Starting phenix.real_space_refine on Mon Mar 11 02:47:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuj_21914/03_2024/6wuj_21914.pdb" } resolution = 3.7 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= 0.015 sd= 0.109 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 13 5.16 5 C 4260 2.51 5 N 1198 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6699 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2191 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 22, 'TRANS': 259} Chain breaks: 2 Chain: "B" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2352 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 19, 'TRANS': 298} Chain breaks: 4 Chain: "C" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2156 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 19, 'TRANS': 264} Chain breaks: 4 Time building chain proxies: 4.14, per 1000 atoms: 0.62 Number of scatterers: 6699 At special positions: 0 Unit cell: (83.74, 81.62, 125.08, 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 13 16.00 O 1228 8.00 N 1198 7.00 C 4260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 38.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.019A pdb=" N LEU A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.152A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 63' Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.666A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.622A pdb=" N TYR A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.734A pdb=" N ASN A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.995A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.667A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.519A pdb=" N ASP A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.956A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.519A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.852A pdb=" N ASP B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.532A pdb=" N VAL B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.753A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.861A pdb=" N SER C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 4.001A pdb=" N SER C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.550A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.570A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 removed outlier: 4.389A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.742A pdb=" N GLY C 277 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 removed outlier: 3.756A pdb=" N MET C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.586A pdb=" N PHE C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.825A pdb=" N LYS C 320 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.950A pdb=" N ALA C 333 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 352 removed outlier: 3.711A pdb=" N LEU C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 376 removed outlier: 4.551A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.246A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.540A pdb=" N VAL B 159 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 168 " --> pdb=" O VAL B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.524A pdb=" N VAL B 171 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.870A pdb=" N THR B 235 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 239 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 397 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.870A pdb=" N THR B 235 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 239 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 397 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 421 Processing sheet with id=AA9, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.607A pdb=" N GLY B 508 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.643A pdb=" N THR C 54 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 62 " --> pdb=" O ASP C 57 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 756 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: 1.96 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1084 1.30 - 1.43: 1844 1.43 - 1.56: 3910 1.56 - 1.68: 0 1.68 - 1.81: 21 Bond restraints: 6859 Sorted by residual: bond pdb=" CA ASP C 286 " pdb=" C ASP C 286 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.27e-02 6.20e+03 3.00e+01 bond pdb=" C VAL A 223 " pdb=" O VAL A 223 " ideal model delta sigma weight residual 1.245 1.177 0.068 1.41e-02 5.03e+03 2.34e+01 bond pdb=" N VAL C 287 " pdb=" CA VAL C 287 " ideal model delta sigma weight residual 1.461 1.406 0.055 1.23e-02 6.61e+03 2.04e+01 bond pdb=" C SER A 224 " pdb=" O SER A 224 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.09e-02 8.42e+03 1.83e+01 bond pdb=" N VAL A 223 " pdb=" CA VAL A 223 " ideal model delta sigma weight residual 1.460 1.424 0.036 8.60e-03 1.35e+04 1.78e+01 ... (remaining 6854 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 227 105.93 - 112.95: 3685 112.95 - 119.98: 2320 119.98 - 127.00: 2999 127.00 - 134.03: 115 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N PHE C 12 " pdb=" CA PHE C 12 " pdb=" C PHE C 12 " ideal model delta sigma weight residual 112.97 119.52 -6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" N VAL C 287 " pdb=" CA VAL C 287 " pdb=" CB VAL C 287 " ideal model delta sigma weight residual 111.21 103.78 7.43 1.40e+00 5.10e-01 2.82e+01 angle pdb=" N ASP C 286 " pdb=" CA ASP C 286 " pdb=" C ASP C 286 " ideal model delta sigma weight residual 107.99 98.90 9.09 1.77e+00 3.19e-01 2.64e+01 angle pdb=" C PRO C 288 " pdb=" N ARG C 289 " pdb=" CA ARG C 289 " ideal model delta sigma weight residual 123.16 116.92 6.24 1.23e+00 6.61e-01 2.58e+01 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 113.71 117.69 -3.98 9.50e-01 1.11e+00 1.76e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3654 17.36 - 34.72: 358 34.72 - 52.09: 44 52.09 - 69.45: 3 69.45 - 86.81: 3 Dihedral angle restraints: 4062 sinusoidal: 1545 harmonic: 2517 Sorted by residual: dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual 180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 958 0.082 - 0.163: 86 0.163 - 0.245: 5 0.245 - 0.326: 2 0.326 - 0.408: 1 Chirality restraints: 1052 Sorted by residual: chirality pdb=" CB VAL A 223 " pdb=" CA VAL A 223 " pdb=" CG1 VAL A 223 " pdb=" CG2 VAL A 223 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA VAL A 223 " pdb=" N VAL A 223 " pdb=" C VAL A 223 " pdb=" CB VAL A 223 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PHE C 12 " pdb=" N PHE C 12 " pdb=" C PHE C 12 " pdb=" CB PHE C 12 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1049 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 287 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO C 288 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 285 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C PRO C 285 " 0.051 2.00e-02 2.50e+03 pdb=" O PRO C 285 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP C 286 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 222 " -0.015 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ILE A 222 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 222 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 223 " -0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 102 2.63 - 3.20: 6170 3.20 - 3.76: 9408 3.76 - 4.33: 13024 4.33 - 4.90: 21934 Nonbonded interactions: 50638 Sorted by model distance: nonbonded pdb=" OG SER B 308 " pdb=" O LEU B 347 " model vdw 2.059 2.440 nonbonded pdb=" OG1 THR B 257 " pdb=" OD2 ASP B 386 " model vdw 2.078 2.440 nonbonded pdb=" O GLY C 13 " pdb=" NH1 ARG C 311 " model vdw 2.128 2.520 nonbonded pdb=" OG1 THR B 230 " pdb=" OD1 ASP B 234 " model vdw 2.155 2.440 nonbonded pdb=" O LEU C 14 " pdb=" N SER C 16 " model vdw 2.165 2.520 ... (remaining 50633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.440 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: 2.200 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:2.590 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 6859 Z= 0.484 Angle : 0.926 9.088 9346 Z= 0.527 Chirality : 0.051 0.408 1052 Planarity : 0.006 0.087 1211 Dihedral : 13.198 86.810 2442 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.08 % Favored : 83.80 % Rotamer: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.22), residues: 858 helix: -3.53 (0.20), residues: 310 sheet: -3.16 (0.41), residues: 148 loop : -4.19 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 8 HIS 0.005 0.001 HIS B 215 PHE 0.015 0.002 PHE B 309 TYR 0.019 0.002 TYR B 421 ARG 0.006 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.8026 (t0) cc_final: 0.7624 (t0) REVERT: B 248 THR cc_start: 0.8891 (p) cc_final: 0.8586 (t) REVERT: C 250 LEU cc_start: 0.8856 (mm) cc_final: 0.8574 (mm) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.2592 time to fit residues: 40.4786 Evaluate side-chains 90 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 178 HIS B 192 ASN B 419 GLN C 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6859 Z= 0.211 Angle : 0.673 8.891 9346 Z= 0.334 Chirality : 0.044 0.161 1052 Planarity : 0.006 0.060 1211 Dihedral : 5.469 43.179 964 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 1.90 % Allowed : 11.52 % Favored : 86.59 % 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: -4.19 (0.26), residues: 858 helix: -1.82 (0.26), residues: 307 sheet: -2.38 (0.49), residues: 127 loop : -3.75 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 8 HIS 0.002 0.001 HIS A 280 PHE 0.028 0.002 PHE C 346 TYR 0.018 0.002 TYR B 289 ARG 0.004 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 248 THR cc_start: 0.8770 (p) cc_final: 0.8494 (t) REVERT: B 378 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8088 (ttpt) REVERT: C 250 LEU cc_start: 0.8750 (mm) cc_final: 0.8428 (mm) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.1721 time to fit residues: 27.2499 Evaluate side-chains 101 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 144 HIS C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6859 Z= 0.345 Angle : 0.714 8.963 9346 Z= 0.351 Chirality : 0.046 0.157 1052 Planarity : 0.006 0.051 1211 Dihedral : 5.477 33.775 964 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 2.62 % Allowed : 14.29 % Favored : 83.09 % 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: -3.56 (0.28), residues: 858 helix: -0.99 (0.29), residues: 296 sheet: -2.28 (0.50), residues: 132 loop : -3.51 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 8 HIS 0.003 0.001 HIS B 215 PHE 0.017 0.002 PHE A 27 TYR 0.017 0.002 TYR B 421 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.8055 (t0) cc_final: 0.7600 (t0) REVERT: B 248 THR cc_start: 0.8848 (p) cc_final: 0.8533 (t) REVERT: B 489 LEU cc_start: 0.8798 (mp) cc_final: 0.8498 (tt) REVERT: B 493 LEU cc_start: 0.8133 (mt) cc_final: 0.7926 (mt) REVERT: C 250 LEU cc_start: 0.8789 (mm) cc_final: 0.8424 (mm) outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.1566 time to fit residues: 24.0951 Evaluate side-chains 104 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6859 Z= 0.209 Angle : 0.648 9.172 9346 Z= 0.317 Chirality : 0.043 0.145 1052 Planarity : 0.005 0.045 1211 Dihedral : 5.092 23.933 964 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.33 % Allowed : 15.16 % Favored : 82.51 % 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: -3.15 (0.28), residues: 858 helix: -0.66 (0.30), residues: 313 sheet: -2.00 (0.52), residues: 127 loop : -3.34 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.004 0.001 HIS C 51 PHE 0.013 0.002 PHE C 276 TYR 0.016 0.001 TYR B 421 ARG 0.003 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7939 (t0) cc_final: 0.7547 (t0) REVERT: B 209 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: B 248 THR cc_start: 0.8741 (p) cc_final: 0.8445 (t) REVERT: B 493 LEU cc_start: 0.7974 (mt) cc_final: 0.7759 (mt) REVERT: C 250 LEU cc_start: 0.8728 (mm) cc_final: 0.8404 (mm) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.1614 time to fit residues: 24.4192 Evaluate side-chains 105 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6859 Z= 0.218 Angle : 0.644 10.287 9346 Z= 0.314 Chirality : 0.043 0.147 1052 Planarity : 0.005 0.045 1211 Dihedral : 4.911 23.182 963 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.77 % Allowed : 16.91 % Favored : 80.32 % 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: -2.77 (0.29), residues: 858 helix: -0.28 (0.31), residues: 309 sheet: -1.79 (0.51), residues: 129 loop : -3.17 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.003 0.001 HIS C 51 PHE 0.019 0.001 PHE C 276 TYR 0.014 0.001 TYR B 421 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.511 Fit side-chains REVERT: B 192 ASN cc_start: 0.7894 (t0) cc_final: 0.7524 (t0) REVERT: B 209 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 248 THR cc_start: 0.8753 (p) cc_final: 0.8442 (t) REVERT: B 493 LEU cc_start: 0.8034 (mt) cc_final: 0.7819 (mt) REVERT: C 40 ILE cc_start: 0.8709 (mm) cc_final: 0.8364 (mt) REVERT: C 250 LEU cc_start: 0.8715 (mm) cc_final: 0.8402 (mm) REVERT: C 351 MET cc_start: 0.8507 (ttm) cc_final: 0.8245 (ttm) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.1512 time to fit residues: 25.4028 Evaluate side-chains 103 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 0.0570 overall best weight: 1.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6859 Z= 0.250 Angle : 0.653 8.561 9346 Z= 0.319 Chirality : 0.044 0.145 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.955 23.815 963 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 3.50 % Allowed : 17.35 % Favored : 79.15 % 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: -2.60 (0.29), residues: 858 helix: -0.12 (0.31), residues: 309 sheet: -1.72 (0.52), residues: 130 loop : -3.07 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.006 0.001 HIS C 51 PHE 0.021 0.002 PHE C 276 TYR 0.012 0.001 TYR B 421 ARG 0.006 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.827 Fit side-chains REVERT: B 192 ASN cc_start: 0.7884 (t0) cc_final: 0.7521 (t0) REVERT: B 209 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: B 248 THR cc_start: 0.8771 (p) cc_final: 0.8469 (t) REVERT: C 40 ILE cc_start: 0.8696 (mm) cc_final: 0.8351 (mt) REVERT: C 250 LEU cc_start: 0.8677 (mm) cc_final: 0.8306 (mm) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.1508 time to fit residues: 23.0417 Evaluate side-chains 109 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 83 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6859 Z= 0.171 Angle : 0.613 11.862 9346 Z= 0.296 Chirality : 0.041 0.140 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.646 22.653 963 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 1.90 % Allowed : 19.24 % Favored : 78.86 % 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: -2.29 (0.30), residues: 858 helix: 0.16 (0.31), residues: 309 sheet: -1.41 (0.52), residues: 128 loop : -2.96 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.006 0.001 HIS C 51 PHE 0.023 0.001 PHE C 276 TYR 0.015 0.001 TYR B 421 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.789 Fit side-chains REVERT: B 202 GLU cc_start: 0.7392 (tt0) cc_final: 0.7125 (tt0) REVERT: B 248 THR cc_start: 0.8687 (p) cc_final: 0.8391 (t) REVERT: C 40 ILE cc_start: 0.8613 (mm) cc_final: 0.8280 (mt) REVERT: C 243 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 250 LEU cc_start: 0.8564 (mm) cc_final: 0.8201 (mm) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 0.1776 time to fit residues: 28.9966 Evaluate side-chains 98 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 78 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 156 ASN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6859 Z= 0.325 Angle : 0.680 7.927 9346 Z= 0.332 Chirality : 0.045 0.150 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.930 24.371 963 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 2.77 % Allowed : 19.53 % Favored : 77.70 % 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: -2.34 (0.29), residues: 858 helix: 0.20 (0.31), residues: 297 sheet: -1.65 (0.51), residues: 131 loop : -2.91 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 8 HIS 0.005 0.001 HIS C 51 PHE 0.018 0.002 PHE C 276 TYR 0.011 0.001 TYR B 240 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.682 Fit side-chains REVERT: B 192 ASN cc_start: 0.7905 (t0) cc_final: 0.7545 (t0) REVERT: B 248 THR cc_start: 0.8791 (p) cc_final: 0.8493 (t) REVERT: C 40 ILE cc_start: 0.8697 (mm) cc_final: 0.8384 (mt) REVERT: C 250 LEU cc_start: 0.8728 (mm) cc_final: 0.8358 (mm) outliers start: 19 outliers final: 11 residues processed: 99 average time/residue: 0.1454 time to fit residues: 21.1144 Evaluate side-chains 101 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 156 ASN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6859 Z= 0.248 Angle : 0.663 11.781 9346 Z= 0.320 Chirality : 0.044 0.148 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.897 24.717 963 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 1.75 % Allowed : 20.41 % Favored : 77.84 % 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: -2.23 (0.29), residues: 858 helix: 0.30 (0.32), residues: 297 sheet: -1.60 (0.51), residues: 131 loop : -2.84 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 8 HIS 0.003 0.001 HIS C 51 PHE 0.020 0.002 PHE C 276 TYR 0.013 0.001 TYR B 240 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.804 Fit side-chains REVERT: B 192 ASN cc_start: 0.7895 (t0) cc_final: 0.7557 (t0) REVERT: B 234 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7862 (p0) REVERT: B 248 THR cc_start: 0.8734 (p) cc_final: 0.8469 (t) REVERT: C 40 ILE cc_start: 0.8675 (mm) cc_final: 0.8367 (mt) REVERT: C 243 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6944 (tm-30) REVERT: C 250 LEU cc_start: 0.8708 (mm) cc_final: 0.8337 (mm) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.1642 time to fit residues: 23.9038 Evaluate side-chains 97 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 8.9990 chunk 79 optimal weight: 0.0870 chunk 69 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 156 ASN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6859 Z= 0.253 Angle : 0.677 12.907 9346 Z= 0.323 Chirality : 0.044 0.149 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.874 24.729 963 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 1.90 % Allowed : 20.70 % Favored : 77.41 % 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: -2.20 (0.30), residues: 858 helix: 0.32 (0.32), residues: 297 sheet: -1.68 (0.51), residues: 131 loop : -2.79 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.004 0.001 HIS C 122 PHE 0.020 0.001 PHE C 276 TYR 0.016 0.001 TYR C 278 ARG 0.003 0.000 ARG C 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.774 Fit side-chains REVERT: B 234 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7947 (p0) REVERT: B 248 THR cc_start: 0.8750 (p) cc_final: 0.8472 (t) REVERT: C 40 ILE cc_start: 0.8677 (mm) cc_final: 0.8377 (mt) REVERT: C 250 LEU cc_start: 0.8711 (mm) cc_final: 0.8318 (mm) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.1642 time to fit residues: 23.1395 Evaluate side-chains 102 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112904 restraints weight = 10100.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115286 restraints weight = 7062.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116909 restraints weight = 5511.153| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6859 Z= 0.170 Angle : 0.639 12.506 9346 Z= 0.304 Chirality : 0.042 0.149 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.625 23.961 963 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.75 % Allowed : 20.99 % Favored : 77.26 % 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: -2.07 (0.30), residues: 858 helix: 0.47 (0.32), residues: 302 sheet: -1.69 (0.50), residues: 134 loop : -2.76 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.005 0.001 HIS C 51 PHE 0.021 0.001 PHE C 276 TYR 0.015 0.001 TYR B 240 ARG 0.003 0.000 ARG C 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.88 seconds wall clock time: 29 minutes 28.19 seconds (1768.19 seconds total)