Starting phenix.real_space_refine on Thu Mar 13 01:09:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2025/7x8s_33058_neut.cif" } resolution = 3.09 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= -0.001 sd= 0.089 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 51 5.16 5 C 5408 2.51 5 N 1468 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1933 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 228} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 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: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} 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: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2496 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 5, 'TRANS': 293} Chain breaks: 3 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'WB2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.63 Number of scatterers: 8480 At special positions: 0 Unit cell: (77.112, 96.39, 154.224, 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 51 16.00 O 1553 8.00 N 1468 7.00 C 5408 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=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 2.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 43.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.977A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.616A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.882A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.290A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.503A 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 351 removed outlier: 3.690A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.557A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.732A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.694A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.704A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 139 through 167 removed outlier: 3.674A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 208 Processing helix chain 'R' and resid 213 through 222 removed outlier: 3.548A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 242 removed outlier: 3.951A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 256 Processing helix chain 'R' and resid 261 through 290 removed outlier: 3.653A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 302 through 338 removed outlier: 4.174A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.794A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.521A pdb=" N PHE R 367 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 404 removed outlier: 3.659A pdb=" N LEU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE R 404 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.364A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.529A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.578A 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 63 removed outlier: 3.934A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.170A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.603A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.267A 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: 7.108A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.485A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.933A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.550A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.826A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1182 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: 2.72 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1372 1.31 - 1.44: 2470 1.44 - 1.56: 4743 1.56 - 1.69: 8 1.69 - 1.81: 71 Bond restraints: 8664 Sorted by residual: bond pdb=" C66 WB2 R 501 " pdb=" C68 WB2 R 501 " ideal model delta sigma weight residual 1.456 1.554 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C51 WB2 R 501 " pdb=" N50 WB2 R 501 " ideal model delta sigma weight residual 1.361 1.458 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C30 WB2 R 501 " pdb=" O29 WB2 R 501 " ideal model delta sigma weight residual 1.340 1.430 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C30 WB2 R 501 " pdb=" C32 WB2 R 501 " ideal model delta sigma weight residual 1.457 1.546 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C37 WB2 R 501 " pdb=" C38 WB2 R 501 " ideal model delta sigma weight residual 1.562 1.650 -0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 11616 2.91 - 5.82: 95 5.82 - 8.73: 19 8.73 - 11.64: 4 11.64 - 14.54: 2 Bond angle restraints: 11736 Sorted by residual: angle pdb=" N LEU R 379 " pdb=" CA LEU R 379 " pdb=" C LEU R 379 " ideal model delta sigma weight residual 112.89 106.51 6.38 1.24e+00 6.50e-01 2.65e+01 angle pdb=" C32 WB2 R 501 " pdb=" C30 WB2 R 501 " pdb=" O29 WB2 R 501 " ideal model delta sigma weight residual 111.75 126.29 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C68 WB2 R 501 " pdb=" C66 WB2 R 501 " pdb=" O65 WB2 R 501 " ideal model delta sigma weight residual 111.81 125.47 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" N PHE R 381 " pdb=" CA PHE R 381 " pdb=" C PHE R 381 " ideal model delta sigma weight residual 112.04 106.03 6.01 1.44e+00 4.82e-01 1.74e+01 angle pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 ... (remaining 11731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4504 17.81 - 35.61: 530 35.61 - 53.42: 100 53.42 - 71.22: 25 71.22 - 89.03: 9 Dihedral angle restraints: 5168 sinusoidal: 2105 harmonic: 3063 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 10.39 82.61 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -150.71 64.71 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1245 0.101 - 0.202: 46 0.202 - 0.303: 2 0.303 - 0.404: 0 0.404 - 0.505: 3 Chirality restraints: 1296 Sorted by residual: chirality pdb=" C56 WB2 R 501 " pdb=" C16 WB2 R 501 " pdb=" C37 WB2 R 501 " pdb=" C57 WB2 R 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.98 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C37 WB2 R 501 " pdb=" C20 WB2 R 501 " pdb=" C38 WB2 R 501 " pdb=" C56 WB2 R 501 " both_signs ideal model delta sigma weight residual False 3.12 3.62 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" C20 WB2 R 501 " pdb=" C16 WB2 R 501 " pdb=" C21 WB2 R 501 " pdb=" C37 WB2 R 501 " both_signs ideal model delta sigma weight residual False -2.61 -3.11 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 1293 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.014 2.00e-02 2.50e+03 1.13e-02 2.53e+00 pdb=" CG TYR B 59 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 280 " -0.012 2.00e-02 2.50e+03 1.20e-02 2.51e+00 pdb=" CG PHE R 280 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 280 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 280 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE R 280 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE R 280 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 280 " -0.000 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 252 2.70 - 3.25: 8336 3.25 - 3.80: 13567 3.80 - 4.35: 17225 4.35 - 4.90: 29608 Nonbonded interactions: 68988 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.155 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.192 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.208 3.040 ... (remaining 68983 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=0.00 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.005 0.098 8664 Z= 0.333 Angle : 0.716 14.545 11736 Z= 0.340 Chirality : 0.051 0.505 1296 Planarity : 0.003 0.048 1489 Dihedral : 15.768 89.030 3179 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % Rotamer: Outliers : 0.22 % Allowed : 0.55 % Favored : 99.22 % 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: 0.09 (0.27), residues: 1032 helix: 1.33 (0.27), residues: 418 sheet: -0.51 (0.34), residues: 215 loop : -0.90 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 417 HIS 0.008 0.001 HIS R 171 PHE 0.027 0.001 PHE R 280 TYR 0.028 0.001 TYR B 59 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.8843 (m) cc_final: 0.8581 (m) REVERT: R 145 TYR cc_start: 0.7805 (t80) cc_final: 0.7414 (t80) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2324 time to fit residues: 52.9281 Evaluate side-chains 149 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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** B 239 ASN B 340 ASN R 300 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154733 restraints weight = 9292.608| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.61 r_work: 0.3441 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8664 Z= 0.163 Angle : 0.530 7.276 11736 Z= 0.282 Chirality : 0.042 0.180 1296 Planarity : 0.003 0.047 1489 Dihedral : 6.181 40.576 1236 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.89 % Allowed : 9.75 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 1032 helix: 1.84 (0.26), residues: 425 sheet: -0.41 (0.34), residues: 217 loop : -0.83 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS R 363 PHE 0.014 0.001 PHE R 381 TYR 0.021 0.001 TYR R 148 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8174 (m-30) cc_final: 0.7605 (m-30) REVERT: N 77 ASN cc_start: 0.7283 (p0) cc_final: 0.7032 (p0) REVERT: R 145 TYR cc_start: 0.7372 (t80) cc_final: 0.6778 (t80) REVERT: R 204 MET cc_start: 0.7261 (mtp) cc_final: 0.6818 (mtp) REVERT: R 397 MET cc_start: 0.8032 (mtm) cc_final: 0.7788 (mtt) outliers start: 8 outliers final: 6 residues processed: 174 average time/residue: 0.2192 time to fit residues: 52.7817 Evaluate side-chains 159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 239 ASN B 268 ASN R 300 ASN ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.205915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153815 restraints weight = 9409.008| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.99 r_work: 0.3358 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8664 Z= 0.229 Angle : 0.531 7.284 11736 Z= 0.282 Chirality : 0.042 0.182 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.641 37.992 1236 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.55 % Allowed : 13.29 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1032 helix: 2.03 (0.26), residues: 421 sheet: -0.40 (0.34), residues: 222 loop : -0.72 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 280 TYR 0.021 0.001 TYR R 148 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6810 (mm-40) REVERT: B 228 ASP cc_start: 0.8322 (m-30) cc_final: 0.7727 (m-30) REVERT: G 44 HIS cc_start: 0.6194 (t70) cc_final: 0.5778 (t-90) REVERT: N 77 ASN cc_start: 0.7378 (p0) cc_final: 0.7109 (p0) REVERT: R 145 TYR cc_start: 0.7308 (t80) cc_final: 0.6644 (t80) REVERT: R 204 MET cc_start: 0.7135 (mtp) cc_final: 0.6884 (mtp) REVERT: R 233 MET cc_start: 0.6187 (tpp) cc_final: 0.5755 (tpt) REVERT: R 397 MET cc_start: 0.8173 (mtm) cc_final: 0.7886 (mtt) outliers start: 14 outliers final: 11 residues processed: 164 average time/residue: 0.2023 time to fit residues: 46.6907 Evaluate side-chains 159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 390 GLN B 239 ASN B 340 ASN R 171 HIS ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.207112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153791 restraints weight = 9399.692| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.60 r_work: 0.3400 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8664 Z= 0.225 Angle : 0.525 7.305 11736 Z= 0.280 Chirality : 0.043 0.185 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.445 36.341 1236 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.66 % Allowed : 15.84 % Favored : 82.50 % 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: 0.73 (0.27), residues: 1032 helix: 2.11 (0.26), residues: 422 sheet: -0.38 (0.34), residues: 222 loop : -0.79 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS R 171 PHE 0.014 0.001 PHE R 280 TYR 0.021 0.001 TYR R 148 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8335 (m-30) cc_final: 0.7758 (m-30) REVERT: G 44 HIS cc_start: 0.6048 (t70) cc_final: 0.5746 (t-90) REVERT: N 77 ASN cc_start: 0.7398 (p0) cc_final: 0.7095 (p0) REVERT: R 145 TYR cc_start: 0.7340 (t80) cc_final: 0.6587 (t80) REVERT: R 233 MET cc_start: 0.6228 (tpp) cc_final: 0.5855 (tpt) REVERT: R 397 MET cc_start: 0.8098 (mtm) cc_final: 0.7814 (mtt) outliers start: 15 outliers final: 14 residues processed: 161 average time/residue: 0.2081 time to fit residues: 46.4106 Evaluate side-chains 161 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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** B 239 ASN B 268 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** 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 = 0.4289 r_free = 0.4289 target = 0.207340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154562 restraints weight = 9483.553| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.59 r_work: 0.3396 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8664 Z= 0.227 Angle : 0.532 7.295 11736 Z= 0.281 Chirality : 0.042 0.177 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.351 35.276 1236 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.55 % Allowed : 17.61 % Favored : 79.84 % 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: 0.76 (0.27), residues: 1032 helix: 2.14 (0.26), residues: 426 sheet: -0.38 (0.34), residues: 222 loop : -0.81 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 280 TYR 0.020 0.001 TYR R 148 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 44 HIS cc_start: 0.6230 (t70) cc_final: 0.5868 (t-90) REVERT: N 77 ASN cc_start: 0.7408 (p0) cc_final: 0.7079 (p0) REVERT: N 117 TYR cc_start: 0.8241 (m-80) cc_final: 0.7845 (m-80) REVERT: R 145 TYR cc_start: 0.7381 (t80) cc_final: 0.6591 (t80) REVERT: R 233 MET cc_start: 0.6251 (tpp) cc_final: 0.5916 (tpt) REVERT: R 397 MET cc_start: 0.8082 (mtm) cc_final: 0.7755 (mtt) outliers start: 23 outliers final: 20 residues processed: 165 average time/residue: 0.2164 time to fit residues: 50.5719 Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** B 239 ASN B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** 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 = 0.4251 r_free = 0.4251 target = 0.203179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150026 restraints weight = 9459.343| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.72 r_work: 0.3340 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8664 Z= 0.368 Angle : 0.601 7.333 11736 Z= 0.317 Chirality : 0.045 0.187 1296 Planarity : 0.004 0.047 1489 Dihedral : 5.535 33.492 1236 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.10 % Allowed : 18.38 % Favored : 78.52 % 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: 0.53 (0.27), residues: 1032 helix: 1.96 (0.26), residues: 426 sheet: -0.54 (0.34), residues: 224 loop : -0.89 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.007 0.002 HIS B 62 PHE 0.019 0.002 PHE N 108 TYR 0.019 0.002 TYR R 148 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 316 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8408 (p) REVERT: G 44 HIS cc_start: 0.6225 (t70) cc_final: 0.5849 (t-90) REVERT: N 39 GLN cc_start: 0.8678 (tt0) cc_final: 0.8464 (tt0) REVERT: N 77 ASN cc_start: 0.7499 (p0) cc_final: 0.7133 (p0) REVERT: N 82 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7514 (tm-30) REVERT: N 117 TYR cc_start: 0.8351 (m-80) cc_final: 0.8021 (m-80) REVERT: R 204 MET cc_start: 0.7763 (tpp) cc_final: 0.7277 (mtt) REVERT: R 233 MET cc_start: 0.6311 (tpp) cc_final: 0.6016 (tpt) REVERT: R 397 MET cc_start: 0.8103 (mtm) cc_final: 0.7780 (mtt) outliers start: 28 outliers final: 25 residues processed: 171 average time/residue: 0.1980 time to fit residues: 47.1828 Evaluate side-chains 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** B 239 ASN B 268 ASN ** G 18 GLN ** 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 = 0.4266 r_free = 0.4266 target = 0.204824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151322 restraints weight = 9478.312| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.66 r_work: 0.3369 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8664 Z= 0.259 Angle : 0.569 7.302 11736 Z= 0.299 Chirality : 0.043 0.187 1296 Planarity : 0.003 0.048 1489 Dihedral : 5.399 33.823 1236 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.43 % Allowed : 18.72 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1032 helix: 2.10 (0.26), residues: 422 sheet: -0.39 (0.35), residues: 223 loop : -0.87 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 280 TYR 0.019 0.001 TYR R 148 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6898 (pt0) REVERT: B 260 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: B 316 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8436 (p) REVERT: G 44 HIS cc_start: 0.6255 (t70) cc_final: 0.5865 (t-90) REVERT: N 77 ASN cc_start: 0.7419 (p0) cc_final: 0.7035 (p0) REVERT: N 82 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7463 (tm-30) REVERT: N 117 TYR cc_start: 0.8263 (m-80) cc_final: 0.7924 (m-80) REVERT: R 204 MET cc_start: 0.7601 (tpp) cc_final: 0.7236 (mtt) REVERT: R 367 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5990 (m-80) REVERT: R 397 MET cc_start: 0.8053 (mtm) cc_final: 0.7730 (mtt) outliers start: 31 outliers final: 24 residues processed: 173 average time/residue: 0.2170 time to fit residues: 52.0236 Evaluate side-chains 171 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 294 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.207604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154231 restraints weight = 9435.941| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.67 r_work: 0.3404 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.003 0.036 8664 Z= 0.176 Angle : 0.539 8.218 11736 Z= 0.283 Chirality : 0.042 0.183 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.235 33.811 1236 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 19.71 % 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: 0.85 (0.27), residues: 1032 helix: 2.28 (0.26), residues: 422 sheet: -0.30 (0.35), residues: 224 loop : -0.83 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS R 171 PHE 0.018 0.001 PHE R 280 TYR 0.019 0.001 TYR R 148 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 TYR cc_start: 0.7824 (m-80) cc_final: 0.7607 (m-80) REVERT: A 392 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6750 (pt0) REVERT: B 217 MET cc_start: 0.8236 (pmm) cc_final: 0.7789 (pmm) REVERT: B 260 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: G 44 HIS cc_start: 0.6181 (t70) cc_final: 0.5797 (t-90) REVERT: N 77 ASN cc_start: 0.7343 (p0) cc_final: 0.6989 (p0) REVERT: N 82 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7543 (tm-30) REVERT: N 117 TYR cc_start: 0.8195 (m-80) cc_final: 0.7826 (m-80) REVERT: R 204 MET cc_start: 0.7561 (tpp) cc_final: 0.7280 (mtp) REVERT: R 307 LEU cc_start: 0.8506 (mm) cc_final: 0.8274 (pp) REVERT: R 367 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: R 394 GLN cc_start: 0.7398 (tp40) cc_final: 0.7134 (tp40) REVERT: R 397 MET cc_start: 0.8049 (mtm) cc_final: 0.7792 (mtt) outliers start: 26 outliers final: 20 residues processed: 172 average time/residue: 0.1982 time to fit residues: 47.5111 Evaluate side-chains 167 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 chunk 65 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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** B 239 ASN B 268 ASN ** G 18 GLN ** 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 = 0.4295 r_free = 0.4295 target = 0.208342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155432 restraints weight = 9485.533| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.65 r_work: 0.3422 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8664 Z= 0.167 Angle : 0.543 7.231 11736 Z= 0.284 Chirality : 0.042 0.179 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.105 33.122 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.77 % Allowed : 19.93 % Favored : 77.30 % 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: 0.97 (0.27), residues: 1032 helix: 2.40 (0.26), residues: 422 sheet: -0.24 (0.35), residues: 225 loop : -0.78 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.015 0.001 PHE R 280 TYR 0.015 0.001 TYR R 148 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6762 (pt0) REVERT: B 260 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: B 316 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8279 (p) REVERT: G 44 HIS cc_start: 0.6247 (t70) cc_final: 0.5880 (t-90) REVERT: N 77 ASN cc_start: 0.7325 (p0) cc_final: 0.6988 (p0) REVERT: N 82 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7622 (tm-30) REVERT: N 117 TYR cc_start: 0.8176 (m-80) cc_final: 0.7801 (m-80) REVERT: R 299 ARG cc_start: 0.8135 (tmt170) cc_final: 0.7902 (ttp80) REVERT: R 307 LEU cc_start: 0.8509 (mm) cc_final: 0.8254 (pp) REVERT: R 367 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5977 (m-80) REVERT: R 394 GLN cc_start: 0.7328 (tp40) cc_final: 0.7058 (tp40) REVERT: R 397 MET cc_start: 0.8090 (mtm) cc_final: 0.7820 (mtt) outliers start: 25 outliers final: 20 residues processed: 172 average time/residue: 0.1955 time to fit residues: 46.4951 Evaluate side-chains 173 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.207770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154970 restraints weight = 9397.493| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.57 r_work: 0.3399 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8664 Z= 0.232 Angle : 0.580 9.632 11736 Z= 0.301 Chirality : 0.043 0.208 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.175 32.025 1236 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.66 % Allowed : 20.71 % Favored : 76.63 % 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: 0.88 (0.27), residues: 1032 helix: 2.31 (0.26), residues: 422 sheet: -0.26 (0.35), residues: 225 loop : -0.82 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE R 280 TYR 0.020 0.001 TYR B 85 ARG 0.007 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8248 (pmm) cc_final: 0.7717 (pmm) REVERT: B 260 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: B 316 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8436 (p) REVERT: G 44 HIS cc_start: 0.6264 (t70) cc_final: 0.5931 (t-90) REVERT: N 77 ASN cc_start: 0.7421 (p0) cc_final: 0.7111 (p0) REVERT: N 117 TYR cc_start: 0.8235 (m-80) cc_final: 0.7903 (m-80) REVERT: R 307 LEU cc_start: 0.8543 (mm) cc_final: 0.8280 (pp) REVERT: R 367 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5948 (m-80) REVERT: R 394 GLN cc_start: 0.7399 (tp40) cc_final: 0.7086 (tp40) REVERT: R 397 MET cc_start: 0.8096 (mtm) cc_final: 0.7825 (mtt) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 0.1931 time to fit residues: 44.9563 Evaluate side-chains 168 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 0.0870 chunk 56 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 16 optimal weight: 0.0030 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- 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** B 88 ASN B 239 ASN B 268 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.208806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.156001 restraints weight = 9515.745| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.60 r_work: 0.3435 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8664 Z= 0.164 Angle : 0.544 9.089 11736 Z= 0.284 Chirality : 0.041 0.202 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.040 32.041 1236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.44 % Allowed : 20.93 % Favored : 76.63 % 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: 1.02 (0.27), residues: 1032 helix: 2.45 (0.26), residues: 422 sheet: -0.18 (0.34), residues: 229 loop : -0.80 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS A 362 PHE 0.015 0.001 PHE R 280 TYR 0.020 0.001 TYR B 85 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.80 seconds wall clock time: 85 minutes 4.66 seconds (5104.66 seconds total)