Starting phenix.real_space_refine on Fri Nov 15 02:26:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_33480.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_33480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_33480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_33480.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hix_33480/11_2024/8hix_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-5513/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: 4.74, per 1000 atoms: 0.57 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 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: 0.96 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: 2.24 Time building geometry restraints manager: 2.43 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.140 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- 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 : 0.937 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: 0.2333 time to fit residues: 50.7156 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 : 0.861 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 : 0.923 Fit side-chains REVERT: A 60 MET cc_start: 0.5211 (ptp) cc_final: 0.4934 (ptp) REVERT: G 21 MET cc_start: 0.4785 (mmt) cc_final: 0.4034 (mmm) outliers start: 10 outliers final: 7 residues processed: 170 average time/residue: 0.2397 time to fit residues: 53.8717 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 : 1.070 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1517 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 : 0.554 7.103 11467 Z= 0.291 Chirality : 0.042 0.137 1286 Planarity : 0.005 0.065 1460 Dihedral : 4.768 23.522 1138 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.44 % Allowed : 14.82 % Favored : 83.74 % 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: -0.18 (0.26), residues: 1029 helix: 1.36 (0.26), residues: 403 sheet: -0.99 (0.34), residues: 208 loop : -1.07 (0.29), residues: 418 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 0.015 0.001 PHE A 212 TYR 0.013 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 169 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.903 Fit side-chains REVERT: G 21 MET cc_start: 0.4613 (mmt) cc_final: 0.3982 (mmm) REVERT: R 173 TYR cc_start: 0.7264 (m-80) cc_final: 0.7003 (m-80) outliers start: 13 outliers final: 12 residues processed: 162 average time/residue: 0.2413 time to fit residues: 51.5646 Evaluate side-chains 155 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 119 ASN 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 69 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 221 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8458 Z= 0.151 Angle : 0.517 6.705 11467 Z= 0.272 Chirality : 0.041 0.143 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.475 22.039 1138 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.77 % Allowed : 17.70 % Favored : 80.53 % 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: 0.13 (0.26), residues: 1029 helix: 1.79 (0.26), residues: 395 sheet: -0.90 (0.35), residues: 203 loop : -1.00 (0.29), residues: 431 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 0.020 0.001 PHE R 287 TYR 0.008 0.001 TYR R 262 ARG 0.008 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 173 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.987 Fit side-chains REVERT: G 21 MET cc_start: 0.4527 (mmt) cc_final: 0.4024 (mmm) REVERT: N 80 TYR cc_start: 0.7465 (m-80) cc_final: 0.7256 (m-80) REVERT: R 173 TYR cc_start: 0.7085 (m-80) cc_final: 0.6863 (m-80) outliers start: 16 outliers final: 10 residues processed: 165 average time/residue: 0.2480 time to fit residues: 53.7811 Evaluate side-chains 157 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 105 TYR 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 N residue 114 THR 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 55 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1799 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= 0.249 Angle : 0.580 6.806 11467 Z= 0.305 Chirality : 0.043 0.146 1286 Planarity : 0.005 0.064 1460 Dihedral : 4.762 22.811 1138 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.77 % Allowed : 18.03 % 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: 0.07 (0.26), residues: 1029 helix: 1.70 (0.26), residues: 395 sheet: -0.94 (0.35), residues: 204 loop : -1.00 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.007 0.001 HIS A 357 PHE 0.028 0.002 PHE R 255 TYR 0.020 0.002 TYR R 200 ARG 0.007 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 175 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.988 Fit side-chains REVERT: A 32 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7452 (ttmm) REVERT: B 105 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6715 (t80) REVERT: G 21 MET cc_start: 0.4788 (mmt) cc_final: 0.4224 (mmm) REVERT: N 21 SER cc_start: 0.7414 (t) cc_final: 0.7047 (t) REVERT: R 173 TYR cc_start: 0.7457 (m-80) cc_final: 0.6932 (m-80) REVERT: R 266 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7971 (tt) outliers start: 25 outliers final: 15 residues processed: 163 average time/residue: 0.2451 time to fit residues: 52.9671 Evaluate side-chains 159 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 109 VAL Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 273 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 87 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 220 HIS ** 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 ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.1927 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= 0.192 Angle : 0.555 7.705 11467 Z= 0.292 Chirality : 0.042 0.138 1286 Planarity : 0.005 0.065 1460 Dihedral : 4.577 22.535 1138 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.32 % Allowed : 20.02 % Favored : 77.65 % 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: 1.87 (0.26), residues: 396 sheet: -0.81 (0.35), residues: 208 loop : -0.94 (0.30), residues: 425 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 0.027 0.002 PHE R 215 TYR 0.023 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 *********************** 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 170 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7417 (ttmm) REVERT: A 358 TYR cc_start: 0.7276 (m-80) cc_final: 0.6599 (m-80) REVERT: B 105 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 256 ARG cc_start: 0.6306 (mtm180) cc_final: 0.6076 (mtm180) REVERT: G 21 MET cc_start: 0.4766 (mmt) cc_final: 0.4213 (mmm) REVERT: N 21 SER cc_start: 0.7295 (t) cc_final: 0.6939 (t) REVERT: R 125 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8072 (mm) REVERT: R 173 TYR cc_start: 0.7371 (m-80) cc_final: 0.6948 (m-80) REVERT: R 266 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7955 (tt) outliers start: 21 outliers final: 15 residues processed: 163 average time/residue: 0.2501 time to fit residues: 53.8781 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 : 0.999 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 109 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 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 220 HIS ** 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 84 ASN N 123 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 0.030 8458 Z= 0.165 Angle : 0.540 7.596 11467 Z= 0.282 Chirality : 0.042 0.140 1286 Planarity : 0.004 0.064 1460 Dihedral : 4.445 21.928 1138 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 20.35 % 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: 0.41 (0.26), residues: 1029 helix: 2.04 (0.26), residues: 395 sheet: -0.74 (0.35), residues: 208 loop : -0.87 (0.30), residues: 426 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 0.023 0.001 PHE R 215 TYR 0.037 0.001 TYR R 200 ARG 0.009 0.000 ARG R 127 *********************** 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 167 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.888 Fit side-chains REVERT: A 358 TYR cc_start: 0.7221 (m-80) cc_final: 0.6569 (m-80) REVERT: G 21 MET cc_start: 0.4754 (mmt) cc_final: 0.4168 (mmm) REVERT: N 21 SER cc_start: 0.7156 (t) cc_final: 0.6732 (t) REVERT: N 80 TYR cc_start: 0.7443 (m-80) cc_final: 0.7205 (m-80) REVERT: R 173 TYR cc_start: 0.7265 (m-80) cc_final: 0.6910 (m-80) REVERT: R 254 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5476 (tt) REVERT: R 266 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (tt) outliers start: 19 outliers final: 14 residues processed: 161 average time/residue: 0.2617 time to fit residues: 54.8221 Evaluate side-chains 157 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 57 SER 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 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 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 220 HIS ** 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 ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8458 Z= 0.160 Angle : 0.536 7.316 11467 Z= 0.280 Chirality : 0.041 0.139 1286 Planarity : 0.005 0.064 1460 Dihedral : 4.387 21.462 1138 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.32 % Allowed : 20.35 % Favored : 77.32 % 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: 0.48 (0.26), residues: 1029 helix: 2.12 (0.25), residues: 395 sheet: -0.71 (0.35), residues: 207 loop : -0.84 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.001 PHE R 287 TYR 0.030 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 *********************** 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 169 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.006 Fit side-chains REVERT: A 358 TYR cc_start: 0.7208 (m-80) cc_final: 0.6564 (m-80) REVERT: G 21 MET cc_start: 0.4682 (mmt) cc_final: 0.4058 (mmm) REVERT: N 21 SER cc_start: 0.7098 (t) cc_final: 0.6685 (t) REVERT: N 65 LYS cc_start: 0.6620 (tppt) cc_final: 0.6401 (tptt) REVERT: N 80 TYR cc_start: 0.7423 (m-80) cc_final: 0.7200 (m-80) REVERT: N 122 THR cc_start: 0.5046 (OUTLIER) cc_final: 0.4842 (t) REVERT: R 125 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8017 (mm) REVERT: R 173 TYR cc_start: 0.7226 (m-80) cc_final: 0.6823 (m-80) REVERT: R 254 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5382 (tt) REVERT: R 266 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8079 (tt) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 0.2510 time to fit residues: 54.0976 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 : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE 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 57 SER 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 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 90 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 220 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2206 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= 0.179 Angle : 0.543 6.929 11467 Z= 0.284 Chirality : 0.042 0.136 1286 Planarity : 0.005 0.063 1460 Dihedral : 4.441 21.469 1138 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.32 % Allowed : 21.35 % Favored : 76.33 % 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: 0.51 (0.26), residues: 1029 helix: 2.10 (0.25), residues: 395 sheet: -0.63 (0.36), residues: 208 loop : -0.82 (0.30), residues: 426 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 0.019 0.001 PHE R 215 TYR 0.040 0.001 TYR R 200 ARG 0.008 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 162 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.938 Fit side-chains REVERT: A 358 TYR cc_start: 0.7214 (m-80) cc_final: 0.6571 (m-80) REVERT: G 21 MET cc_start: 0.4644 (mmt) cc_final: 0.4093 (mmm) REVERT: N 21 SER cc_start: 0.7156 (t) cc_final: 0.6723 (t) REVERT: N 80 TYR cc_start: 0.7453 (m-80) cc_final: 0.7228 (m-80) REVERT: R 125 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8022 (mm) REVERT: R 173 TYR cc_start: 0.7250 (m-80) cc_final: 0.6858 (m-80) REVERT: R 254 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5422 (tt) REVERT: R 266 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8056 (tt) REVERT: R 322 MET cc_start: 0.3109 (tpp) cc_final: 0.2606 (mpp) outliers start: 21 outliers final: 16 residues processed: 157 average time/residue: 0.2513 time to fit residues: 51.7524 Evaluate side-chains 158 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE 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 93 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 220 HIS ** 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 ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8458 Z= 0.190 Angle : 0.549 6.743 11467 Z= 0.286 Chirality : 0.042 0.155 1286 Planarity : 0.005 0.062 1460 Dihedral : 4.505 21.776 1138 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 21.46 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1029 helix: 2.08 (0.25), residues: 394 sheet: -0.64 (0.36), 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 0.005 0.001 HIS A 357 PHE 0.025 0.002 PHE R 287 TYR 0.023 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 ********************** 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 156 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.938 Fit side-chains REVERT: A 358 TYR cc_start: 0.7218 (m-80) cc_final: 0.6574 (m-80) REVERT: G 21 MET cc_start: 0.4645 (mmt) cc_final: 0.4163 (mmm) REVERT: R 125 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8018 (mm) REVERT: R 173 TYR cc_start: 0.7311 (m-80) cc_final: 0.6887 (m-80) REVERT: R 254 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5400 (tt) REVERT: R 266 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8067 (tt) REVERT: R 322 MET cc_start: 0.3027 (tpp) cc_final: 0.2524 (mpp) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.2556 time to fit residues: 50.5504 Evaluate side-chains 155 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.226701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186472 restraints weight = 8293.701| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.71 r_work: 0.3930 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8458 Z= 0.193 Angle : 0.555 6.757 11467 Z= 0.290 Chirality : 0.042 0.155 1286 Planarity : 0.004 0.062 1460 Dihedral : 4.533 26.526 1138 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.32 % Allowed : 21.57 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1029 helix: 2.09 (0.25), residues: 393 sheet: -0.62 (0.36), residues: 208 loop : -0.88 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE R 255 TYR 0.028 0.001 TYR R 200 ARG 0.008 0.000 ARG R 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.84 seconds wall clock time: 39 minutes 55.27 seconds (2395.27 seconds total)