Starting phenix.real_space_refine on Wed Feb 12 14:17:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_24825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_24825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_24825.map" model { file = "/net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_24825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s3i_24825/02_2025/7s3i_24825.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 5.05, per 1000 atoms: 0.62 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: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.87 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: 2.46 Time building geometry restraints manager: 2.21 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- 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 8260 Z= 0.161 Angle : 0.439 6.330 11184 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (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 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE B 234 TYR 0.014 0.001 TYR R 402 ARG 0.004 0.000 ARG A 389 *********************** 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 : 0.814 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: 1.8690 time to fit residues: 258.6840 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 : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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** R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084149 restraints weight = 11822.276| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.23 r_work: 0.2990 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8260 Z= 0.200 Angle : 0.500 5.432 11184 Z= 0.277 Chirality : 0.042 0.153 1255 Planarity : 0.004 0.053 1423 Dihedral : 4.410 21.181 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.50 % Allowed : 8.63 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1005 helix: 2.66 (0.25), residues: 401 sheet: 0.30 (0.36), residues: 209 loop : -0.31 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 357 PHE 0.030 0.001 PHE R 260 TYR 0.013 0.001 TYR R 402 ARG 0.009 0.001 ARG R 326 *********************** 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 130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.866 Fit side-chains REVERT: A 38 ARG cc_start: 0.8611 (mmt180) cc_final: 0.8402 (mmt180) REVERT: B 172 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 217 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8971 (pmt) REVERT: G 32 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8215 (tmtt) REVERT: G 47 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: R 291 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5689 (t80) REVERT: R 292 GLU cc_start: 0.5569 (pm20) cc_final: 0.5055 (pp20) REVERT: R 420 TRP cc_start: 0.7506 (t60) cc_final: 0.7275 (t60) outliers start: 13 outliers final: 2 residues processed: 121 average time/residue: 1.7021 time to fit residues: 215.3683 Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.083877 restraints weight = 11969.224| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.26 r_work: 0.2945 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8260 Z= 0.194 Angle : 0.475 5.411 11184 Z= 0.262 Chirality : 0.041 0.157 1255 Planarity : 0.004 0.050 1423 Dihedral : 4.365 21.321 1115 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.07 % Allowed : 10.24 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1005 helix: 2.78 (0.25), residues: 401 sheet: 0.32 (0.36), residues: 208 loop : -0.37 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.025 0.001 PHE R 260 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG R 421 *********************** 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: 18 poor density : 114 time to evaluate : 0.884 Fit side-chains REVERT: B 172 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7879 (mm-30) REVERT: B 217 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8888 (pmt) REVERT: G 47 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: R 291 TYR cc_start: 0.6463 (OUTLIER) cc_final: 0.5824 (t80) REVERT: R 303 MET cc_start: 0.6340 (mmm) cc_final: 0.6103 (mpm) REVERT: R 411 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7996 (mm) REVERT: R 420 TRP cc_start: 0.7439 (t60) cc_final: 0.7209 (t60) outliers start: 18 outliers final: 6 residues processed: 121 average time/residue: 1.6854 time to fit residues: 213.1658 Evaluate side-chains 109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 68 optimal weight: 0.5980 chunk 16 optimal weight: 0.0170 chunk 88 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.118771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.084006 restraints weight = 11896.245| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.22 r_work: 0.2958 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8260 Z= 0.207 Angle : 0.481 5.469 11184 Z= 0.265 Chirality : 0.042 0.157 1255 Planarity : 0.004 0.048 1423 Dihedral : 4.390 21.710 1115 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.07 % Allowed : 11.62 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1005 helix: 2.81 (0.25), residues: 401 sheet: 0.35 (0.35), residues: 208 loop : -0.39 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS R 363 PHE 0.022 0.001 PHE R 260 TYR 0.013 0.001 TYR B 59 ARG 0.007 0.000 ARG B 96 *********************** 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: 18 poor density : 113 time to evaluate : 0.758 Fit side-chains REVERT: B 172 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 217 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8837 (pmt) REVERT: G 47 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: R 291 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5665 (t80) REVERT: R 292 GLU cc_start: 0.5712 (pm20) cc_final: 0.5066 (pp20) REVERT: R 303 MET cc_start: 0.6355 (mmm) cc_final: 0.6137 (mpm) REVERT: R 420 TRP cc_start: 0.7471 (t60) cc_final: 0.7250 (t60) outliers start: 18 outliers final: 8 residues processed: 121 average time/residue: 1.6649 time to fit residues: 210.7639 Evaluate side-chains 112 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain R residue 291 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.119558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084982 restraints weight = 11745.290| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.21 r_work: 0.2975 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8260 Z= 0.174 Angle : 0.465 5.778 11184 Z= 0.255 Chirality : 0.041 0.155 1255 Planarity : 0.004 0.047 1423 Dihedral : 4.275 21.095 1115 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 12.66 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1005 helix: 2.86 (0.25), residues: 403 sheet: 0.17 (0.35), residues: 214 loop : -0.26 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS A 362 PHE 0.020 0.001 PHE R 260 TYR 0.013 0.001 TYR R 402 ARG 0.006 0.000 ARG B 46 *********************** 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 127 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.874 Fit side-chains REVERT: B 172 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 217 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8850 (pmt) REVERT: G 47 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: R 291 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5758 (t80) REVERT: R 303 MET cc_start: 0.6399 (mmm) cc_final: 0.6189 (mpm) REVERT: R 420 TRP cc_start: 0.7471 (t60) cc_final: 0.7265 (t60) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 1.6901 time to fit residues: 210.3450 Evaluate side-chains 110 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 127 LYS 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 232 LEU Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 320 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS R 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088819 restraints weight = 12495.897| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.07 r_work: 0.3059 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8260 Z= 0.207 Angle : 0.480 5.889 11184 Z= 0.263 Chirality : 0.042 0.154 1255 Planarity : 0.004 0.045 1423 Dihedral : 4.334 21.516 1115 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.84 % Allowed : 13.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1005 helix: 2.84 (0.25), residues: 403 sheet: 0.19 (0.35), residues: 214 loop : -0.28 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.019 0.001 PHE R 260 TYR 0.014 0.001 TYR R 402 ARG 0.007 0.000 ARG B 46 *********************** 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 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.973 Fit side-chains REVERT: B 217 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8842 (pmt) REVERT: G 47 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: R 291 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5883 (t80) REVERT: R 303 MET cc_start: 0.6509 (mmm) cc_final: 0.6300 (mpm) outliers start: 16 outliers final: 8 residues processed: 111 average time/residue: 1.5948 time to fit residues: 185.6525 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 : 0.941 ------------------------------------------------------------------------------- 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 127 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS R 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089613 restraints weight = 12523.647| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8260 Z= 0.180 Angle : 0.473 7.041 11184 Z= 0.259 Chirality : 0.041 0.171 1255 Planarity : 0.003 0.045 1423 Dihedral : 4.249 20.977 1115 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.07 % Allowed : 13.81 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.27), residues: 1005 helix: 2.92 (0.25), residues: 401 sheet: 0.10 (0.35), residues: 214 loop : -0.24 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 420 HIS 0.002 0.001 HIS A 362 PHE 0.017 0.001 PHE R 260 TYR 0.014 0.001 TYR R 402 ARG 0.007 0.000 ARG B 46 *********************** 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: 18 poor density : 107 time to evaluate : 0.876 Fit side-chains REVERT: B 217 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8856 (pmt) REVERT: G 47 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: R 291 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5712 (t80) REVERT: R 292 GLU cc_start: 0.5644 (pm20) cc_final: 0.5189 (pp20) outliers start: 18 outliers final: 10 residues processed: 118 average time/residue: 1.6488 time to fit residues: 203.8420 Evaluate side-chains 112 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 127 LYS 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 4 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089628 restraints weight = 12630.241| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.07 r_work: 0.3073 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8260 Z= 0.186 Angle : 0.478 6.198 11184 Z= 0.261 Chirality : 0.042 0.247 1255 Planarity : 0.004 0.045 1423 Dihedral : 4.250 20.831 1115 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.84 % Allowed : 14.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1005 helix: 2.94 (0.25), residues: 401 sheet: 0.09 (0.35), residues: 211 loop : -0.31 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 420 HIS 0.002 0.001 HIS A 362 PHE 0.018 0.001 PHE R 260 TYR 0.015 0.001 TYR R 402 ARG 0.007 0.000 ARG B 46 *********************** 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 125 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.900 Fit side-chains REVERT: G 47 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: R 291 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5691 (t80) REVERT: R 292 GLU cc_start: 0.5705 (pm20) cc_final: 0.5255 (pp20) outliers start: 16 outliers final: 10 residues processed: 119 average time/residue: 1.7251 time to fit residues: 215.0013 Evaluate side-chains 117 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 127 LYS Chi-restraints excluded: chain B residue 135 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.122060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090115 restraints weight = 12753.319| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.09 r_work: 0.3073 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8260 Z= 0.175 Angle : 0.484 7.990 11184 Z= 0.263 Chirality : 0.041 0.228 1255 Planarity : 0.004 0.044 1423 Dihedral : 4.209 20.304 1115 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 14.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 1005 helix: 2.94 (0.25), residues: 403 sheet: 0.13 (0.35), residues: 212 loop : -0.26 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 420 HIS 0.002 0.001 HIS A 362 PHE 0.018 0.001 PHE R 260 TYR 0.017 0.001 TYR R 402 ARG 0.006 0.000 ARG B 46 *********************** 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 : 0.867 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.9003 (pmt) REVERT: G 47 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: R 291 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5748 (t80) outliers start: 15 outliers final: 8 residues processed: 116 average time/residue: 1.6873 time to fit residues: 204.8823 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 : 0.956 ------------------------------------------------------------------------------- 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 127 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS R 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090533 restraints weight = 12560.475| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.08 r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8260 Z= 0.163 Angle : 0.481 6.930 11184 Z= 0.261 Chirality : 0.041 0.193 1255 Planarity : 0.003 0.045 1423 Dihedral : 4.156 19.829 1115 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.38 % Allowed : 14.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1005 helix: 3.01 (0.25), residues: 403 sheet: 0.11 (0.35), residues: 212 loop : -0.20 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 420 HIS 0.002 0.001 HIS R 363 PHE 0.019 0.001 PHE R 260 TYR 0.017 0.001 TYR R 402 ARG 0.006 0.000 ARG B 46 ********************** 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 119 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.191 Fit side-chains REVERT: B 217 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8975 (pmt) REVERT: G 47 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: R 291 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.5688 (t80) REVERT: R 292 GLU cc_start: 0.5611 (pm20) cc_final: 0.5180 (pp20) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 1.7600 time to fit residues: 209.5349 Evaluate side-chains 112 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089889 restraints weight = 12648.675| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.08 r_work: 0.3067 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8260 Z= 0.188 Angle : 0.489 6.906 11184 Z= 0.266 Chirality : 0.041 0.164 1255 Planarity : 0.004 0.044 1423 Dihedral : 4.219 20.400 1115 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.27 % Allowed : 15.30 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 1005 helix: 3.01 (0.25), residues: 401 sheet: 0.08 (0.34), residues: 216 loop : -0.26 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 420 HIS 0.002 0.001 HIS R 363 PHE 0.020 0.001 PHE R 260 TYR 0.017 0.001 TYR R 402 ARG 0.006 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7525.92 seconds wall clock time: 133 minutes 2.29 seconds (7982.29 seconds total)