Starting phenix.real_space_refine on Wed Mar 12 16:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.map" model { file = "/net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hix_33480/03_2025/8hix_33480.cif" } resolution = 3.12 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5258 2.51 5 N 1433 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1980 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 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: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2297 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 6.06, per 1000 atoms: 0.73 Number of scatterers: 8274 At special positions: 0 Unit cell: (88.4, 98.8, 126.88, 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 53 16.00 O 1530 8.00 N 1433 7.00 C 5258 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=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.966A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.574A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.748A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 4.223A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A 268 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.546A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.531A 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 350 removed outlier: 3.510A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.532A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.606A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.620A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 56 removed outlier: 4.154A pdb=" N LEU R 41 " --> pdb=" O PHE R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 91 removed outlier: 5.071A pdb=" N VAL R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Proline residue: R 85 - end of helix Processing helix chain 'R' and resid 99 through 133 removed outlier: 3.898A pdb=" N GLN R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 107 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER R 119 " --> pdb=" O VAL R 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR R 128 " --> pdb=" O SER R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 161 removed outlier: 3.714A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 167 removed outlier: 3.645A pdb=" N HIS R 167 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 185 removed outlier: 3.863A pdb=" N ALA R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP R 185 " --> pdb=" O CYS R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 199 removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O LEU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 232 removed outlier: 4.083A pdb=" N ALA R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 204 " --> pdb=" O TYR R 200 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 278 Proline residue: R 267 - end of helix removed outlier: 3.567A pdb=" N THR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 295 through 308 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 5.998A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.619A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.780A 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 62 removed outlier: 3.955A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.891A 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: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.859A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.940A 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: 3.652A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.105A 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: 6.313A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.987A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.227A 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 10 through 11 removed outlier: 6.335A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1188 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: 2.36 Time building geometry restraints manager: 2.51 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: 2628 1.34 - 1.46: 1594 1.46 - 1.57: 4164 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8458 Sorted by residual: bond pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 1.502 1.465 0.037 2.30e-02 1.89e+03 2.62e+00 bond pdb=" CG1 ILE A 276 " pdb=" CD1 ILE A 276 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.44e+00 bond pdb=" CG1 ILE R 150 " pdb=" CD1 ILE R 150 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.17e+00 bond pdb=" C THR A 325 " pdb=" N PRO A 326 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.07e+00 ... (remaining 8453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 10991 2.02 - 4.05: 391 4.05 - 6.07: 59 6.07 - 8.09: 17 8.09 - 10.11: 9 Bond angle restraints: 11467 Sorted by residual: angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C TRP R 265 " pdb=" N LEU R 266 " pdb=" CA LEU R 266 " ideal model delta sigma weight residual 120.09 125.86 -5.77 1.25e+00 6.40e-01 2.13e+01 angle pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta sigma weight residual 121.58 113.32 8.26 1.95e+00 2.63e-01 1.79e+01 angle pdb=" N GLN A 59 " pdb=" CA GLN A 59 " pdb=" CB GLN A 59 " ideal model delta sigma weight residual 110.16 115.89 -5.73 1.48e+00 4.57e-01 1.50e+01 angle pdb=" N GLY R 279 " pdb=" CA GLY R 279 " pdb=" C GLY R 279 " ideal model delta sigma weight residual 113.18 121.67 -8.49 2.37e+00 1.78e-01 1.28e+01 ... (remaining 11462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4434 17.90 - 35.81: 475 35.81 - 53.71: 71 53.71 - 71.61: 23 71.61 - 89.51: 7 Dihedral angle restraints: 5010 sinusoidal: 1971 harmonic: 3039 Sorted by residual: dihedral pdb=" CA THR R 278 " pdb=" C THR R 278 " pdb=" N GLY R 279 " pdb=" CA GLY R 279 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 53.86 39.14 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" N THR N 111 " pdb=" CA THR N 111 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1094 0.076 - 0.152: 178 0.152 - 0.228: 10 0.228 - 0.304: 2 0.304 - 0.380: 2 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB THR N 114 " pdb=" CA THR N 114 " pdb=" OG1 THR N 114 " pdb=" CG2 THR N 114 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1283 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 39 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 142 " 0.052 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 143 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 143 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 143 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 52 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ARG B 52 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG B 52 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 53 " -0.016 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 418 2.72 - 3.27: 8249 3.27 - 3.81: 14269 3.81 - 4.36: 17546 4.36 - 4.90: 29638 Nonbonded interactions: 70120 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR R 156 " pdb=" O MET R 198 " model vdw 2.232 3.040 nonbonded pdb=" O SER R 116 " pdb=" OG SER R 119 " model vdw 2.239 3.040 nonbonded pdb=" O PHE R 161 " pdb=" OG SER R 164 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD2 ASP N 106 " model vdw 2.258 3.040 ... (remaining 70115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 24.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 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 : 0.006 0.061 8458 Z= 0.393 Angle : 0.944 10.115 11467 Z= 0.512 Chirality : 0.056 0.380 1286 Planarity : 0.007 0.091 1460 Dihedral : 15.235 89.512 3035 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1029 helix: -0.27 (0.23), residues: 399 sheet: -1.17 (0.34), residues: 201 loop : -1.52 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP N 47 HIS 0.026 0.003 HIS A 220 PHE 0.040 0.003 PHE R 287 TYR 0.029 0.003 TYR B 111 ARG 0.013 0.001 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.919 Fit side-chains REVERT: B 275 SER cc_start: 0.8082 (m) cc_final: 0.7874 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2448 time to fit residues: 53.1435 Evaluate side-chains 132 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 371 ASN B 155 ASN N 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.228541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.186739 restraints weight = 8298.338| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.18 r_work: 0.3909 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8458 Z= 0.195 Angle : 0.582 7.466 11467 Z= 0.307 Chirality : 0.043 0.154 1286 Planarity : 0.005 0.068 1460 Dihedral : 5.099 24.429 1138 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.11 % Allowed : 9.40 % Favored : 89.49 % 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: -0.61 (0.25), residues: 1029 helix: 0.81 (0.25), residues: 403 sheet: -1.05 (0.34), residues: 213 loop : -1.18 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE R 287 TYR 0.016 0.001 TYR R 200 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.777 Fit side-chains REVERT: A 60 MET cc_start: 0.5571 (ptp) cc_final: 0.5299 (ptp) REVERT: A 220 HIS cc_start: 0.7488 (t70) cc_final: 0.7266 (t-90) REVERT: G 21 MET cc_start: 0.4653 (mmt) cc_final: 0.3829 (mmm) REVERT: N 46 GLU cc_start: 0.6912 (pm20) cc_final: 0.6363 (mm-30) outliers start: 10 outliers final: 7 residues processed: 170 average time/residue: 0.2450 time to fit residues: 54.9835 Evaluate side-chains 156 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN R 213 ASN R 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.231171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194306 restraints weight = 8355.142| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.71 r_work: 0.3935 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8458 Z= 0.163 Angle : 0.539 7.053 11467 Z= 0.283 Chirality : 0.042 0.139 1286 Planarity : 0.005 0.065 1460 Dihedral : 4.675 23.249 1138 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.33 % Allowed : 14.71 % Favored : 83.96 % 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: -0.15 (0.26), residues: 1029 helix: 1.38 (0.26), residues: 402 sheet: -0.97 (0.35), residues: 207 loop : -1.04 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.014 0.001 TYR R 200 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.951 Fit side-chains REVERT: A 220 HIS cc_start: 0.7617 (t70) cc_final: 0.7388 (t-90) REVERT: B 297 TRP cc_start: 0.8310 (m100) cc_final: 0.8105 (m100) REVERT: G 21 MET cc_start: 0.4419 (mmt) cc_final: 0.3688 (mmm) REVERT: N 46 GLU cc_start: 0.7153 (pm20) cc_final: 0.6432 (mm-30) REVERT: N 80 TYR cc_start: 0.7766 (m-80) cc_final: 0.7420 (m-80) REVERT: R 173 TYR cc_start: 0.7420 (m-80) cc_final: 0.6866 (m-80) outliers start: 12 outliers final: 11 residues processed: 165 average time/residue: 0.2458 time to fit residues: 53.6636 Evaluate side-chains 158 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.224797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.185438 restraints weight = 8304.872| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.70 r_work: 0.3914 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.209 Angle : 0.556 6.807 11467 Z= 0.292 Chirality : 0.042 0.138 1286 Planarity : 0.005 0.065 1460 Dihedral : 4.695 22.922 1138 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.10 % Allowed : 17.15 % Favored : 80.75 % 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: 0.00 (0.26), residues: 1029 helix: 1.64 (0.25), residues: 396 sheet: -0.91 (0.35), residues: 202 loop : -1.06 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE R 287 TYR 0.012 0.001 TYR B 105 ARG 0.007 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.987 Fit side-chains REVERT: G 21 MET cc_start: 0.4503 (mmt) cc_final: 0.3748 (mmm) REVERT: N 21 SER cc_start: 0.7383 (t) cc_final: 0.7021 (t) REVERT: N 46 GLU cc_start: 0.7348 (pm20) cc_final: 0.6671 (mm-30) REVERT: R 173 TYR cc_start: 0.7617 (m-80) cc_final: 0.6871 (m-80) REVERT: R 266 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7874 (tt) outliers start: 19 outliers final: 11 residues processed: 161 average time/residue: 0.2388 time to fit residues: 50.7320 Evaluate side-chains 157 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN N 123 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.227209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.187841 restraints weight = 8282.593| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.71 r_work: 0.3940 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8458 Z= 0.163 Angle : 0.529 6.704 11467 Z= 0.279 Chirality : 0.042 0.139 1286 Planarity : 0.004 0.063 1460 Dihedral : 4.472 22.168 1138 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.99 % Allowed : 18.81 % Favored : 79.20 % 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: 0.22 (0.26), residues: 1029 helix: 1.86 (0.26), residues: 396 sheet: -0.80 (0.35), residues: 205 loop : -0.97 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 255 TYR 0.020 0.001 TYR R 200 ARG 0.004 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.873 Fit side-chains REVERT: A 343 ASP cc_start: 0.7733 (m-30) cc_final: 0.7529 (m-30) REVERT: A 358 TYR cc_start: 0.7654 (m-80) cc_final: 0.6871 (m-80) REVERT: G 21 MET cc_start: 0.4469 (mmt) cc_final: 0.3746 (mmm) REVERT: N 21 SER cc_start: 0.7295 (t) cc_final: 0.6781 (t) REVERT: N 46 GLU cc_start: 0.7340 (pm20) cc_final: 0.6619 (mm-30) REVERT: N 80 TYR cc_start: 0.7749 (m-80) cc_final: 0.7398 (m-80) REVERT: R 173 TYR cc_start: 0.7408 (m-80) cc_final: 0.6805 (m-80) REVERT: R 266 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7845 (tt) outliers start: 18 outliers final: 12 residues processed: 166 average time/residue: 0.2320 time to fit residues: 51.2169 Evaluate side-chains 159 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.225955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186781 restraints weight = 8324.241| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.69 r_work: 0.3926 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8458 Z= 0.192 Angle : 0.545 6.761 11467 Z= 0.286 Chirality : 0.042 0.138 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.500 22.198 1138 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.21 % Allowed : 19.03 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.26), residues: 1029 helix: 2.02 (0.25), residues: 394 sheet: -0.80 (0.35), residues: 208 loop : -0.94 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 255 TYR 0.015 0.001 TYR R 200 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.879 Fit side-chains REVERT: A 32 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7779 (ttmm) REVERT: A 358 TYR cc_start: 0.7656 (m-80) cc_final: 0.6879 (m-80) REVERT: B 217 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5825 (tmm) REVERT: G 21 MET cc_start: 0.4584 (mmt) cc_final: 0.3836 (mmm) REVERT: N 46 GLU cc_start: 0.7350 (pm20) cc_final: 0.6671 (mm-30) REVERT: N 80 TYR cc_start: 0.7785 (m-80) cc_final: 0.7576 (m-80) REVERT: R 173 TYR cc_start: 0.7554 (m-80) cc_final: 0.6845 (m-80) REVERT: R 200 TYR cc_start: 0.6826 (m-80) cc_final: 0.6567 (m-80) REVERT: R 266 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7886 (tt) outliers start: 20 outliers final: 12 residues processed: 161 average time/residue: 0.2435 time to fit residues: 51.3901 Evaluate side-chains 161 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN N 84 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.228059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.188825 restraints weight = 8324.804| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.70 r_work: 0.3949 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.163 Angle : 0.529 7.311 11467 Z= 0.278 Chirality : 0.041 0.137 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.375 21.643 1138 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.99 % Allowed : 20.02 % Favored : 77.99 % 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: 0.45 (0.26), residues: 1029 helix: 2.15 (0.26), residues: 394 sheet: -0.75 (0.35), residues: 207 loop : -0.90 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.026 0.001 PHE R 255 TYR 0.011 0.001 TYR B 105 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.967 Fit side-chains REVERT: A 32 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7774 (ttmm) REVERT: A 358 TYR cc_start: 0.7619 (m-80) cc_final: 0.6864 (m-80) REVERT: B 217 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5799 (tmm) REVERT: G 21 MET cc_start: 0.4560 (mmt) cc_final: 0.3814 (mmm) REVERT: N 46 GLU cc_start: 0.7370 (pm20) cc_final: 0.6663 (mm-30) REVERT: N 80 TYR cc_start: 0.7759 (m-80) cc_final: 0.7367 (m-80) REVERT: R 125 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (mm) REVERT: R 173 TYR cc_start: 0.7483 (m-80) cc_final: 0.6714 (m-80) REVERT: R 200 TYR cc_start: 0.6734 (m-80) cc_final: 0.6528 (m-80) REVERT: R 254 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5396 (tt) REVERT: R 266 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7896 (tt) outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 0.2447 time to fit residues: 52.2615 Evaluate side-chains 163 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.227025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.187639 restraints weight = 8386.225| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.70 r_work: 0.3930 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8458 Z= 0.182 Angle : 0.543 7.311 11467 Z= 0.284 Chirality : 0.042 0.137 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.419 21.940 1138 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.88 % Allowed : 20.35 % Favored : 77.77 % 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: 0.46 (0.26), residues: 1029 helix: 2.13 (0.25), residues: 394 sheet: -0.73 (0.35), residues: 208 loop : -0.87 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.023 0.002 PHE R 287 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.860 Fit side-chains REVERT: A 358 TYR cc_start: 0.7651 (m-80) cc_final: 0.6896 (m-80) REVERT: B 217 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5783 (tmm) REVERT: G 21 MET cc_start: 0.4566 (mmt) cc_final: 0.3832 (mmm) REVERT: N 46 GLU cc_start: 0.7397 (pm20) cc_final: 0.6716 (mm-30) REVERT: N 80 TYR cc_start: 0.7790 (m-80) cc_final: 0.7429 (m-80) REVERT: R 125 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8331 (mm) REVERT: R 173 TYR cc_start: 0.7541 (m-80) cc_final: 0.6774 (m-80) REVERT: R 254 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5611 (tt) REVERT: R 266 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7916 (tt) outliers start: 17 outliers final: 12 residues processed: 161 average time/residue: 0.2331 time to fit residues: 49.4934 Evaluate side-chains 165 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.223088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183572 restraints weight = 8454.013| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.73 r_work: 0.3890 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8458 Z= 0.268 Angle : 0.602 7.155 11467 Z= 0.315 Chirality : 0.044 0.151 1286 Planarity : 0.005 0.064 1460 Dihedral : 4.740 22.914 1138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.21 % Allowed : 20.35 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1029 helix: 1.91 (0.26), residues: 394 sheet: -0.90 (0.35), residues: 210 loop : -0.91 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 265 HIS 0.013 0.001 HIS A 220 PHE 0.023 0.002 PHE R 255 TYR 0.037 0.002 TYR R 200 ARG 0.006 0.000 ARG R 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.948 Fit side-chains REVERT: A 32 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7755 (ttmm) REVERT: A 339 TYR cc_start: 0.8343 (m-80) cc_final: 0.8050 (m-80) REVERT: A 358 TYR cc_start: 0.7737 (m-80) cc_final: 0.6960 (m-80) REVERT: G 21 MET cc_start: 0.4387 (mmt) cc_final: 0.3745 (mmm) REVERT: N 46 GLU cc_start: 0.7418 (pm20) cc_final: 0.6775 (mm-30) REVERT: N 65 LYS cc_start: 0.6511 (tppt) cc_final: 0.6164 (tptt) REVERT: R 173 TYR cc_start: 0.7747 (m-80) cc_final: 0.6853 (m-80) REVERT: R 200 TYR cc_start: 0.6510 (m-80) cc_final: 0.6194 (m-80) REVERT: R 254 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5492 (tt) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 0.2551 time to fit residues: 53.0581 Evaluate side-chains 162 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 82 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.226400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.187870 restraints weight = 8248.194| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.67 r_work: 0.3929 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.176 Angle : 0.552 7.301 11467 Z= 0.288 Chirality : 0.042 0.149 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.478 22.160 1138 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 21.02 % Favored : 77.10 % 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: 0.40 (0.26), residues: 1029 helix: 2.06 (0.26), residues: 394 sheet: -0.77 (0.35), residues: 208 loop : -0.87 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.011 0.001 HIS A 220 PHE 0.024 0.002 PHE R 287 TYR 0.017 0.001 TYR R 200 ARG 0.007 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.877 Fit side-chains REVERT: A 32 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7710 (ttmm) REVERT: A 358 TYR cc_start: 0.7642 (m-80) cc_final: 0.6899 (m-80) REVERT: G 21 MET cc_start: 0.4376 (mmt) cc_final: 0.3716 (mmm) REVERT: N 46 GLU cc_start: 0.7398 (pm20) cc_final: 0.6765 (mm-30) REVERT: N 65 LYS cc_start: 0.6547 (tppt) cc_final: 0.6170 (tptt) REVERT: R 125 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8357 (mm) REVERT: R 173 TYR cc_start: 0.7518 (m-80) cc_final: 0.6786 (m-80) REVERT: R 254 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5573 (tt) REVERT: R 269 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (mm) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 0.2435 time to fit residues: 51.4951 Evaluate side-chains 162 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 288 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.228096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.188782 restraints weight = 8422.685| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.70 r_work: 0.3949 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8458 Z= 0.173 Angle : 0.548 7.225 11467 Z= 0.285 Chirality : 0.042 0.158 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.475 21.766 1138 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 21.02 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.26), residues: 1029 helix: 2.08 (0.25), residues: 394 sheet: -0.68 (0.35), residues: 206 loop : -0.84 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.012 0.001 HIS A 220 PHE 0.019 0.001 PHE R 215 TYR 0.023 0.001 TYR R 200 ARG 0.006 0.000 ARG R 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5039.15 seconds wall clock time: 87 minutes 27.40 seconds (5247.40 seconds total)