Starting phenix.real_space_refine on Tue Mar 3 20:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_33058_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_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 { model { file = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_33058_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_33058_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_33058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8s_33058/03_2026/7x8s_33058.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'GLU:plan': 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: 2.21, per 1000 atoms: 0.26 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: 0.67 Conformation dependent library (CDL) restraints added in 311.5 milliseconds 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: 0.26 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: 1.32 Time building geometry restraints manager: 0.91 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: 1.080 Set stop_for_unknowns flag: 0.010 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.650 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- 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 8667 Z= 0.261 Angle : 0.717 14.545 11742 Z= 0.341 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 : 9.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.000 ARG A 333 TYR 0.028 0.001 TYR B 59 PHE 0.027 0.001 PHE R 280 TRP 0.014 0.001 TRP R 417 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8664) covalent geometry : angle 0.71566 (11736) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.91012 ( 6) hydrogen bonds : bond 0.16280 ( 412) hydrogen bonds : angle 5.93785 ( 1182) *********************** 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 : 0.314 Fit side-chains revert: symmetry clash 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: 0.7413 (t80) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0947 time to fit residues: 21.7079 Evaluate side-chains 148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0030 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 239 ASN B 340 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 = 0.4287 r_free = 0.4287 target = 0.207060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.155375 restraints weight = 9382.192| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.83 r_work: 0.3397 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8667 Z= 0.123 Angle : 0.531 7.288 11742 Z= 0.283 Chirality : 0.042 0.168 1296 Planarity : 0.003 0.047 1489 Dihedral : 6.116 39.841 1236 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.00 % Allowed : 10.19 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 1032 helix: 1.82 (0.26), residues: 425 sheet: -0.44 (0.34), residues: 217 loop : -0.84 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.021 0.001 TYR R 148 PHE 0.011 0.001 PHE R 381 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8664) covalent geometry : angle 0.53051 (11736) SS BOND : bond 0.00167 ( 3) SS BOND : angle 1.27664 ( 6) hydrogen bonds : bond 0.03936 ( 412) hydrogen bonds : angle 4.42204 ( 1182) *********************** 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 178 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.6656 (mmt180) cc_final: 0.6410 (mmt180) REVERT: B 228 ASP cc_start: 0.8198 (m-30) cc_final: 0.7592 (m-30) REVERT: N 77 ASN cc_start: 0.7299 (p0) cc_final: 0.7038 (p0) REVERT: R 145 TYR cc_start: 0.7393 (t80) cc_final: 0.6788 (t80) REVERT: R 204 MET cc_start: 0.7273 (mtp) cc_final: 0.6834 (mtp) REVERT: R 397 MET cc_start: 0.8081 (mtm) cc_final: 0.7835 (mtt) outliers start: 9 outliers final: 7 residues processed: 174 average time/residue: 0.0966 time to fit residues: 23.3304 Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 355 THR 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 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.203215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148725 restraints weight = 9440.022| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.87 r_work: 0.3360 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8667 Z= 0.236 Angle : 0.600 7.437 11742 Z= 0.318 Chirality : 0.045 0.191 1296 Planarity : 0.004 0.049 1489 Dihedral : 5.842 36.797 1236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.66 % Allowed : 14.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 1032 helix: 1.80 (0.26), residues: 425 sheet: -0.59 (0.33), residues: 228 loop : -0.81 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.019 0.002 TYR R 148 PHE 0.020 0.002 PHE N 108 TRP 0.014 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 8664) covalent geometry : angle 0.59902 (11736) SS BOND : bond 0.00201 ( 3) SS BOND : angle 1.44080 ( 6) hydrogen bonds : bond 0.04313 ( 412) hydrogen bonds : angle 4.44398 ( 1182) *********************** 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 169 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6958 (mm-40) REVERT: G 44 HIS cc_start: 0.6245 (t70) cc_final: 0.5861 (t-90) REVERT: N 77 ASN cc_start: 0.7556 (p0) cc_final: 0.7294 (p0) REVERT: N 117 TYR cc_start: 0.8319 (m-80) cc_final: 0.7974 (m-80) REVERT: R 233 MET cc_start: 0.6177 (tpp) cc_final: 0.5758 (tpt) REVERT: R 367 PHE cc_start: 0.5977 (t80) cc_final: 0.5675 (t80) REVERT: R 397 MET cc_start: 0.8095 (mtm) cc_final: 0.7771 (mtt) REVERT: R 420 TRP cc_start: 0.7673 (t60) cc_final: 0.7468 (t-100) outliers start: 15 outliers final: 13 residues processed: 164 average time/residue: 0.0855 time to fit residues: 19.9586 Evaluate side-chains 158 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 50 ASP 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 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 92 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 340 ASN ** 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 = 0.4281 r_free = 0.4281 target = 0.206526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153350 restraints weight = 9557.462| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.62 r_work: 0.3393 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.146 Angle : 0.527 7.314 11742 Z= 0.282 Chirality : 0.043 0.186 1296 Planarity : 0.003 0.049 1489 Dihedral : 5.540 36.477 1236 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 16.39 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 1032 helix: 2.07 (0.26), residues: 420 sheet: -0.42 (0.34), residues: 222 loop : -0.76 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.020 0.001 TYR R 148 PHE 0.015 0.001 PHE R 280 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8664) covalent geometry : angle 0.52698 (11736) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.95296 ( 6) hydrogen bonds : bond 0.03669 ( 412) hydrogen bonds : angle 4.19926 ( 1182) *********************** 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 172 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8345 (m-30) cc_final: 0.7632 (m-30) REVERT: G 44 HIS cc_start: 0.6159 (t70) cc_final: 0.5810 (t-90) REVERT: N 77 ASN cc_start: 0.7382 (p0) cc_final: 0.7066 (p0) REVERT: N 117 TYR cc_start: 0.8245 (m-80) cc_final: 0.7996 (m-80) REVERT: R 145 TYR cc_start: 0.7277 (t80) cc_final: 0.6540 (t80) REVERT: R 233 MET cc_start: 0.6222 (tpp) cc_final: 0.5867 (tpt) REVERT: R 300 ASN cc_start: 0.7901 (m110) cc_final: 0.7698 (m110) REVERT: R 367 PHE cc_start: 0.5934 (t80) cc_final: 0.5689 (t80) REVERT: R 397 MET cc_start: 0.8101 (mtm) cc_final: 0.7753 (mtt) REVERT: R 420 TRP cc_start: 0.7757 (t60) cc_final: 0.7488 (t-100) outliers start: 19 outliers final: 15 residues processed: 166 average time/residue: 0.0868 time to fit residues: 20.1085 Evaluate side-chains 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 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 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 268 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 = 0.4282 r_free = 0.4282 target = 0.206655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152971 restraints weight = 9488.177| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.67 r_work: 0.3406 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.126 Angle : 0.516 7.281 11742 Z= 0.274 Chirality : 0.042 0.191 1296 Planarity : 0.003 0.048 1489 Dihedral : 5.352 35.747 1236 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.77 % Allowed : 17.28 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1032 helix: 2.22 (0.26), residues: 420 sheet: -0.32 (0.34), residues: 226 loop : -0.72 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.020 0.001 TYR R 148 PHE 0.016 0.001 PHE R 280 TRP 0.010 0.001 TRP A 234 HIS 0.007 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8664) covalent geometry : angle 0.51582 (11736) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.83186 ( 6) hydrogen bonds : bond 0.03451 ( 412) hydrogen bonds : angle 4.06641 ( 1182) *********************** 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 173 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6944 (pt0) REVERT: B 228 ASP cc_start: 0.8304 (m-30) cc_final: 0.7647 (m-30) REVERT: G 44 HIS cc_start: 0.6090 (t70) cc_final: 0.5709 (t-90) REVERT: N 77 ASN cc_start: 0.7370 (p0) cc_final: 0.7031 (p0) REVERT: N 117 TYR cc_start: 0.8187 (m-80) cc_final: 0.7907 (m-80) REVERT: R 145 TYR cc_start: 0.7292 (t80) cc_final: 0.7054 (t80) REVERT: R 233 MET cc_start: 0.6198 (tpp) cc_final: 0.5876 (tpt) REVERT: R 367 PHE cc_start: 0.5747 (t80) cc_final: 0.5470 (t80) REVERT: R 397 MET cc_start: 0.8037 (mtm) cc_final: 0.7724 (mtt) REVERT: R 420 TRP cc_start: 0.7760 (t60) cc_final: 0.7461 (t-100) outliers start: 25 outliers final: 21 residues processed: 165 average time/residue: 0.0885 time to fit residues: 20.5672 Evaluate side-chains 167 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 220 HIS 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 234 PHE 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 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 46 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4293 r_free = 0.4293 target = 0.207812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153333 restraints weight = 9404.315| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.71 r_work: 0.3425 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.117 Angle : 0.505 7.258 11742 Z= 0.269 Chirality : 0.041 0.192 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.193 34.833 1236 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.10 % Allowed : 18.05 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1032 helix: 2.32 (0.26), residues: 420 sheet: -0.30 (0.34), residues: 228 loop : -0.69 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.020 0.001 TYR R 148 PHE 0.016 0.001 PHE R 280 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8664) covalent geometry : angle 0.50499 (11736) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.75278 ( 6) hydrogen bonds : bond 0.03276 ( 412) hydrogen bonds : angle 3.97011 ( 1182) *********************** 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 174 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8276 (m-30) cc_final: 0.7724 (m-30) REVERT: B 316 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8246 (p) REVERT: G 44 HIS cc_start: 0.6138 (t70) cc_final: 0.5747 (t-90) REVERT: N 77 ASN cc_start: 0.7340 (p0) cc_final: 0.7033 (p0) REVERT: R 145 TYR cc_start: 0.7345 (t80) cc_final: 0.7068 (t80) REVERT: R 204 MET cc_start: 0.7061 (mtp) cc_final: 0.6586 (mtp) REVERT: R 233 MET cc_start: 0.6202 (tpp) cc_final: 0.5902 (tpt) REVERT: R 367 PHE cc_start: 0.5581 (t80) cc_final: 0.5019 (t80) REVERT: R 397 MET cc_start: 0.8061 (mtm) cc_final: 0.7761 (mtt) REVERT: R 420 TRP cc_start: 0.7641 (t60) cc_final: 0.7367 (t-100) outliers start: 28 outliers final: 22 residues processed: 166 average time/residue: 0.0868 time to fit residues: 20.4007 Evaluate side-chains 167 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 234 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 268 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.208413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157157 restraints weight = 9502.266| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.80 r_work: 0.3380 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.126 Angle : 0.518 7.255 11742 Z= 0.274 Chirality : 0.041 0.191 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.141 33.867 1236 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.10 % Allowed : 18.83 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.27), residues: 1032 helix: 2.36 (0.26), residues: 420 sheet: -0.26 (0.34), residues: 228 loop : -0.70 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.019 0.001 TYR R 148 PHE 0.017 0.001 PHE R 280 TRP 0.010 0.001 TRP A 234 HIS 0.007 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8664) covalent geometry : angle 0.51815 (11736) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.76367 ( 6) hydrogen bonds : bond 0.03302 ( 412) hydrogen bonds : angle 3.95518 ( 1182) *********************** 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 173 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8329 (m-30) cc_final: 0.7679 (m-30) REVERT: B 260 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: B 316 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8245 (p) REVERT: G 44 HIS cc_start: 0.6286 (t70) cc_final: 0.5916 (t-90) REVERT: N 77 ASN cc_start: 0.7376 (p0) cc_final: 0.7052 (p0) REVERT: N 117 TYR cc_start: 0.8212 (m-80) cc_final: 0.7938 (m-80) REVERT: R 145 TYR cc_start: 0.7425 (t80) cc_final: 0.7196 (t80) REVERT: R 204 MET cc_start: 0.7099 (mtp) cc_final: 0.6634 (mtp) REVERT: R 367 PHE cc_start: 0.5554 (t80) cc_final: 0.5000 (t80) REVERT: R 397 MET cc_start: 0.8101 (mtm) cc_final: 0.7798 (mtt) REVERT: R 420 TRP cc_start: 0.7625 (t60) cc_final: 0.7346 (t-100) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.0870 time to fit residues: 20.2992 Evaluate side-chains 168 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 355 THR Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 71 optimal weight: 0.0170 chunk 30 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4299 r_free = 0.4299 target = 0.208605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155661 restraints weight = 9427.622| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.68 r_work: 0.3438 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8667 Z= 0.107 Angle : 0.518 8.071 11742 Z= 0.273 Chirality : 0.042 0.327 1296 Planarity : 0.003 0.047 1489 Dihedral : 5.007 33.269 1236 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.33 % Allowed : 19.60 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1032 helix: 2.42 (0.26), residues: 421 sheet: -0.21 (0.34), residues: 229 loop : -0.71 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.014 0.001 TYR R 148 PHE 0.016 0.001 PHE R 280 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8664) covalent geometry : angle 0.51792 (11736) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.64979 ( 6) hydrogen bonds : bond 0.03093 ( 412) hydrogen bonds : angle 3.86163 ( 1182) *********************** 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 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6837 (pt0) REVERT: B 217 MET cc_start: 0.8206 (pmm) cc_final: 0.7787 (pmm) REVERT: B 228 ASP cc_start: 0.8282 (m-30) cc_final: 0.7679 (m-30) REVERT: B 260 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: B 316 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8252 (p) REVERT: G 44 HIS cc_start: 0.6226 (t70) cc_final: 0.5855 (t-90) REVERT: N 77 ASN cc_start: 0.7332 (p0) cc_final: 0.7018 (p0) REVERT: N 117 TYR cc_start: 0.8157 (m-80) cc_final: 0.7844 (m-80) REVERT: R 145 TYR cc_start: 0.7409 (t80) cc_final: 0.7087 (t80) REVERT: R 204 MET cc_start: 0.6992 (mtp) cc_final: 0.6617 (mtp) REVERT: R 367 PHE cc_start: 0.5456 (t80) cc_final: 0.4901 (t80) REVERT: R 394 GLN cc_start: 0.7339 (tp40) cc_final: 0.7036 (tp40) REVERT: R 397 MET cc_start: 0.8033 (mtm) cc_final: 0.7771 (mtt) REVERT: R 420 TRP cc_start: 0.7617 (t60) cc_final: 0.7344 (t-100) outliers start: 21 outliers final: 19 residues processed: 165 average time/residue: 0.0857 time to fit residues: 20.0764 Evaluate side-chains 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 R residue 144 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.209184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158422 restraints weight = 9391.981| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.81 r_work: 0.3390 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8667 Z= 0.109 Angle : 0.533 8.250 11742 Z= 0.279 Chirality : 0.042 0.302 1296 Planarity : 0.003 0.046 1489 Dihedral : 4.946 32.403 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.44 % Allowed : 19.82 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 1032 helix: 2.49 (0.26), residues: 421 sheet: -0.17 (0.34), residues: 229 loop : -0.71 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.015 0.001 TYR R 148 PHE 0.016 0.001 PHE R 280 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8664) covalent geometry : angle 0.53336 (11736) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.64057 ( 6) hydrogen bonds : bond 0.03085 ( 412) hydrogen bonds : angle 3.84929 ( 1182) *********************** 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 170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6848 (pt0) REVERT: B 217 MET cc_start: 0.8238 (pmm) cc_final: 0.7738 (pmm) REVERT: B 228 ASP cc_start: 0.8297 (m-30) cc_final: 0.8042 (m-30) REVERT: B 260 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: B 316 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8243 (p) REVERT: G 44 HIS cc_start: 0.6198 (t70) cc_final: 0.5853 (t-90) REVERT: N 77 ASN cc_start: 0.7351 (p0) cc_final: 0.7061 (p0) REVERT: N 117 TYR cc_start: 0.8189 (m-80) cc_final: 0.7787 (m-80) REVERT: R 145 TYR cc_start: 0.7449 (t80) cc_final: 0.7123 (t80) REVERT: R 204 MET cc_start: 0.7017 (mtp) cc_final: 0.6658 (mtp) REVERT: R 367 PHE cc_start: 0.5460 (t80) cc_final: 0.4960 (t80) REVERT: R 394 GLN cc_start: 0.7360 (tp40) cc_final: 0.7024 (tp40) REVERT: R 397 MET cc_start: 0.8070 (mtm) cc_final: 0.7810 (mtt) REVERT: R 420 TRP cc_start: 0.7609 (t60) cc_final: 0.7340 (t-100) outliers start: 22 outliers final: 19 residues processed: 166 average time/residue: 0.0878 time to fit residues: 20.5907 Evaluate side-chains 167 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 R residue 144 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** 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 = 0.4287 r_free = 0.4287 target = 0.207428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154729 restraints weight = 9392.673| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.73 r_work: 0.3404 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.137 Angle : 0.555 10.080 11742 Z= 0.287 Chirality : 0.043 0.291 1296 Planarity : 0.003 0.047 1489 Dihedral : 4.995 31.162 1236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.44 % Allowed : 20.04 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 1032 helix: 2.37 (0.26), residues: 425 sheet: -0.19 (0.34), residues: 229 loop : -0.70 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.015 0.001 TYR R 148 PHE 0.014 0.001 PHE R 280 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8664) covalent geometry : angle 0.55454 (11736) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.82989 ( 6) hydrogen bonds : bond 0.03317 ( 412) hydrogen bonds : angle 3.89425 ( 1182) ********************** 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 165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6879 (pt0) REVERT: B 260 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: B 316 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8219 (p) REVERT: G 44 HIS cc_start: 0.6255 (t70) cc_final: 0.5899 (t-90) REVERT: N 77 ASN cc_start: 0.7376 (p0) cc_final: 0.7070 (p0) REVERT: N 117 TYR cc_start: 0.8187 (m-80) cc_final: 0.7782 (m-80) REVERT: R 204 MET cc_start: 0.7025 (mtp) cc_final: 0.6697 (mtp) REVERT: R 367 PHE cc_start: 0.5374 (t80) cc_final: 0.4906 (t80) REVERT: R 394 GLN cc_start: 0.7381 (tp40) cc_final: 0.7016 (tp40) REVERT: R 397 MET cc_start: 0.8059 (mtm) cc_final: 0.7799 (mtt) REVERT: R 420 TRP cc_start: 0.7617 (t60) cc_final: 0.7360 (t-100) outliers start: 22 outliers final: 20 residues processed: 160 average time/residue: 0.0885 time to fit residues: 19.9882 Evaluate side-chains 166 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 268 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.207164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154501 restraints weight = 9315.918| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.59 r_work: 0.3410 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8667 Z= 0.133 Angle : 0.560 10.204 11742 Z= 0.290 Chirality : 0.043 0.283 1296 Planarity : 0.003 0.046 1489 Dihedral : 4.988 30.833 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 20.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 1032 helix: 2.30 (0.26), residues: 431 sheet: -0.17 (0.34), residues: 229 loop : -0.73 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.015 0.001 TYR R 148 PHE 0.015 0.001 PHE R 280 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8664) covalent geometry : angle 0.55993 (11736) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.80722 ( 6) hydrogen bonds : bond 0.03284 ( 412) hydrogen bonds : angle 3.88242 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2385.16 seconds wall clock time: 41 minutes 29.55 seconds (2489.55 seconds total)