " pdb=" SD MET B 188 " pdb=" CE MET B 188 " ideal model delta sinusoidal sigma weight residual 180.00 122.61 57.39 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 4477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 960 0.055 - 0.111: 124 0.111 - 0.166: 32 0.166 - 0.222: 2 0.222 - 0.277: 4 Chirality restraints: 1122 Sorted by residual: 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 -2.59 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.25 2.00e-01 2.50e+01 1.54e+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 -2.56 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1119 not shown) Planarity restraints: 1187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 J40 R 502 " 0.148 2.00e-02 2.50e+03 2.68e-01 7.18e+02 pdb=" C21 J40 R 502 " -0.349 2.00e-02 2.50e+03 pdb=" C22 J40 R 502 " 0.349 2.00e-02 2.50e+03 pdb=" C23 J40 R 502 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 J40 R 502 " -0.141 2.00e-02 2.50e+03 2.45e-01 5.99e+02 pdb=" C24 J40 R 502 " 0.316 2.00e-02 2.50e+03 pdb=" C25 J40 R 502 " -0.316 2.00e-02 2.50e+03 pdb=" C26 J40 R 502 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 J40 R 502 " 0.161 2.00e-02 2.50e+03 1.61e-01 2.58e+02 pdb=" C15 J40 R 502 " -0.161 2.00e-02 2.50e+03 pdb=" C16 J40 R 502 " -0.161 2.00e-02 2.50e+03 pdb=" C17 J40 R 502 " 0.161 2.00e-02 2.50e+03 ... (remaining 1184 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 81 2.62 - 3.19: 6243 3.19 - 3.76: 10198 3.76 - 4.33: 14178 4.33 - 4.90: 23753 Nonbonded interactions: 54453 Sorted by model distance: nonbonded pdb=" O43 J40 R 502 " pdb=" O5 J40 R 502 " model vdw 2.050 3.040 nonbonded pdb=" O11 J40 R 502 " pdb=" O6 J40 R 502 " model vdw 2.131 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.138 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" O THR B 221 " model vdw 2.165 3.120 nonbonded pdb=" O ASP A 272 " pdb=" OE1 GLU A 276 " model vdw 2.218 3.040 ... (remaining 54448 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: 0.440 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.030 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:5.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.008 0.198 7132 Z= 0.391 Angle : 0.822 17.823 9674 Z= 0.343 Chirality : 0.045 0.277 1122 Planarity : 0.012 0.268 1187 Dihedral : 12.222 104.603 2836 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.91 (0.30), residues: 852 helix: 2.99 (0.27), residues: 385 sheet: 0.55 (0.43), residues: 157 loop : -0.62 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.010 0.001 TYR R 144 PHE 0.009 0.001 PHE B 222 TRP 0.005 0.001 TRP R 358 HIS 0.003 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.39 ( 7130) covalent geometry : angle 0.82225 / 0.34 ( 9670) SS BOND : bond 0.00468 / 0.25 ( 2) SS BOND : angle 1.09093 / 0.50 ( 4) hydrogen bonds : bond 0.16638 / 11.11 ( 361) hydrogen bonds : angle 5.89214 / 4.20 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 293 ASN cc_start: 0.7047 (m110) cc_final: 0.6648 (p0) REVERT: B 298 ASP cc_start: 0.6967 (t70) cc_final: 0.6256 (t0) REVERT: R 386 ASN cc_start: 0.7577 (t0) cc_final: 0.7355 (t0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.4048 time to fit residues: 72.2023 Evaluate side-chains 136 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.213440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166311 restraints weight = 7648.563| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.59 r_work: 0.3865 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7132 Z= 0.130 Angle : 0.574 8.339 9674 Z= 0.290 Chirality : 0.042 0.163 1122 Planarity : 0.004 0.035 1187 Dihedral : 8.861 66.148 1270 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.25 % Allowed : 12.04 % Favored : 84.71 % 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: 1.54 (0.30), residues: 852 helix: 2.76 (0.27), residues: 388 sheet: 0.36 (0.43), residues: 155 loop : -0.94 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 227 TYR 0.014 0.001 TYR R 96 PHE 0.017 0.002 PHE R 224 TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7130) covalent geometry : angle 0.57341 / 0.29 ( 9670) SS BOND : bond 0.00967 / 0.50 ( 2) SS BOND : angle 1.65009 / 0.90 ( 4) hydrogen bonds : bond 0.03759 / 2.50 ( 361) hydrogen bonds : angle 4.39402 / 3.17 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7872 (ptp90) cc_final: 0.7316 (mtm-85) REVERT: A 330 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6621 (mppt) REVERT: A 349 LYS cc_start: 0.7126 (mttt) cc_final: 0.6911 (mttm) REVERT: B 134 ARG cc_start: 0.6947 (ptt90) cc_final: 0.6513 (ppt170) REVERT: B 219 ARG cc_start: 0.7262 (mmt90) cc_final: 0.7002 (mmt90) REVERT: B 266 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6772 (t-170) REVERT: B 293 ASN cc_start: 0.7082 (m110) cc_final: 0.6416 (p0) REVERT: B 298 ASP cc_start: 0.7400 (t70) cc_final: 0.7136 (t0) REVERT: B 335 PHE cc_start: 0.6792 (m-10) cc_final: 0.6428 (m-10) REVERT: R 377 MET cc_start: 0.7488 (pmm) cc_final: 0.5233 (ptm) outliers start: 24 outliers final: 7 residues processed: 153 average time/residue: 0.3625 time to fit residues: 59.0394 Evaluate side-chains 132 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.150284 restraints weight = 7644.820| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.55 r_work: 0.3680 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 7132 Z= 0.226 Angle : 0.683 8.059 9674 Z= 0.349 Chirality : 0.045 0.160 1122 Planarity : 0.004 0.052 1187 Dihedral : 8.493 75.242 1270 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.25 % Allowed : 13.80 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 852 helix: 2.07 (0.26), residues: 393 sheet: 0.05 (0.42), residues: 161 loop : -1.22 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.015 0.002 TYR A 320 PHE 0.024 0.003 PHE R 354 TRP 0.013 0.002 TRP B 99 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 ( 7130) covalent geometry : angle 0.68155 / 0.35 ( 9670) SS BOND : bond 0.01472 / 0.77 ( 2) SS BOND : angle 2.52798 / 1.26 ( 4) hydrogen bonds : bond 0.05117 / 3.37 ( 361) hydrogen bonds : angle 4.67074 / 3.40 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6314 (ttpp) cc_final: 0.6006 (pttm) REVERT: A 193 ASP cc_start: 0.6533 (t0) cc_final: 0.6268 (t0) REVERT: A 198 MET cc_start: 0.8459 (ttp) cc_final: 0.8219 (ttm) REVERT: A 216 GLU cc_start: 0.8145 (pt0) cc_final: 0.7789 (tt0) REVERT: A 251 ASP cc_start: 0.7392 (t0) cc_final: 0.7188 (t70) REVERT: A 266 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8412 (tt) REVERT: A 330 LYS cc_start: 0.7388 (mmtt) cc_final: 0.6849 (mppt) REVERT: B 52 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7527 (mtm110) REVERT: B 134 ARG cc_start: 0.7129 (ptt90) cc_final: 0.6613 (ppt170) REVERT: B 184 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7647 (p) REVERT: B 205 ASP cc_start: 0.7751 (m-30) cc_final: 0.7356 (m-30) REVERT: B 217 MET cc_start: 0.6332 (pp-130) cc_final: 0.5775 (ppp) REVERT: B 266 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6767 (t-170) REVERT: R 351 MET cc_start: 0.7709 (mmt) cc_final: 0.7486 (mmt) outliers start: 24 outliers final: 11 residues processed: 148 average time/residue: 0.3927 time to fit residues: 61.7818 Evaluate side-chains 134 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 230 ASN B 239 ASN R 69 ASN R 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.203285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155309 restraints weight = 7577.997| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.58 r_work: 0.3738 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7132 Z= 0.119 Angle : 0.560 8.327 9674 Z= 0.284 Chirality : 0.041 0.135 1122 Planarity : 0.003 0.044 1187 Dihedral : 7.829 79.470 1270 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.19 % Allowed : 16.37 % Favored : 79.43 % 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: 1.21 (0.29), residues: 852 helix: 2.58 (0.26), residues: 386 sheet: -0.03 (0.42), residues: 170 loop : -1.14 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 227 TYR 0.010 0.001 TYR R 96 PHE 0.023 0.001 PHE R 224 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7130) covalent geometry : angle 0.55979 / 0.28 ( 9670) SS BOND : bond 0.00681 / 0.36 ( 2) SS BOND : angle 1.11363 / 0.52 ( 4) hydrogen bonds : bond 0.03821 / 2.54 ( 361) hydrogen bonds : angle 4.23935 / 3.06 ( 1053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.175 Fit side-chains REVERT: A 24 ARG cc_start: 0.6393 (ttm110) cc_final: 0.6088 (ttm110) REVERT: A 198 MET cc_start: 0.8416 (ttp) cc_final: 0.8207 (ttm) REVERT: A 266 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8373 (tt) REVERT: A 306 GLN cc_start: 0.7389 (tp40) cc_final: 0.6859 (mt0) REVERT: A 330 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6843 (mppt) REVERT: B 51 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 52 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7319 (mtm110) REVERT: B 134 ARG cc_start: 0.7083 (ptt90) cc_final: 0.6587 (ppt170) REVERT: B 184 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 205 ASP cc_start: 0.7712 (m-30) cc_final: 0.7393 (m-30) REVERT: B 219 ARG cc_start: 0.7108 (mmt90) cc_final: 0.6877 (mmt90) REVERT: B 234 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 267 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (t0) REVERT: B 293 ASN cc_start: 0.7251 (m110) cc_final: 0.6259 (p0) REVERT: B 298 ASP cc_start: 0.7009 (t0) cc_final: 0.6739 (t0) REVERT: R 96 TYR cc_start: 0.7470 (t80) cc_final: 0.6919 (t80) REVERT: R 227 ARG cc_start: 0.5833 (mmm160) cc_final: 0.5546 (mpt-90) REVERT: R 347 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7130 (mt) REVERT: R 377 MET cc_start: 0.7576 (pmm) cc_final: 0.5253 (ptm) REVERT: R 392 ASN cc_start: 0.8427 (t0) cc_final: 0.8048 (t0) REVERT: R 393 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7533 (m) outliers start: 31 outliers final: 8 residues processed: 150 average time/residue: 0.3502 time to fit residues: 56.0761 Evaluate side-chains 138 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.201873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153862 restraints weight = 7658.702| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.60 r_work: 0.3729 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7132 Z= 0.126 Angle : 0.565 7.777 9674 Z= 0.285 Chirality : 0.041 0.147 1122 Planarity : 0.003 0.042 1187 Dihedral : 7.809 84.585 1270 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.47 % Allowed : 18.00 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.29), residues: 852 helix: 2.58 (0.26), residues: 387 sheet: -0.01 (0.41), residues: 170 loop : -1.11 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 227 TYR 0.009 0.001 TYR R 195 PHE 0.016 0.001 PHE R 354 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7130) covalent geometry : angle 0.56493 / 0.29 ( 9670) SS BOND : bond 0.00815 / 0.43 ( 2) SS BOND : angle 1.31412 / 0.61 ( 4) hydrogen bonds : bond 0.03799 / 2.51 ( 361) hydrogen bonds : angle 4.06117 / 2.95 ( 1053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 198 MET cc_start: 0.8491 (ttp) cc_final: 0.8260 (ttm) REVERT: A 266 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 306 GLN cc_start: 0.7480 (tp40) cc_final: 0.7013 (mt0) REVERT: A 330 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6718 (mppt) REVERT: B 51 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 52 ARG cc_start: 0.7668 (ptt-90) cc_final: 0.7390 (mtm110) REVERT: B 134 ARG cc_start: 0.7008 (ptt90) cc_final: 0.6618 (ppt170) REVERT: B 184 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7744 (p) REVERT: B 186 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7433 (p0) REVERT: B 205 ASP cc_start: 0.7714 (m-30) cc_final: 0.7447 (m-30) REVERT: B 220 GLN cc_start: 0.7422 (tp-100) cc_final: 0.6639 (tm-30) REVERT: B 234 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6799 (t80) REVERT: B 293 ASN cc_start: 0.7341 (m110) cc_final: 0.6308 (p0) REVERT: B 298 ASP cc_start: 0.7090 (t0) cc_final: 0.6864 (t0) REVERT: R 96 TYR cc_start: 0.7403 (t80) cc_final: 0.6883 (t80) REVERT: R 227 ARG cc_start: 0.5882 (mmm160) cc_final: 0.5592 (mpt-90) REVERT: R 347 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7152 (mt) REVERT: R 393 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7649 (m) outliers start: 33 outliers final: 11 residues processed: 148 average time/residue: 0.3412 time to fit residues: 53.8730 Evaluate side-chains 139 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain R residue 147 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.215302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167139 restraints weight = 7538.910| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.56 r_work: 0.4012 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7132 Z= 0.116 Angle : 0.547 7.647 9674 Z= 0.276 Chirality : 0.041 0.139 1122 Planarity : 0.003 0.040 1187 Dihedral : 7.781 86.216 1270 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.06 % Allowed : 20.30 % Favored : 75.64 % 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: 1.32 (0.29), residues: 852 helix: 2.66 (0.26), residues: 385 sheet: 0.07 (0.41), residues: 170 loop : -1.09 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 227 TYR 0.008 0.001 TYR R 195 PHE 0.026 0.001 PHE R 224 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7130) covalent geometry : angle 0.54702 / 0.28 ( 9670) SS BOND : bond 0.00722 / 0.38 ( 2) SS BOND : angle 1.22502 / 0.58 ( 4) hydrogen bonds : bond 0.03613 / 2.41 ( 361) hydrogen bonds : angle 3.98762 / 2.88 ( 1053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.260 Fit side-chains REVERT: A 197 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7622 (mtpt) REVERT: A 198 MET cc_start: 0.8489 (ttp) cc_final: 0.8274 (ttm) REVERT: A 266 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 306 GLN cc_start: 0.7795 (tp40) cc_final: 0.7365 (mt0) REVERT: A 330 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6997 (mppt) REVERT: B 51 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 127 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7768 (ptpp) REVERT: B 134 ARG cc_start: 0.7145 (ptt90) cc_final: 0.6792 (ppt170) REVERT: B 184 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 205 ASP cc_start: 0.7742 (m-30) cc_final: 0.7520 (m-30) REVERT: B 217 MET cc_start: 0.6165 (ppp) cc_final: 0.5642 (pp-130) REVERT: B 220 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7221 (tm-30) REVERT: B 234 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7144 (t80) REVERT: B 293 ASN cc_start: 0.7587 (m110) cc_final: 0.6790 (p0) REVERT: B 325 MET cc_start: 0.7842 (mmt) cc_final: 0.7282 (ptp) REVERT: R 344 VAL cc_start: 0.8437 (p) cc_final: 0.8186 (t) REVERT: R 347 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7367 (mt) REVERT: R 377 MET cc_start: 0.7385 (pmm) cc_final: 0.5044 (ttm) REVERT: R 393 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7857 (m) outliers start: 30 outliers final: 9 residues processed: 143 average time/residue: 0.3682 time to fit residues: 56.1297 Evaluate side-chains 130 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.0570 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 chunk 80 optimal weight: 0.4980 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.217016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.168817 restraints weight = 7453.208| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.57 r_work: 0.4032 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7132 Z= 0.106 Angle : 0.542 7.745 9674 Z= 0.275 Chirality : 0.040 0.138 1122 Planarity : 0.003 0.039 1187 Dihedral : 7.767 86.251 1270 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.25 % Allowed : 21.92 % Favored : 74.83 % 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: 1.42 (0.30), residues: 852 helix: 2.68 (0.26), residues: 384 sheet: 0.19 (0.42), residues: 162 loop : -0.94 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 52 TYR 0.008 0.001 TYR R 198 PHE 0.011 0.001 PHE R 354 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7130) covalent geometry : angle 0.54202 / 0.27 ( 9670) SS BOND : bond 0.00575 / 0.30 ( 2) SS BOND : angle 1.00270 / 0.46 ( 4) hydrogen bonds : bond 0.03357 / 2.23 ( 361) hydrogen bonds : angle 3.95781 / 2.87 ( 1053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.7892 (tp40) cc_final: 0.7471 (mt0) REVERT: A 315 ASP cc_start: 0.6879 (p0) cc_final: 0.6581 (m-30) REVERT: A 330 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6757 (mppt) REVERT: B 184 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7849 (p) REVERT: B 186 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7467 (p0) REVERT: B 217 MET cc_start: 0.6109 (ppp) cc_final: 0.5570 (pp-130) REVERT: B 220 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7153 (tm-30) REVERT: B 234 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6970 (t80) REVERT: B 293 ASN cc_start: 0.7621 (m110) cc_final: 0.6885 (p0) REVERT: B 325 MET cc_start: 0.7752 (mmt) cc_final: 0.7282 (ptp) REVERT: G 46 LYS cc_start: 0.7341 (ptpt) cc_final: 0.6710 (mptp) REVERT: R 65 ARG cc_start: 0.6776 (mpt-90) cc_final: 0.6567 (mtm-85) REVERT: R 344 VAL cc_start: 0.8411 (p) cc_final: 0.8178 (t) REVERT: R 347 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7368 (mt) REVERT: R 377 MET cc_start: 0.7412 (pmm) cc_final: 0.5058 (ttm) REVERT: R 393 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.7880 (m) REVERT: R 394 LEU cc_start: 0.8508 (pp) cc_final: 0.8155 (tp) outliers start: 24 outliers final: 8 residues processed: 135 average time/residue: 0.3619 time to fit residues: 52.1305 Evaluate side-chains 118 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 147 LYS Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.212612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164211 restraints weight = 7548.159| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.58 r_work: 0.3984 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7132 Z= 0.148 Angle : 0.597 8.079 9674 Z= 0.303 Chirality : 0.041 0.140 1122 Planarity : 0.004 0.040 1187 Dihedral : 7.875 88.446 1270 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.25 % Allowed : 22.33 % Favored : 74.42 % 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: 1.20 (0.30), residues: 852 helix: 2.35 (0.26), residues: 392 sheet: 0.18 (0.42), residues: 167 loop : -1.01 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 52 TYR 0.011 0.001 TYR R 195 PHE 0.024 0.002 PHE R 224 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7130) covalent geometry : angle 0.59606 / 0.30 ( 9670) SS BOND : bond 0.00911 / 0.48 ( 2) SS BOND : angle 1.51885 / 0.70 ( 4) hydrogen bonds : bond 0.03982 / 2.62 ( 361) hydrogen bonds : angle 4.12043 / 3.00 ( 1053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7521 (tt0) cc_final: 0.7227 (pp20) REVERT: A 306 GLN cc_start: 0.7637 (tp40) cc_final: 0.7252 (mt0) REVERT: A 315 ASP cc_start: 0.7007 (p0) cc_final: 0.6670 (m-30) REVERT: A 330 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6744 (mppt) REVERT: B 134 ARG cc_start: 0.7598 (ptm-80) cc_final: 0.7375 (ptm-80) REVERT: B 184 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7844 (p) REVERT: B 186 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7560 (p0) REVERT: B 220 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7299 (tm-30) REVERT: B 234 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7110 (t80) REVERT: B 293 ASN cc_start: 0.7665 (m110) cc_final: 0.6882 (p0) REVERT: B 325 MET cc_start: 0.7757 (mmt) cc_final: 0.7180 (ptp) REVERT: G 46 LYS cc_start: 0.7328 (ptpt) cc_final: 0.6705 (mptp) REVERT: R 47 ILE cc_start: 0.8309 (mp) cc_final: 0.8052 (mp) REVERT: R 96 TYR cc_start: 0.8006 (t80) cc_final: 0.7394 (t80) REVERT: R 344 VAL cc_start: 0.8457 (p) cc_final: 0.8202 (t) REVERT: R 347 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7413 (mt) REVERT: R 393 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.7917 (m) outliers start: 24 outliers final: 7 residues processed: 135 average time/residue: 0.4041 time to fit residues: 57.9577 Evaluate side-chains 126 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.215113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.167153 restraints weight = 7468.226| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.57 r_work: 0.4013 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7132 Z= 0.122 Angle : 0.582 8.698 9674 Z= 0.296 Chirality : 0.041 0.133 1122 Planarity : 0.004 0.062 1187 Dihedral : 7.736 87.576 1270 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 24.09 % Favored : 73.88 % 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: 1.25 (0.30), residues: 852 helix: 2.39 (0.26), residues: 394 sheet: 0.26 (0.42), residues: 167 loop : -1.05 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 227 TYR 0.008 0.001 TYR R 198 PHE 0.013 0.001 PHE R 354 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS R 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7130) covalent geometry : angle 0.58123 / 0.30 ( 9670) SS BOND : bond 0.00639 / 0.33 ( 2) SS BOND : angle 1.05634 / 0.48 ( 4) hydrogen bonds : bond 0.03595 / 2.37 ( 361) hydrogen bonds : angle 4.05946 / 2.95 ( 1053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7276 (pp20) cc_final: 0.6920 (pp20) REVERT: A 197 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7725 (mtpm) REVERT: A 306 GLN cc_start: 0.7569 (tp40) cc_final: 0.7156 (mt0) REVERT: A 315 ASP cc_start: 0.6998 (p0) cc_final: 0.6698 (m-30) REVERT: A 330 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6747 (mppt) REVERT: B 134 ARG cc_start: 0.7591 (ptm-80) cc_final: 0.7364 (ptm-80) REVERT: B 170 ASP cc_start: 0.8616 (m-30) cc_final: 0.7979 (t70) REVERT: B 172 GLU cc_start: 0.7199 (pm20) cc_final: 0.6428 (pm20) REVERT: B 184 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 186 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7473 (p0) REVERT: B 217 MET cc_start: 0.6367 (pp-130) cc_final: 0.6065 (pp-130) REVERT: B 220 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7202 (tm-30) REVERT: B 234 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 293 ASN cc_start: 0.7725 (m110) cc_final: 0.7052 (p0) REVERT: B 325 MET cc_start: 0.7714 (mmt) cc_final: 0.7206 (ptp) REVERT: G 46 LYS cc_start: 0.7378 (ptpt) cc_final: 0.6782 (mptp) REVERT: R 96 TYR cc_start: 0.7938 (t80) cc_final: 0.7268 (t80) REVERT: R 344 VAL cc_start: 0.8455 (p) cc_final: 0.8209 (t) REVERT: R 347 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7373 (mt) REVERT: R 377 MET cc_start: 0.7424 (pmm) cc_final: 0.5052 (ttm) REVERT: R 393 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7798 (m) outliers start: 15 outliers final: 6 residues processed: 131 average time/residue: 0.3858 time to fit residues: 53.6722 Evaluate side-chains 126 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.0770 chunk 36 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5344 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.204075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.157293 restraints weight = 7522.303| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.58 r_work: 0.3757 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7132 Z= 0.114 Angle : 0.577 8.113 9674 Z= 0.296 Chirality : 0.041 0.150 1122 Planarity : 0.004 0.075 1187 Dihedral : 7.639 87.138 1270 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.35 % Allowed : 25.03 % Favored : 73.61 % 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: 1.32 (0.30), residues: 852 helix: 2.49 (0.26), residues: 388 sheet: 0.41 (0.43), residues: 161 loop : -1.05 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 227 TYR 0.008 0.001 TYR R 198 PHE 0.026 0.001 PHE R 224 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 7130) covalent geometry : angle 0.57730 / 0.30 ( 9670) SS BOND : bond 0.00550 / 0.29 ( 2) SS BOND : angle 0.93089 / 0.43 ( 4) hydrogen bonds : bond 0.03346 / 2.22 ( 361) hydrogen bonds : angle 4.05548 / 2.95 ( 1053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6937 (pp20) cc_final: 0.6598 (pp20) REVERT: A 193 ASP cc_start: 0.6588 (t0) cc_final: 0.6349 (t0) REVERT: A 197 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7060 (mtpm) REVERT: A 306 GLN cc_start: 0.7362 (tp40) cc_final: 0.6955 (mt0) REVERT: A 315 ASP cc_start: 0.6935 (p0) cc_final: 0.6594 (m-30) REVERT: A 330 LYS cc_start: 0.6732 (mmtt) cc_final: 0.6243 (mppt) REVERT: B 134 ARG cc_start: 0.7277 (ptm-80) cc_final: 0.7058 (ptm-80) REVERT: B 170 ASP cc_start: 0.8347 (m-30) cc_final: 0.7582 (t70) REVERT: B 172 GLU cc_start: 0.7237 (pm20) cc_final: 0.6386 (pm20) REVERT: B 217 MET cc_start: 0.6246 (pp-130) cc_final: 0.5916 (pp-130) REVERT: B 220 GLN cc_start: 0.7417 (tp-100) cc_final: 0.6866 (tm-30) REVERT: B 234 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6761 (t80) REVERT: B 293 ASN cc_start: 0.7439 (m110) cc_final: 0.6767 (p0) REVERT: B 325 MET cc_start: 0.7688 (mmt) cc_final: 0.7040 (ptp) REVERT: G 46 LYS cc_start: 0.7257 (ptpt) cc_final: 0.6587 (mptp) REVERT: R 65 ARG cc_start: 0.6582 (mpt-90) cc_final: 0.6370 (mtm-85) REVERT: R 96 TYR cc_start: 0.7542 (t80) cc_final: 0.6907 (t80) REVERT: R 347 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7102 (mt) REVERT: R 377 MET cc_start: 0.7594 (pmm) cc_final: 0.5092 (ttm) REVERT: R 393 SER cc_start: 0.7922 (OUTLIER) cc_final: 0.7527 (m) REVERT: R 394 LEU cc_start: 0.8424 (pp) cc_final: 0.7964 (tp) outliers start: 10 outliers final: 4 residues processed: 132 average time/residue: 0.4077 time to fit residues: 57.2924 Evaluate side-chains 123 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.0050 overall best weight: 1.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.213894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.165700 restraints weight = 7393.251| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.55 r_work: 0.4000 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7132 Z= 0.140 Angle : 0.606 8.065 9674 Z= 0.310 Chirality : 0.042 0.178 1122 Planarity : 0.004 0.071 1187 Dihedral : 7.762 88.029 1270 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.62 % Allowed : 24.90 % Favored : 73.48 % 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: 1.25 (0.30), residues: 852 helix: 2.38 (0.26), residues: 390 sheet: 0.35 (0.43), residues: 167 loop : -1.04 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 227 TYR 0.011 0.001 TYR B 289 PHE 0.016 0.001 PHE R 354 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7130) covalent geometry : angle 0.60591 / 0.31 ( 9670) SS BOND : bond 0.00806 / 0.42 ( 2) SS BOND : angle 1.30061 / 0.60 ( 4) hydrogen bonds : bond 0.03845 / 2.53 ( 361) hydrogen bonds : angle 4.16260 / 3.03 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.57 seconds wall clock time: 34 minutes 7.90 seconds (2047.90 seconds total)