Starting phenix.real_space_refine on Sat Dec 28 21:19:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.map" model { file = "/net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y36_33590/12_2024/7y36_33590.cif" } resolution = 2.8 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 58 5.16 5 C 5851 2.51 5 N 1616 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9206 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' OH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.60 Number of scatterers: 9206 At special positions: 0 Unit cell: (124.722, 97.344, 152.1, 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 58 16.00 O 1681 8.00 N 1616 7.00 C 5851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 43.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 removed outlier: 3.522A pdb=" N ARG R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.348A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.681A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.067A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.566A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.633A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.605A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.925A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.864A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.556A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.615A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.002A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.797A 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 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.787A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.093A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.690A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.812A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.502A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.786A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.591A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.522A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.170A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1359 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: 2.79 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1503 1.31 - 1.44: 2663 1.44 - 1.56: 5159 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9407 Sorted by residual: bond pdb=" C GLN A 227 " pdb=" N ARG A 228 " ideal model delta sigma weight residual 1.330 1.403 -0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.98e+01 bond pdb=" CA THR R 178 " pdb=" C THR R 178 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.59e+01 bond pdb=" N LEU R 174 " pdb=" CA LEU R 174 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.23e-02 6.61e+03 1.58e+01 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.22e-02 6.72e+03 1.42e+01 ... (remaining 9402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12457 2.04 - 4.08: 233 4.08 - 6.12: 28 6.12 - 8.17: 10 8.17 - 10.21: 4 Bond angle restraints: 12732 Sorted by residual: angle pdb=" N GLU R 169 " pdb=" CA GLU R 169 " pdb=" C GLU R 169 " ideal model delta sigma weight residual 111.71 102.90 8.81 1.15e+00 7.56e-01 5.87e+01 angle pdb=" C GLN A 227 " pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 121.06 131.27 -10.21 1.88e+00 2.83e-01 2.95e+01 angle pdb=" C LEU P 24 " pdb=" N ARG P 25 " pdb=" CA ARG P 25 " ideal model delta sigma weight residual 120.44 113.12 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" N LEU R 174 " pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 111.33 117.63 -6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" N LYS R 172 " pdb=" CA LYS R 172 " pdb=" C LYS R 172 " ideal model delta sigma weight residual 112.38 118.55 -6.17 1.22e+00 6.72e-01 2.56e+01 ... (remaining 12727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5106 17.75 - 35.51: 391 35.51 - 53.26: 69 53.26 - 71.01: 8 71.01 - 88.77: 5 Dihedral angle restraints: 5579 sinusoidal: 2231 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CA CYS R 351 " pdb=" C CYS R 351 " pdb=" N TRP R 352 " pdb=" CA TRP R 352 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1097 0.056 - 0.111: 260 0.111 - 0.167: 40 0.167 - 0.223: 6 0.223 - 0.278: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA LEU R 174 " pdb=" N LEU R 174 " pdb=" C LEU R 174 " pdb=" CB LEU R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR R 178 " pdb=" N THR R 178 " pdb=" C THR R 178 " pdb=" CB THR R 178 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1402 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 168 " 0.035 2.00e-02 2.50e+03 7.17e-02 5.15e+01 pdb=" C SER R 168 " -0.124 2.00e-02 2.50e+03 pdb=" O SER R 168 " 0.048 2.00e-02 2.50e+03 pdb=" N GLU R 169 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.016 2.00e-02 2.50e+03 1.54e-02 4.73e+00 pdb=" CG TYR B 59 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 8791 3.25 - 3.80: 14683 3.80 - 4.35: 19212 4.35 - 4.90: 32425 Nonbonded interactions: 75371 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ASP R 113 " pdb=" CG1 VAL P 31 " model vdw 2.178 3.460 nonbonded pdb=" OG1 THR R 218 " pdb=" OE2 GLU R 317 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.207 3.040 nonbonded pdb=" CG2 ILE R 115 " pdb=" NZ LYS P 27 " model vdw 2.229 3.540 ... (remaining 75366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.040 Process input model: 24.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 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 : 0.007 0.072 9407 Z= 0.421 Angle : 0.732 10.207 12732 Z= 0.445 Chirality : 0.049 0.278 1405 Planarity : 0.005 0.072 1621 Dihedral : 12.892 88.766 3395 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -1.26 (0.22), residues: 1127 helix: -0.23 (0.22), residues: 449 sheet: -0.68 (0.31), residues: 227 loop : -1.41 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.002 PHE R 335 TYR 0.038 0.002 TYR B 59 ARG 0.009 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 1.1916 time to fit residues: 395.5853 Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 458 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 HIS R 216 HIS R 463 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 41 HIS B 62 HIS B 75 GLN B 91 HIS B 119 ASN B 176 GLN B 266 HIS B 295 ASN B 313 ASN N 77 ASN N 82 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9407 Z= 0.286 Angle : 0.738 13.282 12732 Z= 0.390 Chirality : 0.046 0.169 1405 Planarity : 0.005 0.071 1621 Dihedral : 5.056 28.989 1261 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.04 % Allowed : 15.76 % Favored : 80.20 % 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: -0.14 (0.24), residues: 1127 helix: 0.87 (0.24), residues: 448 sheet: -0.14 (0.32), residues: 222 loop : -0.97 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.010 0.002 HIS B 183 PHE 0.036 0.002 PHE R 335 TYR 0.040 0.002 TYR R 191 ARG 0.011 0.001 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 469 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6860 (mm-30) REVERT: A 347 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6758 (ptp-110) REVERT: B 81 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5954 (pt) outliers start: 40 outliers final: 10 residues processed: 293 average time/residue: 1.1277 time to fit residues: 355.3914 Evaluate side-chains 203 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 ASN P 32 HIS B 266 HIS B 295 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9407 Z= 0.223 Angle : 0.670 11.148 12732 Z= 0.350 Chirality : 0.044 0.156 1405 Planarity : 0.004 0.057 1621 Dihedral : 4.602 28.454 1259 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.05 % Allowed : 20.51 % Favored : 74.44 % 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: 0.52 (0.25), residues: 1127 helix: 1.61 (0.24), residues: 451 sheet: 0.05 (0.32), residues: 229 loop : -0.76 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 36 HIS 0.003 0.001 HIS R 420 PHE 0.015 0.002 PHE A 315 TYR 0.027 0.002 TYR R 191 ARG 0.010 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.6047 (ppp) cc_final: 0.5798 (ptm) REVERT: A 386 MET cc_start: 0.6987 (tmm) cc_final: 0.6730 (ttt) REVERT: A 389 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6744 (ttm110) REVERT: N 59 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7308 (p) REVERT: N 73 ASP cc_start: 0.5512 (p0) cc_final: 0.5234 (p0) outliers start: 50 outliers final: 16 residues processed: 253 average time/residue: 1.2583 time to fit residues: 339.8462 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 HIS ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 266 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.8656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9407 Z= 0.202 Angle : 0.645 9.770 12732 Z= 0.337 Chirality : 0.043 0.157 1405 Planarity : 0.004 0.041 1621 Dihedral : 4.434 29.280 1259 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.75 % Allowed : 24.14 % Favored : 71.11 % 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: 0.72 (0.25), residues: 1127 helix: 1.85 (0.24), residues: 450 sheet: 0.29 (0.34), residues: 204 loop : -0.76 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 420 PHE 0.015 0.001 PHE B 292 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 LEU cc_start: 0.7553 (mt) cc_final: 0.7353 (mt) REVERT: A 347 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7198 (ptp-110) REVERT: A 389 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6806 (ttm110) outliers start: 47 outliers final: 19 residues processed: 240 average time/residue: 1.2708 time to fit residues: 325.3500 Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 293 ASN G 18 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.9549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9407 Z= 0.190 Angle : 0.620 9.105 12732 Z= 0.325 Chirality : 0.043 0.157 1405 Planarity : 0.004 0.038 1621 Dihedral : 4.296 23.422 1259 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.95 % Allowed : 26.06 % Favored : 68.99 % 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: 0.87 (0.25), residues: 1127 helix: 1.89 (0.24), residues: 450 sheet: 0.40 (0.33), residues: 230 loop : -0.67 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 420 PHE 0.014 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 441 MET cc_start: 0.7061 (mmm) cc_final: 0.6838 (mmm) REVERT: A 14 ASN cc_start: 0.5696 (OUTLIER) cc_final: 0.5149 (p0) outliers start: 49 outliers final: 21 residues processed: 252 average time/residue: 1.2789 time to fit residues: 343.0779 Evaluate side-chains 199 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 353 ASP Chi-restraints excluded: chain R residue 470 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 1.0139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9407 Z= 0.205 Angle : 0.642 9.460 12732 Z= 0.334 Chirality : 0.044 0.266 1405 Planarity : 0.004 0.029 1621 Dihedral : 4.362 26.932 1259 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.24 % Allowed : 28.28 % Favored : 67.47 % 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: 0.96 (0.25), residues: 1127 helix: 1.92 (0.24), residues: 450 sheet: 0.68 (0.35), residues: 215 loop : -0.66 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 437 HIS 0.004 0.001 HIS R 420 PHE 0.011 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.5682 (OUTLIER) cc_final: 0.5294 (p0) REVERT: A 310 ASP cc_start: 0.6096 (p0) cc_final: 0.5850 (p0) outliers start: 42 outliers final: 26 residues processed: 228 average time/residue: 1.2391 time to fit residues: 301.9296 Evaluate side-chains 206 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 1.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9407 Z= 0.215 Angle : 0.645 9.940 12732 Z= 0.337 Chirality : 0.043 0.274 1405 Planarity : 0.004 0.032 1621 Dihedral : 4.350 25.131 1259 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.15 % Allowed : 28.18 % Favored : 66.67 % 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: 1.07 (0.26), residues: 1127 helix: 2.00 (0.24), residues: 448 sheet: 0.78 (0.35), residues: 219 loop : -0.62 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 23 HIS 0.004 0.001 HIS R 420 PHE 0.024 0.001 PHE R 314 TYR 0.029 0.001 TYR R 191 ARG 0.010 0.001 ARG R 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.5955 (OUTLIER) cc_final: 0.5651 (p0) REVERT: A 310 ASP cc_start: 0.6289 (p0) cc_final: 0.6071 (p0) REVERT: N 83 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6926 (mtt) outliers start: 51 outliers final: 29 residues processed: 251 average time/residue: 1.1802 time to fit residues: 317.0564 Evaluate side-chains 220 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 1.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9407 Z= 0.201 Angle : 0.691 12.080 12732 Z= 0.358 Chirality : 0.043 0.309 1405 Planarity : 0.004 0.033 1621 Dihedral : 4.343 23.563 1259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.84 % Allowed : 30.00 % Favored : 66.16 % 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: 1.08 (0.26), residues: 1127 helix: 2.02 (0.24), residues: 448 sheet: 0.95 (0.36), residues: 218 loop : -0.73 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 23 HIS 0.003 0.001 HIS R 420 PHE 0.018 0.001 PHE R 335 TYR 0.031 0.001 TYR R 191 ARG 0.009 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7149 (ppp) cc_final: 0.6672 (ptm) REVERT: A 14 ASN cc_start: 0.5814 (OUTLIER) cc_final: 0.5594 (p0) REVERT: N 73 ASP cc_start: 0.6250 (p0) cc_final: 0.5703 (p0) outliers start: 38 outliers final: 21 residues processed: 236 average time/residue: 1.2480 time to fit residues: 315.1288 Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 103 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 266 HIS N 84 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 1.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9407 Z= 0.200 Angle : 0.697 11.831 12732 Z= 0.359 Chirality : 0.043 0.278 1405 Planarity : 0.004 0.033 1621 Dihedral : 4.332 24.028 1259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 30.51 % Favored : 66.46 % 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: 1.10 (0.26), residues: 1127 helix: 1.95 (0.25), residues: 448 sheet: 0.99 (0.35), residues: 227 loop : -0.65 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 23 HIS 0.004 0.001 HIS R 420 PHE 0.021 0.001 PHE R 314 TYR 0.033 0.001 TYR R 191 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7254 (ppp) cc_final: 0.6782 (ptm) outliers start: 30 outliers final: 22 residues processed: 231 average time/residue: 1.3240 time to fit residues: 325.3835 Evaluate side-chains 216 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 1.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9407 Z= 0.230 Angle : 0.758 11.034 12732 Z= 0.388 Chirality : 0.045 0.278 1405 Planarity : 0.004 0.042 1621 Dihedral : 4.506 22.721 1259 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.83 % Allowed : 32.32 % Favored : 64.85 % 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: 1.09 (0.26), residues: 1127 helix: 1.89 (0.25), residues: 449 sheet: 1.03 (0.36), residues: 225 loop : -0.61 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 298 HIS 0.004 0.001 HIS R 143 PHE 0.021 0.001 PHE R 335 TYR 0.036 0.001 TYR R 191 ARG 0.015 0.001 ARG B 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 425 MET cc_start: 0.7258 (ppp) cc_final: 0.6809 (ptm) REVERT: G 46 LYS cc_start: 0.7191 (ttpp) cc_final: 0.6498 (ptmm) outliers start: 28 outliers final: 20 residues processed: 221 average time/residue: 1.2782 time to fit residues: 301.8967 Evaluate side-chains 211 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109403 restraints weight = 14676.254| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.48 r_work: 0.3281 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 1.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9407 Z= 0.254 Angle : 0.765 11.275 12732 Z= 0.393 Chirality : 0.045 0.273 1405 Planarity : 0.005 0.081 1621 Dihedral : 4.646 24.025 1259 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.83 % Allowed : 32.22 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.26), residues: 1127 helix: 1.79 (0.25), residues: 448 sheet: 1.04 (0.36), residues: 226 loop : -0.61 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 298 HIS 0.005 0.001 HIS R 420 PHE 0.023 0.001 PHE R 335 TYR 0.034 0.001 TYR R 191 ARG 0.014 0.001 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.98 seconds wall clock time: 90 minutes 18.12 seconds (5418.12 seconds total)