Starting phenix.real_space_refine on Tue Mar 3 18:28:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2026/7s3i_24825.map" } resolution = 2.51 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5147 2.51 5 N 1403 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8094 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1929 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Chain: "B" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2615 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2133 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 1.45, per 1000 atoms: 0.18 Number of scatterers: 8094 At special positions: 0 Unit cell: (87.15, 123.67, 97.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1496 8.00 N 1403 7.00 C 5147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.49 Conformation dependent library (CDL) restraints added in 289.2 milliseconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 44.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.612A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.622A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.709A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.310A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.704A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.863A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.594A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.726A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.635A 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 'G' and resid 55 through 59 removed outlier: 3.516A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.854A pdb=" N LEU R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.856A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.757A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 338 removed outlier: 3.855A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.557A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 361 removed outlier: 3.689A pdb=" N ARG R 348 " --> pdb=" O ASP R 344 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 371 Processing helix chain 'R' and resid 377 through 404 removed outlier: 4.065A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.320A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.458A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.528A 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: 3.837A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.089A 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: 6.745A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.242A 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 153 removed outlier: 6.918A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.032A 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: 6.894A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.319A 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: 3.615A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.969A 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: 3.848A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.038A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2642 1.34 - 1.46: 1862 1.46 - 1.58: 3690 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 8260 Sorted by residual: bond pdb=" N TYR N 117 " pdb=" CA TYR N 117 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.48e-02 4.57e+03 3.96e+00 bond pdb=" C ASP B 291 " pdb=" N PHE B 292 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.73e-02 3.34e+03 2.79e+00 bond pdb=" CA GLY R 151 " pdb=" C GLY R 151 " ideal model delta sigma weight residual 1.517 1.500 0.016 1.14e-02 7.69e+03 2.02e+00 bond pdb=" CA TYR N 117 " pdb=" CB TYR N 117 " ideal model delta sigma weight residual 1.531 1.545 -0.014 1.53e-02 4.27e+03 8.26e-01 bond pdb=" C ASP B 118 " pdb=" N ASN B 119 " ideal model delta sigma weight residual 1.331 1.317 0.015 1.62e-02 3.81e+03 8.12e-01 ... (remaining 8255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 10981 1.27 - 2.53: 158 2.53 - 3.80: 35 3.80 - 5.06: 6 5.06 - 6.33: 4 Bond angle restraints: 11184 Sorted by residual: angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 109.59 103.26 6.33 1.61e+00 3.86e-01 1.55e+01 angle pdb=" N GLY R 151 " pdb=" CA GLY R 151 " pdb=" C GLY R 151 " ideal model delta sigma weight residual 112.77 108.86 3.91 1.28e+00 6.10e-01 9.35e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 122.55 116.92 5.63 2.03e+00 2.43e-01 7.69e+00 angle pdb=" N TYR N 117 " pdb=" CA TYR N 117 " pdb=" CB TYR N 117 " ideal model delta sigma weight residual 112.47 115.72 -3.25 1.52e+00 4.33e-01 4.57e+00 angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" C THR B 128 " ideal model delta sigma weight residual 108.63 112.03 -3.40 1.60e+00 3.91e-01 4.52e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4412 17.33 - 34.65: 407 34.65 - 51.98: 56 51.98 - 69.30: 17 69.30 - 86.63: 8 Dihedral angle restraints: 4900 sinusoidal: 1922 harmonic: 2978 Sorted by residual: dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1063 0.055 - 0.110: 170 0.110 - 0.166: 20 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA TYR N 117 " pdb=" N TYR N 117 " pdb=" C TYR N 117 " pdb=" CB TYR N 117 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1252 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 332 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO G 53 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO G 55 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.020 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 92 2.65 - 3.21: 7346 3.21 - 3.78: 12729 3.78 - 4.34: 18270 4.34 - 4.90: 29474 Nonbonded interactions: 67911 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.223 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.242 3.040 nonbonded pdb=" ND2 ASN R 320 " pdb=" O LEU R 360 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 306 " model vdw 2.283 3.040 ... (remaining 67906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.002 0.029 8263 Z= 0.117 Angle : 0.440 6.330 11190 Z= 0.246 Chirality : 0.041 0.276 1255 Planarity : 0.004 0.057 1423 Dihedral : 13.630 86.629 2965 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.36 (0.27), residues: 1005 helix: 2.43 (0.26), residues: 395 sheet: 0.36 (0.35), residues: 217 loop : -0.34 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.014 0.001 TYR R 402 PHE 0.012 0.001 PHE B 234 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8260) covalent geometry : angle 0.43946 (11184) SS BOND : bond 0.00108 ( 3) SS BOND : angle 1.23589 ( 6) hydrogen bonds : bond 0.17543 ( 433) hydrogen bonds : angle 6.41800 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.298 Fit side-chains REVERT: A 294 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7664 (tp40) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.8206 time to fit residues: 113.4453 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS A 390 GLN N 3 GLN N 13 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085431 restraints weight = 11900.633| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.24 r_work: 0.3013 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8263 Z= 0.117 Angle : 0.483 5.403 11190 Z= 0.267 Chirality : 0.041 0.153 1255 Planarity : 0.004 0.052 1423 Dihedral : 4.295 20.167 1115 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.38 % Allowed : 8.86 % Favored : 89.76 % 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: 1.55 (0.27), residues: 1005 helix: 2.72 (0.25), residues: 401 sheet: 0.25 (0.36), residues: 211 loop : -0.29 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 326 TYR 0.013 0.001 TYR R 402 PHE 0.032 0.001 PHE R 260 TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8260) covalent geometry : angle 0.48298 (11184) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.73683 ( 6) hydrogen bonds : bond 0.04179 ( 433) hydrogen bonds : angle 4.55875 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.366 Fit side-chains REVERT: A 38 ARG cc_start: 0.8613 (mmt180) cc_final: 0.8409 (mmt180) REVERT: A 253 TYR cc_start: 0.8679 (p90) cc_final: 0.8462 (p90) REVERT: B 217 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8974 (pmt) REVERT: G 32 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8225 (tmtt) REVERT: G 47 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: R 291 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.5647 (t80) REVERT: R 292 GLU cc_start: 0.5485 (pm20) cc_final: 0.4779 (pp20) REVERT: R 420 TRP cc_start: 0.7505 (t60) cc_final: 0.7269 (t60) outliers start: 12 outliers final: 2 residues processed: 125 average time/residue: 0.7052 time to fit residues: 92.1876 Evaluate side-chains 109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 3 GLN N 13 GLN R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090276 restraints weight = 12461.923| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.07 r_work: 0.3072 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8263 Z= 0.119 Angle : 0.463 5.277 11190 Z= 0.255 Chirality : 0.041 0.156 1255 Planarity : 0.004 0.048 1423 Dihedral : 4.236 20.106 1115 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.73 % Allowed : 10.82 % Favored : 87.46 % 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: 1.63 (0.27), residues: 1005 helix: 2.85 (0.25), residues: 401 sheet: 0.34 (0.36), residues: 208 loop : -0.35 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 421 TYR 0.013 0.001 TYR B 59 PHE 0.024 0.001 PHE R 260 TRP 0.013 0.001 TRP A 234 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8260) covalent geometry : angle 0.46313 (11184) SS BOND : bond 0.00107 ( 3) SS BOND : angle 0.56761 ( 6) hydrogen bonds : bond 0.03896 ( 433) hydrogen bonds : angle 4.31628 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.338 Fit side-chains REVERT: B 217 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8962 (pmt) REVERT: G 47 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: R 291 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5794 (t80) REVERT: R 303 MET cc_start: 0.6410 (mmm) cc_final: 0.6102 (mpm) REVERT: R 411 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8097 (mm) REVERT: R 420 TRP cc_start: 0.7550 (t60) cc_final: 0.7346 (t60) outliers start: 15 outliers final: 4 residues processed: 123 average time/residue: 0.7319 time to fit residues: 94.1097 Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 3 GLN N 13 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089048 restraints weight = 12712.421| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.09 r_work: 0.3048 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8263 Z= 0.143 Angle : 0.481 5.453 11190 Z= 0.265 Chirality : 0.042 0.155 1255 Planarity : 0.004 0.046 1423 Dihedral : 4.362 21.249 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.19 % Allowed : 11.39 % Favored : 86.42 % 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: 1.64 (0.26), residues: 1005 helix: 2.81 (0.25), residues: 403 sheet: 0.36 (0.35), residues: 213 loop : -0.33 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 421 TYR 0.013 0.001 TYR B 59 PHE 0.025 0.001 PHE R 260 TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8260) covalent geometry : angle 0.48097 (11184) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.61407 ( 6) hydrogen bonds : bond 0.03912 ( 433) hydrogen bonds : angle 4.29716 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.321 Fit side-chains REVERT: B 217 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (pmt) REVERT: G 47 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: R 291 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5689 (t80) REVERT: R 303 MET cc_start: 0.6437 (mmm) cc_final: 0.6177 (mpm) REVERT: R 411 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8158 (mm) outliers start: 19 outliers final: 7 residues processed: 120 average time/residue: 0.7377 time to fit residues: 92.6129 Evaluate side-chains 110 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 3 GLN N 13 GLN R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090216 restraints weight = 12595.826| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.09 r_work: 0.3083 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8263 Z= 0.115 Angle : 0.462 5.768 11190 Z= 0.254 Chirality : 0.041 0.155 1255 Planarity : 0.003 0.045 1423 Dihedral : 4.229 20.655 1115 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 12.66 % Favored : 85.39 % 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: 1.67 (0.27), residues: 1005 helix: 2.88 (0.25), residues: 403 sheet: 0.20 (0.35), residues: 214 loop : -0.24 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 46 TYR 0.014 0.001 TYR R 402 PHE 0.020 0.001 PHE R 260 TRP 0.019 0.001 TRP R 420 HIS 0.002 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8260) covalent geometry : angle 0.46161 (11184) SS BOND : bond 0.00207 ( 3) SS BOND : angle 1.06093 ( 6) hydrogen bonds : bond 0.03632 ( 433) hydrogen bonds : angle 4.18279 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.316 Fit side-chains REVERT: B 217 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8874 (pmt) REVERT: G 47 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: R 291 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.5750 (t80) REVERT: R 303 MET cc_start: 0.6469 (mmm) cc_final: 0.6237 (mpm) outliers start: 17 outliers final: 7 residues processed: 111 average time/residue: 0.7365 time to fit residues: 85.6129 Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 13 GLN R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089875 restraints weight = 12470.437| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.08 r_work: 0.3069 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8263 Z= 0.121 Angle : 0.465 5.868 11190 Z= 0.255 Chirality : 0.041 0.154 1255 Planarity : 0.003 0.044 1423 Dihedral : 4.221 20.474 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 13.35 % Favored : 84.93 % 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: 1.66 (0.27), residues: 1005 helix: 2.90 (0.25), residues: 403 sheet: 0.13 (0.35), residues: 214 loop : -0.25 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.013 0.001 TYR R 402 PHE 0.018 0.001 PHE R 260 TRP 0.021 0.001 TRP R 420 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8260) covalent geometry : angle 0.46385 (11184) SS BOND : bond 0.00150 ( 3) SS BOND : angle 1.21066 ( 6) hydrogen bonds : bond 0.03647 ( 433) hydrogen bonds : angle 4.15746 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.304 Fit side-chains REVERT: B 217 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8868 (pmt) REVERT: G 47 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: R 291 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5825 (t80) REVERT: R 303 MET cc_start: 0.6507 (mmm) cc_final: 0.6287 (mpm) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.7467 time to fit residues: 84.2565 Evaluate side-chains 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 320 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 68 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 13 GLN R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089500 restraints weight = 12632.722| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.10 r_work: 0.3063 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8263 Z= 0.129 Angle : 0.476 7.014 11190 Z= 0.260 Chirality : 0.041 0.185 1255 Planarity : 0.003 0.043 1423 Dihedral : 4.246 20.795 1115 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.84 % Allowed : 13.92 % Favored : 84.23 % 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: 1.65 (0.27), residues: 1005 helix: 2.93 (0.25), residues: 401 sheet: 0.13 (0.34), residues: 216 loop : -0.28 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.013 0.001 TYR R 402 PHE 0.018 0.001 PHE R 260 TRP 0.025 0.001 TRP R 420 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8260) covalent geometry : angle 0.47515 (11184) SS BOND : bond 0.00217 ( 3) SS BOND : angle 1.17210 ( 6) hydrogen bonds : bond 0.03666 ( 433) hydrogen bonds : angle 4.15894 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.313 Fit side-chains REVERT: B 217 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8836 (pmt) REVERT: G 47 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: R 291 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5699 (t80) REVERT: R 292 GLU cc_start: 0.5631 (pm20) cc_final: 0.5156 (pp20) outliers start: 16 outliers final: 9 residues processed: 118 average time/residue: 0.7579 time to fit residues: 93.4800 Evaluate side-chains 110 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 13 GLN R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090444 restraints weight = 12555.863| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.09 r_work: 0.3080 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8263 Z= 0.114 Angle : 0.465 6.187 11190 Z= 0.254 Chirality : 0.041 0.215 1255 Planarity : 0.003 0.043 1423 Dihedral : 4.168 20.200 1115 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.50 % Allowed : 14.61 % Favored : 83.89 % 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: 1.69 (0.27), residues: 1005 helix: 2.95 (0.25), residues: 403 sheet: 0.11 (0.35), residues: 214 loop : -0.23 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.015 0.001 TYR R 402 PHE 0.018 0.001 PHE R 260 TRP 0.028 0.002 TRP R 420 HIS 0.002 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8260) covalent geometry : angle 0.46483 (11184) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.95154 ( 6) hydrogen bonds : bond 0.03523 ( 433) hydrogen bonds : angle 4.09647 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.323 Fit side-chains REVERT: B 217 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8865 (pmt) REVERT: G 47 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: R 291 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.5730 (t80) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 0.7787 time to fit residues: 93.5262 Evaluate side-chains 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.120745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088431 restraints weight = 12595.250| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.09 r_work: 0.3044 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8263 Z= 0.159 Angle : 0.517 7.920 11190 Z= 0.281 Chirality : 0.043 0.206 1255 Planarity : 0.004 0.043 1423 Dihedral : 4.389 21.771 1115 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.73 % Allowed : 14.50 % Favored : 83.77 % 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: 1.62 (0.26), residues: 1005 helix: 2.92 (0.25), residues: 401 sheet: 0.14 (0.35), residues: 211 loop : -0.34 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.017 0.002 TYR R 402 PHE 0.018 0.001 PHE R 260 TRP 0.033 0.002 TRP R 420 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8260) covalent geometry : angle 0.51678 (11184) SS BOND : bond 0.00132 ( 3) SS BOND : angle 1.17314 ( 6) hydrogen bonds : bond 0.03854 ( 433) hydrogen bonds : angle 4.23133 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.323 Fit side-chains REVERT: G 47 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: R 291 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5776 (t80) outliers start: 15 outliers final: 8 residues processed: 114 average time/residue: 0.8016 time to fit residues: 95.4178 Evaluate side-chains 115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 340 ASN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089021 restraints weight = 12553.271| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.08 r_work: 0.3054 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8263 Z= 0.144 Angle : 0.507 6.938 11190 Z= 0.276 Chirality : 0.042 0.164 1255 Planarity : 0.004 0.043 1423 Dihedral : 4.365 22.048 1115 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 14.84 % Favored : 83.66 % 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: 1.62 (0.26), residues: 1005 helix: 2.91 (0.25), residues: 401 sheet: 0.11 (0.34), residues: 216 loop : -0.30 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.017 0.001 TYR R 402 PHE 0.019 0.001 PHE R 260 TRP 0.034 0.002 TRP R 420 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8260) covalent geometry : angle 0.50667 (11184) SS BOND : bond 0.00135 ( 3) SS BOND : angle 1.03023 ( 6) hydrogen bonds : bond 0.03773 ( 433) hydrogen bonds : angle 4.20515 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.240 Fit side-chains REVERT: B 217 MET cc_start: 0.9216 (pmm) cc_final: 0.8974 (pmt) REVERT: G 47 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: R 291 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5843 (t80) outliers start: 13 outliers final: 7 residues processed: 111 average time/residue: 0.8312 time to fit residues: 96.2306 Evaluate side-chains 113 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090780 restraints weight = 12578.283| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.08 r_work: 0.3092 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8263 Z= 0.111 Angle : 0.480 6.966 11190 Z= 0.261 Chirality : 0.041 0.156 1255 Planarity : 0.003 0.044 1423 Dihedral : 4.190 20.625 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.27 % Allowed : 15.19 % Favored : 83.54 % 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: 1.71 (0.27), residues: 1005 helix: 3.00 (0.25), residues: 401 sheet: 0.12 (0.35), residues: 212 loop : -0.25 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 46 TYR 0.016 0.001 TYR R 402 PHE 0.020 0.001 PHE R 260 TRP 0.034 0.002 TRP R 420 HIS 0.002 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8260) covalent geometry : angle 0.47965 (11184) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.89424 ( 6) hydrogen bonds : bond 0.03475 ( 433) hydrogen bonds : angle 4.09066 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.94 seconds wall clock time: 61 minutes 32.20 seconds (3692.20 seconds total)