Starting phenix.real_space_refine on Wed Mar 12 14:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s3i_24825/03_2025/7s3i_24825.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s3i_24825/03_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_24825/03_2025/7s3i_24825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2025/7s3i_24825.map" model { file = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_2025/7s3i_24825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s3i_24825/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.13, per 1000 atoms: 0.63 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 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: 0.86 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: 2.40 Time building geometry restraints manager: 2.20 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: 0.960 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.710 Find NCS groups from input model: 0.090 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- 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 : 0.979 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: 1.8619 time to fit residues: 257.9059 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 : 0.897 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084135 restraints weight = 11822.275| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.23 r_work: 0.2990 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- 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 : 0.885 Fit side-chains REVERT: A 38 ARG cc_start: 0.8611 (mmt180) cc_final: 0.8402 (mmt180) REVERT: B 172 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 217 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8972 (pmt) REVERT: G 32 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8215 (tmtt) REVERT: G 47 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: R 291 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5689 (t80) REVERT: R 292 GLU cc_start: 0.5568 (pm20) cc_final: 0.5054 (pp20) REVERT: R 420 TRP cc_start: 0.7507 (t60) cc_final: 0.7277 (t60) outliers start: 13 outliers final: 2 residues processed: 121 average time/residue: 1.6593 time to fit residues: 210.4465 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 : 0.899 ------------------------------------------------------------------------------- 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: 0.7980 chunk 98 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 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 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 = 0.3643 r_free = 0.3643 target = 0.119922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084472 restraints weight = 11970.412| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.25 r_work: 0.2996 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8260 Z= 0.175 Angle : 0.467 5.247 11184 Z= 0.258 Chirality : 0.041 0.159 1255 Planarity : 0.004 0.050 1423 Dihedral : 4.307 20.826 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 : 10.36 % 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 (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: 1.59 (0.27), residues: 1005 helix: 2.81 (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 0.004 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 134 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.908 Fit side-chains REVERT: A 253 TYR cc_start: 0.8491 (p90) cc_final: 0.8286 (p90) REVERT: B 172 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 217 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8892 (pmt) REVERT: G 47 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: R 291 TYR cc_start: 0.6448 (OUTLIER) cc_final: 0.5813 (t80) REVERT: R 303 MET cc_start: 0.6338 (mmm) cc_final: 0.6094 (mpm) REVERT: R 411 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7998 (mm) REVERT: R 420 TRP cc_start: 0.7426 (t60) cc_final: 0.7196 (t60) outliers start: 19 outliers final: 7 residues processed: 122 average time/residue: 1.6719 time to fit residues: 213.3030 Evaluate side-chains 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 270 ILE 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: 0.4980 chunk 16 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 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: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082889 restraints weight = 11910.721| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.20 r_work: 0.2936 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8260 Z= 0.266 Angle : 0.509 5.435 11184 Z= 0.281 Chirality : 0.043 0.156 1255 Planarity : 0.004 0.049 1423 Dihedral : 4.550 22.944 1115 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.42 % Allowed : 11.51 % Favored : 86.08 % 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: 1.51 (0.26), residues: 1005 helix: 2.72 (0.25), residues: 401 sheet: 0.32 (0.35), residues: 208 loop : -0.41 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.021 0.002 PHE R 260 TYR 0.016 0.002 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 134 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.956 Fit side-chains REVERT: B 172 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 217 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8824 (pmt) REVERT: G 47 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: R 291 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5701 (t80) REVERT: R 292 GLU cc_start: 0.5805 (pm20) cc_final: 0.5186 (pp20) REVERT: R 303 MET cc_start: 0.6359 (mmm) cc_final: 0.6137 (mpm) REVERT: R 411 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8054 (mm) REVERT: R 420 TRP cc_start: 0.7465 (t60) cc_final: 0.7242 (t60) outliers start: 21 outliers final: 9 residues processed: 122 average time/residue: 1.5995 time to fit residues: 204.6779 Evaluate side-chains 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 320 ASN 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 88 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.117476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082654 restraints weight = 11760.321| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.20 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8260 Z= 0.271 Angle : 0.505 5.609 11184 Z= 0.278 Chirality : 0.043 0.156 1255 Planarity : 0.004 0.049 1423 Dihedral : 4.569 23.680 1115 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.19 % Allowed : 12.77 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.26), residues: 1005 helix: 2.69 (0.25), residues: 401 sheet: 0.21 (0.35), residues: 209 loop : -0.40 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.019 0.001 PHE R 260 TYR 0.016 0.002 TYR B 59 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 131 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.881 Fit side-chains REVERT: B 172 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7960 (mm-30) REVERT: G 47 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: R 291 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.5778 (t80) REVERT: R 364 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7568 (mm-30) REVERT: R 411 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8130 (mm) REVERT: R 420 TRP cc_start: 0.7438 (t60) cc_final: 0.7227 (t60) outliers start: 19 outliers final: 9 residues processed: 121 average time/residue: 1.6020 time to fit residues: 202.8068 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 : 0.889 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.117476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.082705 restraints weight = 11829.159| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.20 r_work: 0.2933 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8260 Z= 0.264 Angle : 0.506 5.833 11184 Z= 0.278 Chirality : 0.043 0.155 1255 Planarity : 0.004 0.048 1423 Dihedral : 4.574 23.737 1115 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.07 % Allowed : 14.15 % 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: 1.43 (0.26), residues: 1005 helix: 2.70 (0.25), residues: 401 sheet: 0.22 (0.35), residues: 198 loop : -0.46 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.019 0.001 PHE R 260 TYR 0.016 0.002 TYR B 59 ARG 0.006 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: 18 poor density : 99 time to evaluate : 0.927 Fit side-chains REVERT: B 172 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 217 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8968 (pmt) REVERT: G 47 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: N 13 GLN cc_start: 0.8204 (mm110) cc_final: 0.7998 (mm-40) REVERT: R 291 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5750 (t80) REVERT: R 411 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8124 (mm) outliers start: 18 outliers final: 9 residues processed: 109 average time/residue: 1.5232 time to fit residues: 174.3505 Evaluate side-chains 109 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 92 optimal weight: 0.0070 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085347 restraints weight = 11837.721| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.20 r_work: 0.2981 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.002 0.031 8260 Z= 0.148 Angle : 0.462 7.136 11184 Z= 0.254 Chirality : 0.040 0.157 1255 Planarity : 0.004 0.048 1423 Dihedral : 4.254 21.360 1115 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.96 % Allowed : 14.38 % 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: 1.61 (0.26), residues: 1005 helix: 2.91 (0.25), residues: 401 sheet: 0.18 (0.35), residues: 205 loop : -0.36 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 420 HIS 0.002 0.001 HIS B 54 PHE 0.019 0.001 PHE R 260 TYR 0.013 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 124 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.908 Fit side-chains REVERT: B 217 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8946 (pmt) REVERT: G 47 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: R 291 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5815 (t80) REVERT: R 292 GLU cc_start: 0.5845 (pm20) cc_final: 0.5351 (pp20) outliers start: 17 outliers final: 7 residues processed: 117 average time/residue: 1.6556 time to fit residues: 202.9510 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 : 0.975 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.119170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084752 restraints weight = 11907.578| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.21 r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8260 Z= 0.180 Angle : 0.476 6.372 11184 Z= 0.260 Chirality : 0.041 0.169 1255 Planarity : 0.004 0.047 1423 Dihedral : 4.253 20.975 1115 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.96 % Allowed : 14.73 % Favored : 83.31 % 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 (0.27), residues: 1005 helix: 2.93 (0.25), residues: 401 sheet: 0.06 (0.35), residues: 209 loop : -0.33 (0.30), residues: 395 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 0.019 0.001 PHE R 260 TYR 0.015 0.001 TYR R 402 ARG 0.006 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 115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.914 Fit side-chains REVERT: B 217 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8936 (pmt) REVERT: G 47 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: R 291 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5822 (t80) outliers start: 17 outliers final: 7 residues processed: 108 average time/residue: 1.6564 time to fit residues: 188.3741 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 : 1.582 ------------------------------------------------------------------------------- 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 25 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089361 restraints weight = 12749.808| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.09 r_work: 0.3072 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8260 Z= 0.185 Angle : 0.485 7.277 11184 Z= 0.265 Chirality : 0.042 0.216 1255 Planarity : 0.004 0.046 1423 Dihedral : 4.261 20.855 1115 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.50 % Allowed : 15.30 % Favored : 83.20 % 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 (0.27), residues: 1005 helix: 2.93 (0.25), residues: 401 sheet: 0.10 (0.35), residues: 212 loop : -0.29 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 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 0.006 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 119 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.878 Fit side-chains REVERT: B 217 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8901 (pmt) REVERT: G 47 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: N 13 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8061 (mm-40) REVERT: R 291 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5786 (t80) REVERT: R 364 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7745 (mm-30) outliers start: 13 outliers final: 6 residues processed: 114 average time/residue: 1.6797 time to fit residues: 200.2278 Evaluate side-chains 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 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 N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089510 restraints weight = 12519.581| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.07 r_work: 0.3065 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8260 Z= 0.181 Angle : 0.489 6.953 11184 Z= 0.266 Chirality : 0.042 0.205 1255 Planarity : 0.004 0.046 1423 Dihedral : 4.263 20.732 1115 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.27 % Allowed : 15.07 % 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: 1.64 (0.27), residues: 1005 helix: 2.95 (0.25), residues: 401 sheet: 0.10 (0.35), residues: 212 loop : -0.29 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 420 HIS 0.002 0.001 HIS A 362 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 116 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.975 Fit side-chains REVERT: B 217 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8893 (pmt) REVERT: G 47 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: R 291 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.5682 (t80) REVERT: R 292 GLU cc_start: 0.5784 (pm20) cc_final: 0.5329 (pp20) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 1.6946 time to fit residues: 196.7220 Evaluate side-chains 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.119246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086794 restraints weight = 12718.505| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.10 r_work: 0.3013 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8260 Z= 0.348 Angle : 0.567 8.095 11184 Z= 0.308 Chirality : 0.045 0.174 1255 Planarity : 0.004 0.046 1423 Dihedral : 4.624 23.516 1115 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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 (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: 1.43 (0.26), residues: 1005 helix: 2.68 (0.25), residues: 401 sheet: 0.13 (0.34), residues: 215 loop : -0.39 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 420 HIS 0.004 0.001 HIS A 362 PHE 0.018 0.002 PHE R 260 TYR 0.021 0.002 TYR B 124 ARG 0.005 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8058.21 seconds wall clock time: 139 minutes 11.30 seconds (8351.30 seconds total)