Starting phenix.real_space_refine on Fri Jun 6 18:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hix_33480/06_2025/8hix_33480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hix_33480/06_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_33480/06_2025/8hix_33480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hix_33480/06_2025/8hix_33480.map" model { file = "/net/cci-nas-00/data/ceres_data/8hix_33480/06_2025/8hix_33480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hix_33480/06_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-5710/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: 4.93, per 1000 atoms: 0.60 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: 1.85 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: 0.86 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: 2.37 Time building geometry restraints manager: 2.09 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.070 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: 0.010 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: 25.380 ------------------------------------------------------------------------------- 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 8461 Z= 0.265 Angle : 0.945 10.115 11473 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 Details of bonding type rmsd hydrogen bonds : bond 0.12973 ( 412) hydrogen bonds : angle 6.63425 ( 1188) SS BOND : bond 0.00766 ( 3) SS BOND : angle 1.76711 ( 6) covalent geometry : bond 0.00594 ( 8458) covalent geometry : angle 0.94439 (11467) *********************** 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 : 0.768 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: 0.2552 time to fit residues: 55.1635 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 : 0.902 ------------------------------------------------------------------------------- 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 8461 Z= 0.137 Angle : 0.582 7.466 11473 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 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 412) hydrogen bonds : angle 4.87777 ( 1188) SS BOND : bond 0.00518 ( 3) SS BOND : angle 0.97171 ( 6) covalent geometry : bond 0.00302 ( 8458) covalent geometry : angle 0.58170 (11467) *********************** 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 : 1.191 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: 0.2796 time to fit residues: 62.7418 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 : 0.900 ------------------------------------------------------------------------------- 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 8461 Z= 0.117 Angle : 0.539 7.053 11473 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 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 412) hydrogen bonds : angle 4.57457 ( 1188) SS BOND : bond 0.00385 ( 3) SS BOND : angle 0.53178 ( 6) covalent geometry : bond 0.00254 ( 8458) covalent geometry : angle 0.53870 (11467) *********************** 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 : 0.845 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: 0.2345 time to fit residues: 51.5956 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 : 0.835 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.6994 ------------------------------------------------------------------------------- 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** N 123 GLN ** 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 = 0.4495 r_free = 0.4495 target = 0.227327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.187954 restraints weight = 8295.983| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.69 r_work: 0.3936 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8461 Z= 0.118 Angle : 0.524 6.744 11473 Z= 0.276 Chirality : 0.041 0.142 1286 Planarity : 0.004 0.065 1460 Dihedral : 4.507 22.235 1138 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.99 % Allowed : 16.92 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1029 helix: 1.77 (0.26), residues: 396 sheet: -0.77 (0.36), residues: 199 loop : -1.05 (0.29), residues: 434 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 0.021 0.001 PHE R 287 TYR 0.009 0.001 TYR B 105 ARG 0.007 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 412) hydrogen bonds : angle 4.44451 ( 1188) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.48926 ( 6) covalent geometry : bond 0.00257 ( 8458) covalent geometry : angle 0.52419 (11467) *********************** 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 175 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.834 Fit side-chains REVERT: A 266 LEU cc_start: 0.7940 (mt) cc_final: 0.7705 (tp) REVERT: G 21 MET cc_start: 0.4402 (mmt) cc_final: 0.3713 (mmm) REVERT: N 21 SER cc_start: 0.7296 (t) cc_final: 0.6900 (t) REVERT: N 46 GLU cc_start: 0.7366 (pm20) cc_final: 0.6585 (mm-30) REVERT: R 173 TYR cc_start: 0.7398 (m-80) cc_final: 0.6799 (m-80) REVERT: R 266 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7880 (tt) outliers start: 18 outliers final: 11 residues processed: 167 average time/residue: 0.2290 time to fit residues: 50.8033 Evaluate side-chains 160 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4497 r_free = 0.4497 target = 0.227523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188270 restraints weight = 8258.748| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.70 r_work: 0.3940 rms_B_bonded: 2.87 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: 0.7047 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8461 Z= 0.120 Angle : 0.530 6.716 11473 Z= 0.278 Chirality : 0.042 0.140 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.442 21.940 1138 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.21 % Allowed : 19.36 % Favored : 78.43 % 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: 0.27 (0.26), residues: 1029 helix: 1.89 (0.26), residues: 396 sheet: -0.81 (0.35), residues: 207 loop : -0.92 (0.30), residues: 426 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 0.026 0.001 PHE R 255 TYR 0.020 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 412) hydrogen bonds : angle 4.42124 ( 1188) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.43607 ( 6) covalent geometry : bond 0.00265 ( 8458) covalent geometry : angle 0.52991 (11467) *********************** 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 175 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.816 Fit side-chains REVERT: A 32 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7830 (ttmm) REVERT: A 358 TYR cc_start: 0.7626 (m-80) cc_final: 0.6873 (m-80) REVERT: G 21 MET cc_start: 0.4437 (mmt) cc_final: 0.3726 (mmm) REVERT: N 21 SER cc_start: 0.7282 (t) cc_final: 0.6755 (t) REVERT: N 46 GLU cc_start: 0.7346 (pm20) cc_final: 0.6648 (mm-30) REVERT: N 80 TYR cc_start: 0.7743 (m-80) cc_final: 0.7377 (m-80) REVERT: R 173 TYR cc_start: 0.7432 (m-80) cc_final: 0.6848 (m-80) REVERT: R 229 GLN cc_start: 0.7312 (mm-40) cc_final: 0.7101 (mm110) REVERT: R 266 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7808 (tt) outliers start: 20 outliers final: 13 residues processed: 167 average time/residue: 0.2287 time to fit residues: 50.1970 Evaluate side-chains 164 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 N residue 122 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: 1.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4540 r_free = 0.4540 target = 0.232773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193819 restraints weight = 8296.987| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.90 r_work: 0.3949 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8461 Z= 0.116 Angle : 0.524 6.713 11473 Z= 0.276 Chirality : 0.041 0.142 1286 Planarity : 0.004 0.063 1460 Dihedral : 4.341 21.643 1138 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.88 % Allowed : 20.02 % Favored : 78.10 % 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: 0.44 (0.26), residues: 1029 helix: 2.09 (0.26), residues: 394 sheet: -0.74 (0.35), residues: 207 loop : -0.87 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.022 0.001 PHE R 287 TYR 0.014 0.001 TYR R 200 ARG 0.004 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 412) hydrogen bonds : angle 4.36981 ( 1188) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.39611 ( 6) covalent geometry : bond 0.00253 ( 8458) covalent geometry : angle 0.52434 (11467) *********************** 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 173 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.844 Fit side-chains REVERT: A 32 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7809 (ttmm) REVERT: A 358 TYR cc_start: 0.7639 (m-80) cc_final: 0.6900 (m-80) REVERT: G 21 MET cc_start: 0.4414 (mmt) cc_final: 0.3709 (mmm) REVERT: N 21 SER cc_start: 0.7186 (t) cc_final: 0.6713 (t) REVERT: N 46 GLU cc_start: 0.7304 (pm20) cc_final: 0.6624 (mm-30) REVERT: N 80 TYR cc_start: 0.7714 (m-80) cc_final: 0.7393 (m-80) REVERT: R 173 TYR cc_start: 0.7421 (m-80) cc_final: 0.6760 (m-80) REVERT: R 200 TYR cc_start: 0.6827 (m-80) cc_final: 0.6444 (m-80) REVERT: R 254 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5491 (tt) REVERT: R 266 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 17 outliers final: 12 residues processed: 167 average time/residue: 0.2375 time to fit residues: 52.1621 Evaluate side-chains 165 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain N residue 122 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 0.0000 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.234468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194317 restraints weight = 8269.555| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.09 r_work: 0.3968 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8461 Z= 0.107 Angle : 0.515 6.689 11473 Z= 0.270 Chirality : 0.041 0.147 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.225 21.151 1138 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.88 % Allowed : 20.02 % Favored : 78.10 % 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: 0.56 (0.27), residues: 1029 helix: 2.21 (0.26), residues: 395 sheet: -0.52 (0.36), residues: 203 loop : -0.91 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.021 0.001 PHE R 215 TYR 0.009 0.001 TYR R 200 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 412) hydrogen bonds : angle 4.30798 ( 1188) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.38292 ( 6) covalent geometry : bond 0.00231 ( 8458) covalent geometry : angle 0.51530 (11467) *********************** 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 175 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.888 Fit side-chains REVERT: G 21 MET cc_start: 0.4306 (mmt) cc_final: 0.3569 (mmm) REVERT: N 21 SER cc_start: 0.7148 (t) cc_final: 0.6705 (t) REVERT: N 46 GLU cc_start: 0.7288 (pm20) cc_final: 0.6689 (mm-30) REVERT: N 80 TYR cc_start: 0.7672 (m-80) cc_final: 0.7185 (m-80) REVERT: R 173 TYR cc_start: 0.7430 (m-80) cc_final: 0.6809 (m-80) REVERT: R 200 TYR cc_start: 0.6634 (m-80) cc_final: 0.6383 (m-80) REVERT: R 254 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5398 (tt) REVERT: R 266 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7853 (tt) outliers start: 17 outliers final: 11 residues processed: 169 average time/residue: 0.2539 time to fit residues: 56.3992 Evaluate side-chains 160 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 N residue 122 THR 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: 1.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.226150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.188053 restraints weight = 8408.619| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.77 r_work: 0.3919 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8461 Z= 0.138 Angle : 0.556 7.168 11473 Z= 0.291 Chirality : 0.042 0.146 1286 Planarity : 0.004 0.061 1460 Dihedral : 4.453 21.648 1138 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.99 % Allowed : 20.46 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1029 helix: 2.12 (0.25), residues: 394 sheet: -0.63 (0.36), residues: 205 loop : -0.87 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 PHE 0.024 0.002 PHE R 215 TYR 0.011 0.001 TYR B 105 ARG 0.007 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 412) hydrogen bonds : angle 4.42130 ( 1188) SS BOND : bond 0.00392 ( 3) SS BOND : angle 0.44228 ( 6) covalent geometry : bond 0.00309 ( 8458) covalent geometry : angle 0.55604 (11467) *********************** 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 163 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.941 Fit side-chains REVERT: A 32 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7825 (ttmm) REVERT: A 343 ASP cc_start: 0.7456 (m-30) cc_final: 0.7142 (m-30) REVERT: A 358 TYR cc_start: 0.7693 (m-80) cc_final: 0.6907 (m-80) REVERT: B 105 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6872 (t80) REVERT: G 21 MET cc_start: 0.4515 (mmt) cc_final: 0.3820 (mmm) REVERT: N 46 GLU cc_start: 0.7422 (pm20) cc_final: 0.6760 (mm-30) REVERT: R 125 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8316 (mm) REVERT: R 173 TYR cc_start: 0.7545 (m-80) cc_final: 0.6838 (m-80) REVERT: R 254 LEU cc_start: 0.5718 (OUTLIER) cc_final: 0.5360 (tt) REVERT: R 266 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7910 (tt) outliers start: 18 outliers final: 13 residues processed: 157 average time/residue: 0.2457 time to fit residues: 51.0508 Evaluate side-chains 161 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 105 TYR 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 N residue 122 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: 0.8980 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.228017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.189880 restraints weight = 8426.743| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.70 r_work: 0.3942 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8461 Z= 0.126 Angle : 0.543 7.257 11473 Z= 0.284 Chirality : 0.042 0.138 1286 Planarity : 0.004 0.060 1460 Dihedral : 4.393 21.593 1138 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.43 % Allowed : 20.58 % Favored : 76.99 % 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: 0.52 (0.27), residues: 1029 helix: 2.15 (0.26), residues: 394 sheet: -0.63 (0.36), residues: 208 loop : -0.85 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 265 HIS 0.010 0.001 HIS A 220 PHE 0.020 0.002 PHE R 215 TYR 0.033 0.001 TYR R 200 ARG 0.007 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 412) hydrogen bonds : angle 4.39922 ( 1188) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.35271 ( 6) covalent geometry : bond 0.00279 ( 8458) covalent geometry : angle 0.54278 (11467) *********************** 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 164 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.925 Fit side-chains REVERT: A 32 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7829 (ttmm) REVERT: A 358 TYR cc_start: 0.7634 (m-80) cc_final: 0.6882 (m-80) REVERT: B 105 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6843 (t80) REVERT: G 21 MET cc_start: 0.4531 (mmt) cc_final: 0.3830 (mmm) REVERT: N 46 GLU cc_start: 0.7347 (pm20) cc_final: 0.6740 (mm-30) REVERT: R 125 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8265 (mm) REVERT: R 173 TYR cc_start: 0.7491 (m-80) cc_final: 0.6736 (m-80) REVERT: R 200 TYR cc_start: 0.6427 (m-80) cc_final: 0.5937 (m-80) REVERT: R 254 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5419 (tt) REVERT: R 322 MET cc_start: 0.2830 (tpp) cc_final: 0.2367 (mpp) outliers start: 22 outliers final: 15 residues processed: 157 average time/residue: 0.2373 time to fit residues: 49.3839 Evaluate side-chains 157 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 105 TYR 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 N residue 122 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 273 LEU 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: 2.9990 chunk 16 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.227492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.187327 restraints weight = 8277.528| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.72 r_work: 0.3931 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8461 Z= 0.132 Angle : 0.551 7.038 11473 Z= 0.287 Chirality : 0.042 0.152 1286 Planarity : 0.004 0.060 1460 Dihedral : 4.447 21.706 1138 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.99 % Allowed : 21.24 % Favored : 76.77 % 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: 0.49 (0.26), residues: 1029 helix: 2.12 (0.25), residues: 394 sheet: -0.64 (0.35), residues: 208 loop : -0.86 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.013 0.001 HIS A 220 PHE 0.024 0.002 PHE R 287 TYR 0.027 0.001 TYR R 200 ARG 0.007 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 412) hydrogen bonds : angle 4.43878 ( 1188) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.38598 ( 6) covalent geometry : bond 0.00295 ( 8458) covalent geometry : angle 0.55144 (11467) ********************** 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 161 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.812 Fit side-chains REVERT: A 16 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7072 (mp0) REVERT: A 32 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7829 (ttmm) REVERT: A 358 TYR cc_start: 0.7632 (m-80) cc_final: 0.6881 (m-80) REVERT: B 105 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6746 (t80) REVERT: G 21 MET cc_start: 0.4527 (mmt) cc_final: 0.3820 (mmm) REVERT: N 46 GLU cc_start: 0.7382 (pm20) cc_final: 0.6751 (mm-30) REVERT: R 125 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8311 (mm) REVERT: R 173 TYR cc_start: 0.7542 (m-80) cc_final: 0.6756 (m-80) REVERT: R 200 TYR cc_start: 0.6392 (m-80) cc_final: 0.6095 (m-80) REVERT: R 254 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5359 (tt) REVERT: R 322 MET cc_start: 0.2852 (tpp) cc_final: 0.2388 (mpp) outliers start: 18 outliers final: 15 residues processed: 156 average time/residue: 0.2468 time to fit residues: 50.4282 Evaluate side-chains 160 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 105 TYR 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 N residue 122 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 273 LEU 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: 3.9990 chunk 95 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.229701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.190405 restraints weight = 8435.544| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.71 r_work: 0.3953 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8461 Z= 0.109 Angle : 0.529 7.275 11473 Z= 0.274 Chirality : 0.041 0.147 1286 Planarity : 0.004 0.060 1460 Dihedral : 4.277 20.961 1138 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.21 % Allowed : 21.24 % Favored : 76.55 % 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 (0.27), residues: 1029 helix: 2.22 (0.26), residues: 396 sheet: -0.53 (0.36), residues: 205 loop : -0.84 (0.30), residues: 428 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 0.018 0.001 PHE R 215 TYR 0.021 0.001 TYR R 200 ARG 0.007 0.000 ARG R 127 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 412) hydrogen bonds : angle 4.34943 ( 1188) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.30119 ( 6) covalent geometry : bond 0.00239 ( 8458) covalent geometry : angle 0.52888 (11467) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5325.18 seconds wall clock time: 92 minutes 14.88 seconds (5534.88 seconds total)