Starting phenix.real_space_refine on Tue Mar 3 20:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2026/7vvl_32143.cif" } resolution = 2.8 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5546 2.51 5 N 1523 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 8725 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1901 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2519 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 392 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 280 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2664 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'PHE:plan': 2, 'HIS:plan': 3, 'ASP:plan': 3, 'TRP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 152 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.25, per 1000 atoms: 0.26 Number of scatterers: 8725 At special positions: 0 Unit cell: (128.374, 99.6003, 127.267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1603 8.00 N 1523 7.00 C 5546 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=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.07 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 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: 0.71 Conformation dependent library (CDL) restraints added in 378.0 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 41.8% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.787A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.520A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.632A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.568A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.163A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.537A pdb=" N TYR A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.540A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 3.511A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.800A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.835A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.196A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 removed outlier: 3.555A pdb=" N ILE R 222 " --> pdb=" O THR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 312 removed outlier: 3.545A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 344 removed outlier: 3.541A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.648A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 removed outlier: 4.090A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.503A pdb=" N ASN R 374 " --> pdb=" O SER R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 400 No H-bonds generated for 'chain 'R' and resid 398 through 400' Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.756A pdb=" N LEU R 406 " --> pdb=" O GLN R 402 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU R 407 " --> pdb=" O TYR R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 419 through 423 removed outlier: 3.702A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.531A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 477 removed outlier: 3.692A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER R 473 " --> pdb=" O GLU R 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.984A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.812A 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: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.935A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.020A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.373A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.617A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.520A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.639A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 128 through 130 453 hydrogen bonds defined for protein. 1290 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: 1.57 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1424 1.30 - 1.43: 2492 1.43 - 1.56: 4915 1.56 - 1.69: 1 1.69 - 1.83: 78 Bond restraints: 8910 Sorted by residual: bond pdb=" CE1 HIS R 307 " pdb=" NE2 HIS R 307 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.79e+01 bond pdb=" C ARG R 150 " pdb=" O ARG R 150 " ideal model delta sigma weight residual 1.236 1.301 -0.064 1.26e-02 6.30e+03 2.61e+01 bond pdb=" C PRO A 351 " pdb=" O PRO A 351 " ideal model delta sigma weight residual 1.233 1.180 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C ASN R 139 " pdb=" O ASN R 139 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.35e-02 5.49e+03 2.18e+01 bond pdb=" N VAL R 157 " pdb=" CA VAL R 157 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.11e+01 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 8531 1.81 - 3.61: 3236 3.61 - 5.42: 298 5.42 - 7.23: 18 7.23 - 9.03: 7 Bond angle restraints: 12090 Sorted by residual: angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.35 121.98 -7.63 1.25e+00 6.40e-01 3.72e+01 angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 122.63 118.12 4.51 8.70e-01 1.32e+00 2.69e+01 angle pdb=" N GLU P 4 " pdb=" CA GLU P 4 " pdb=" C GLU P 4 " ideal model delta sigma weight residual 111.14 105.80 5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" C GLU B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.94 125.41 -5.47 1.11e+00 8.12e-01 2.43e+01 angle pdb=" CB GLU A 312 " pdb=" CG GLU A 312 " pdb=" CD GLU A 312 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.70e+00 3.46e-01 2.14e+01 ... (remaining 12085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4523 17.64 - 35.27: 513 35.27 - 52.90: 167 52.90 - 70.54: 34 70.54 - 88.17: 18 Dihedral angle restraints: 5255 sinusoidal: 1978 harmonic: 3277 Sorted by residual: 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 -146.52 60.52 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.34 43.66 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CA THR A 359 " pdb=" C THR A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 752 0.068 - 0.136: 443 0.136 - 0.204: 138 0.204 - 0.272: 24 0.272 - 0.340: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE R 135 " pdb=" CA ILE R 135 " pdb=" CG1 ILE R 135 " pdb=" CG2 ILE R 135 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1358 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 329 " -0.017 2.00e-02 2.50e+03 8.90e-03 1.98e+00 pdb=" CG TRP R 329 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 329 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 329 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 329 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 329 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 329 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 329 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 329 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.019 2.00e-02 2.50e+03 8.80e-03 1.94e+00 pdb=" CG TRP A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 134 " 0.004 2.00e-02 2.50e+03 8.46e-03 1.43e+00 pdb=" CG TYR R 134 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR R 134 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR R 134 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR R 134 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR R 134 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 134 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR R 134 " 0.001 2.00e-02 2.50e+03 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 561 2.74 - 3.28: 8583 3.28 - 3.82: 14112 3.82 - 4.36: 19286 4.36 - 4.90: 31185 Nonbonded interactions: 73727 Sorted by model distance: nonbonded pdb=" O SER R 356 " pdb=" OG SER R 356 " model vdw 2.204 3.040 nonbonded pdb=" O GLN R 438 " pdb=" ND1 HIS R 442 " model vdw 2.262 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.289 3.120 nonbonded pdb=" NH1 ARG R 282 " pdb=" OD1 ASN R 348 " model vdw 2.303 3.120 ... (remaining 73722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.260 Find NCS groups from input model: 0.050 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:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.014 0.066 8913 Z= 1.025 Angle : 1.690 9.035 12096 Z= 1.234 Chirality : 0.089 0.340 1361 Planarity : 0.003 0.012 1545 Dihedral : 17.696 88.173 3126 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 7.24 % Allowed : 19.15 % Favored : 73.61 % 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: -0.88 (0.24), residues: 1104 helix: -0.35 (0.23), residues: 426 sheet: 0.15 (0.37), residues: 206 loop : -1.03 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 49 TYR 0.016 0.003 TYR R 134 PHE 0.012 0.003 PHE R 378 TRP 0.019 0.004 TRP A 271 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.01411 ( 8910) covalent geometry : angle 1.68841 (12090) SS BOND : bond 0.02342 ( 3) SS BOND : angle 3.81664 ( 6) hydrogen bonds : bond 0.22680 ( 453) hydrogen bonds : angle 8.18422 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 0.219 Fit side-chains REVERT: A 21 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: A 27 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6753 (tp30) REVERT: A 28 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6648 (ttmm) REVERT: A 49 ASP cc_start: 0.7293 (m-30) cc_final: 0.6698 (t0) REVERT: A 289 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: A 371 ASP cc_start: 0.8221 (t70) cc_final: 0.7731 (t0) REVERT: B 32 GLN cc_start: 0.5824 (pt0) cc_final: 0.5403 (tp40) REVERT: B 38 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 59 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8578 (t80) REVERT: B 78 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8068 (tppp) REVERT: B 96 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7208 (ttm-80) REVERT: B 101 MET cc_start: 0.8775 (mtp) cc_final: 0.8350 (mtp) REVERT: B 137 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6541 (ttm110) REVERT: B 138 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 146 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (tt) REVERT: B 156 GLN cc_start: 0.7526 (mt0) cc_final: 0.7310 (mt0) REVERT: B 175 GLN cc_start: 0.7620 (pt0) cc_final: 0.6779 (mm-40) REVERT: B 219 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6731 (mmt-90) REVERT: B 220 GLN cc_start: 0.8781 (mt0) cc_final: 0.8335 (mt0) REVERT: B 270 ILE cc_start: 0.7915 (pt) cc_final: 0.7654 (pp) REVERT: B 277 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 301 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7382 (mtpt) REVERT: G 44 HIS cc_start: 0.7802 (m90) cc_final: 0.7551 (m-70) REVERT: N 3 GLN cc_start: 0.6596 (tt0) cc_final: 0.6179 (tt0) REVERT: N 6 GLU cc_start: 0.6681 (mp0) cc_final: 0.6269 (mp0) REVERT: N 34 MET cc_start: 0.8507 (mmm) cc_final: 0.8299 (mmm) REVERT: N 39 GLN cc_start: 0.8408 (tt0) cc_final: 0.8012 (tt0) REVERT: N 53 GLN cc_start: 0.7523 (mp10) cc_final: 0.6943 (mp10) REVERT: N 76 LYS cc_start: 0.7068 (mppt) cc_final: 0.6567 (mttt) REVERT: N 83 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6351 (mtt) REVERT: N 95 TYR cc_start: 0.8530 (m-80) cc_final: 0.7898 (m-80) REVERT: N 104 THR cc_start: 0.8362 (p) cc_final: 0.8074 (p) REVERT: N 123 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6464 (tp40) REVERT: R 36 GLU cc_start: 0.5469 (tt0) cc_final: 0.4930 (tp30) REVERT: R 133 ASP cc_start: 0.3942 (OUTLIER) cc_final: 0.3682 (t0) REVERT: R 182 GLU cc_start: 0.7675 (tt0) cc_final: 0.7447 (tt0) REVERT: R 186 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6590 (ttp-110) REVERT: R 189 MET cc_start: 0.7426 (tpt) cc_final: 0.7101 (tpp) REVERT: R 218 THR cc_start: 0.8351 (t) cc_final: 0.8144 (m) REVERT: R 220 ASN cc_start: 0.7906 (m-40) cc_final: 0.7698 (m-40) REVERT: R 224 MET cc_start: 0.6932 (mtt) cc_final: 0.6688 (mtm) REVERT: R 240 LYS cc_start: 0.6731 (ttpt) cc_final: 0.6371 (ttpp) REVERT: R 389 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7262 (mp) REVERT: R 405 LYS cc_start: 0.5768 (tptm) cc_final: 0.4801 (ttmm) REVERT: R 408 LYS cc_start: 0.7381 (tmtp) cc_final: 0.7118 (tptt) REVERT: R 441 MET cc_start: 0.8493 (mmt) cc_final: 0.8217 (mmt) REVERT: R 445 MET cc_start: 0.8425 (mmp) cc_final: 0.8184 (mmm) REVERT: R 469 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5624 (mm-30) outliers start: 65 outliers final: 23 residues processed: 214 average time/residue: 0.6086 time to fit residues: 137.7848 Evaluate side-chains 174 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 186 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 341 SER Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 389 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN G 59 ASN P 16 ASN R 374 ASN R 402 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116691 restraints weight = 10374.405| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.00 r_work: 0.3209 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8913 Z= 0.124 Angle : 0.525 6.619 12096 Z= 0.292 Chirality : 0.041 0.162 1361 Planarity : 0.004 0.045 1545 Dihedral : 8.767 76.323 1291 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.23 % Allowed : 22.27 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.25), residues: 1104 helix: 1.38 (0.25), residues: 444 sheet: -0.08 (0.34), residues: 212 loop : -0.66 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 72 TYR 0.024 0.001 TYR R 191 PHE 0.017 0.001 PHE A 212 TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8910) covalent geometry : angle 0.52505 (12090) SS BOND : bond 0.00431 ( 3) SS BOND : angle 0.75105 ( 6) hydrogen bonds : bond 0.05090 ( 453) hydrogen bonds : angle 5.10123 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6450 (pt0) REVERT: A 27 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6495 (mm-30) REVERT: A 28 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6670 (mtpt) REVERT: A 49 ASP cc_start: 0.6931 (m-30) cc_final: 0.6513 (t0) REVERT: A 58 LYS cc_start: 0.6600 (mtpp) cc_final: 0.6248 (mmtp) REVERT: A 208 PHE cc_start: 0.7723 (m-80) cc_final: 0.7446 (m-80) REVERT: A 289 GLU cc_start: 0.7499 (pp20) cc_final: 0.6984 (tp30) REVERT: A 346 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6466 (mtm-85) REVERT: B 27 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5852 (p0) REVERT: B 32 GLN cc_start: 0.6276 (pt0) cc_final: 0.5768 (tp40) REVERT: B 66 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7092 (p0) REVERT: B 70 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 96 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7141 (ttm-80) REVERT: B 101 MET cc_start: 0.8787 (mtp) cc_final: 0.8361 (mtp) REVERT: B 137 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7066 (tpp80) REVERT: B 138 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 146 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8561 (mm) REVERT: B 156 GLN cc_start: 0.7609 (mt0) cc_final: 0.7326 (mt0) REVERT: B 175 GLN cc_start: 0.7624 (pt0) cc_final: 0.7399 (pt0) REVERT: B 220 GLN cc_start: 0.7977 (mt0) cc_final: 0.7725 (mt0) REVERT: B 301 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7667 (mtpt) REVERT: G 44 HIS cc_start: 0.7865 (m90) cc_final: 0.7603 (m-70) REVERT: N 3 GLN cc_start: 0.6954 (tt0) cc_final: 0.6331 (tt0) REVERT: N 39 GLN cc_start: 0.8437 (tt0) cc_final: 0.8027 (tt0) REVERT: N 53 GLN cc_start: 0.7303 (mp10) cc_final: 0.6818 (mp10) REVERT: N 80 TYR cc_start: 0.7842 (m-80) cc_final: 0.6260 (m-80) REVERT: N 83 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7017 (mtt) REVERT: N 95 TYR cc_start: 0.8669 (m-80) cc_final: 0.8225 (m-80) REVERT: N 104 THR cc_start: 0.8055 (p) cc_final: 0.7702 (p) REVERT: N 105 ARG cc_start: 0.6647 (ttt180) cc_final: 0.6274 (mmm-85) REVERT: N 106 ASP cc_start: 0.8577 (p0) cc_final: 0.8336 (p0) REVERT: N 123 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6654 (tp-100) REVERT: R 182 GLU cc_start: 0.7502 (tt0) cc_final: 0.7160 (tt0) REVERT: R 189 MET cc_start: 0.7729 (tpt) cc_final: 0.7434 (tpp) REVERT: R 196 SER cc_start: 0.7489 (m) cc_final: 0.7243 (t) REVERT: R 224 MET cc_start: 0.7532 (mtt) cc_final: 0.7318 (mtm) REVERT: R 305 TYR cc_start: 0.8316 (t80) cc_final: 0.7529 (t80) REVERT: R 308 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7768 (p) REVERT: R 318 LYS cc_start: 0.6150 (mppt) cc_final: 0.5804 (mmtt) REVERT: R 346 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7258 (mm) REVERT: R 390 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6956 (ttp-110) REVERT: R 404 ARG cc_start: 0.6162 (tmm160) cc_final: 0.5267 (tmt-80) REVERT: R 441 MET cc_start: 0.8262 (mmt) cc_final: 0.8041 (mmt) outliers start: 47 outliers final: 21 residues processed: 182 average time/residue: 0.5814 time to fit residues: 112.3454 Evaluate side-chains 168 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 103 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 0.0010 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 176 GLN B 237 ASN B 340 ASN N 31 ASN P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117208 restraints weight = 10296.099| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.00 r_work: 0.3242 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8913 Z= 0.124 Angle : 0.487 6.194 12096 Z= 0.269 Chirality : 0.041 0.157 1361 Planarity : 0.004 0.052 1545 Dihedral : 7.513 73.553 1258 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.46 % Allowed : 22.61 % Favored : 71.94 % 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: 0.71 (0.25), residues: 1104 helix: 1.86 (0.25), residues: 444 sheet: -0.09 (0.33), residues: 218 loop : -0.63 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.024 0.001 TYR R 191 PHE 0.016 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8910) covalent geometry : angle 0.48643 (12090) SS BOND : bond 0.00041 ( 3) SS BOND : angle 0.76503 ( 6) hydrogen bonds : bond 0.04627 ( 453) hydrogen bonds : angle 4.73579 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6511 (pt0) REVERT: A 27 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 28 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6713 (mtpt) REVERT: A 49 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6594 (t0) REVERT: A 208 PHE cc_start: 0.7718 (m-80) cc_final: 0.7480 (m-80) REVERT: A 289 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: B 32 GLN cc_start: 0.6153 (pt0) cc_final: 0.5923 (tp40) REVERT: B 38 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6822 (p0) REVERT: B 66 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7269 (p0) REVERT: B 96 ARG cc_start: 0.7537 (mtm110) cc_final: 0.7107 (ttm-80) REVERT: B 101 MET cc_start: 0.8782 (mtp) cc_final: 0.8280 (mtp) REVERT: B 124 TYR cc_start: 0.8482 (m-80) cc_final: 0.8024 (m-80) REVERT: B 130 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5505 (tt0) REVERT: B 137 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7192 (ttm110) REVERT: B 138 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7349 (mt-10) REVERT: B 146 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 156 GLN cc_start: 0.7644 (mt0) cc_final: 0.7335 (mt0) REVERT: B 175 GLN cc_start: 0.7616 (pt0) cc_final: 0.7402 (pt0) REVERT: B 176 GLN cc_start: 0.8219 (tt0) cc_final: 0.7909 (tt0) REVERT: G 44 HIS cc_start: 0.7913 (m90) cc_final: 0.7669 (m-70) REVERT: G 62 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.4357 (ppt170) REVERT: N 3 GLN cc_start: 0.6894 (tt0) cc_final: 0.6135 (tt0) REVERT: N 39 GLN cc_start: 0.8474 (tt0) cc_final: 0.8170 (tt0) REVERT: N 53 GLN cc_start: 0.7267 (mp10) cc_final: 0.6822 (mp10) REVERT: N 80 TYR cc_start: 0.7768 (m-80) cc_final: 0.6101 (m-80) REVERT: N 86 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7173 (mp) REVERT: N 105 ARG cc_start: 0.6707 (ttt180) cc_final: 0.6224 (ttp-170) REVERT: N 106 ASP cc_start: 0.8589 (p0) cc_final: 0.8379 (p0) REVERT: N 123 GLN cc_start: 0.7298 (mm-40) cc_final: 0.6922 (tp-100) REVERT: R 45 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.4824 (tt0) REVERT: R 189 MET cc_start: 0.7590 (tpt) cc_final: 0.7363 (tpp) REVERT: R 240 LYS cc_start: 0.7375 (ttpt) cc_final: 0.6994 (ttpp) REVERT: R 305 TYR cc_start: 0.8431 (t80) cc_final: 0.8011 (t80) REVERT: R 318 LYS cc_start: 0.6135 (mppt) cc_final: 0.5883 (mmtt) REVERT: R 348 ASN cc_start: 0.8732 (t0) cc_final: 0.8500 (t0) REVERT: R 390 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7084 (ttp-110) REVERT: R 404 ARG cc_start: 0.6242 (tmm160) cc_final: 0.5514 (tmt-80) outliers start: 49 outliers final: 22 residues processed: 176 average time/residue: 0.6070 time to fit residues: 112.9327 Evaluate side-chains 167 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 14 optimal weight: 0.0570 chunk 100 optimal weight: 1.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115989 restraints weight = 10406.703| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.97 r_work: 0.3241 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8913 Z= 0.210 Angle : 0.570 8.210 12096 Z= 0.310 Chirality : 0.044 0.177 1361 Planarity : 0.005 0.056 1545 Dihedral : 7.114 63.882 1251 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.57 % Allowed : 23.61 % Favored : 69.82 % 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: 0.42 (0.25), residues: 1104 helix: 1.63 (0.25), residues: 439 sheet: -0.37 (0.33), residues: 222 loop : -0.69 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.023 0.002 TYR R 191 PHE 0.018 0.002 PHE A 212 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8910) covalent geometry : angle 0.56973 (12090) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.97142 ( 6) hydrogen bonds : bond 0.05060 ( 453) hydrogen bonds : angle 4.88257 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: A 27 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6789 (mm-30) REVERT: A 28 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6885 (mtpt) REVERT: A 35 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6502 (mt0) REVERT: A 208 PHE cc_start: 0.7824 (m-80) cc_final: 0.7617 (m-80) REVERT: A 289 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: B 27 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.5822 (p0) REVERT: B 32 GLN cc_start: 0.6304 (pt0) cc_final: 0.5979 (tp40) REVERT: B 38 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6770 (p0) REVERT: B 66 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7341 (p0) REVERT: B 96 ARG cc_start: 0.7523 (mtm110) cc_final: 0.7128 (ttm-80) REVERT: B 101 MET cc_start: 0.8803 (mtp) cc_final: 0.8384 (mtp) REVERT: B 124 TYR cc_start: 0.8502 (m-80) cc_final: 0.8007 (m-80) REVERT: B 130 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5511 (tt0) REVERT: B 137 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7224 (ttm110) REVERT: B 138 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 146 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8804 (tt) REVERT: B 156 GLN cc_start: 0.7768 (mt0) cc_final: 0.7486 (mt0) REVERT: G 44 HIS cc_start: 0.7976 (m90) cc_final: 0.7688 (m-70) REVERT: N 3 GLN cc_start: 0.6986 (tt0) cc_final: 0.6328 (tt0) REVERT: N 39 GLN cc_start: 0.8497 (tt0) cc_final: 0.8091 (tt0) REVERT: N 53 GLN cc_start: 0.7401 (mp10) cc_final: 0.6964 (mp10) REVERT: N 80 TYR cc_start: 0.7987 (m-80) cc_final: 0.6611 (m-80) REVERT: N 86 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7398 (mp) REVERT: R 34 LYS cc_start: 0.5919 (ttpm) cc_final: 0.5461 (tttp) REVERT: R 179 ARG cc_start: 0.5834 (mmt90) cc_final: 0.4933 (mmm-85) REVERT: R 305 TYR cc_start: 0.8460 (t80) cc_final: 0.8152 (t80) REVERT: R 318 LYS cc_start: 0.6163 (mppt) cc_final: 0.5831 (mmpt) REVERT: R 469 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5702 (mm-30) outliers start: 59 outliers final: 35 residues processed: 180 average time/residue: 0.5834 time to fit residues: 111.4115 Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 175 GLN B 176 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116231 restraints weight = 10331.952| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.96 r_work: 0.3243 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8913 Z= 0.205 Angle : 0.568 7.664 12096 Z= 0.309 Chirality : 0.044 0.171 1361 Planarity : 0.005 0.057 1545 Dihedral : 7.086 63.990 1251 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 7.35 % Allowed : 23.16 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.25), residues: 1104 helix: 1.50 (0.25), residues: 439 sheet: -0.42 (0.33), residues: 220 loop : -0.77 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.025 0.002 TYR R 191 PHE 0.017 0.002 PHE R 230 TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8910) covalent geometry : angle 0.56738 (12090) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.98258 ( 6) hydrogen bonds : bond 0.04940 ( 453) hydrogen bonds : angle 4.86601 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 133 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: A 27 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6746 (mm-30) REVERT: A 28 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6998 (mtpt) REVERT: A 35 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: A 58 LYS cc_start: 0.6607 (mtpp) cc_final: 0.6274 (mmtp) REVERT: A 208 PHE cc_start: 0.7797 (m-80) cc_final: 0.7574 (m-80) REVERT: A 289 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: B 27 ASP cc_start: 0.6514 (OUTLIER) cc_final: 0.5855 (p0) REVERT: B 32 GLN cc_start: 0.6217 (pt0) cc_final: 0.5931 (tp40) REVERT: B 38 ASP cc_start: 0.6955 (p0) cc_final: 0.6685 (p0) REVERT: B 101 MET cc_start: 0.8767 (mtp) cc_final: 0.8395 (mtp) REVERT: B 130 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5357 (tt0) REVERT: B 137 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7098 (tpp80) REVERT: B 138 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 156 GLN cc_start: 0.7699 (mt0) cc_final: 0.7444 (mt0) REVERT: B 201 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8512 (p) REVERT: G 36 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: G 44 HIS cc_start: 0.7981 (m90) cc_final: 0.7708 (m-70) REVERT: N 3 GLN cc_start: 0.7002 (tt0) cc_final: 0.6369 (tt0) REVERT: N 39 GLN cc_start: 0.8510 (tt0) cc_final: 0.8049 (tt0) REVERT: N 53 GLN cc_start: 0.7381 (mp10) cc_final: 0.6924 (mp10) REVERT: N 86 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7360 (mp) REVERT: N 105 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6285 (mmm-85) REVERT: N 125 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7938 (p) REVERT: R 34 LYS cc_start: 0.5818 (ttpm) cc_final: 0.5414 (tttp) REVERT: R 179 ARG cc_start: 0.5956 (mmt90) cc_final: 0.5080 (mmm-85) REVERT: R 212 PHE cc_start: 0.6200 (m-80) cc_final: 0.5776 (m-10) REVERT: R 305 TYR cc_start: 0.8464 (t80) cc_final: 0.8210 (t80) REVERT: R 390 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7263 (ttp-110) REVERT: R 425 MET cc_start: 0.8715 (pp-130) cc_final: 0.8376 (ptm) REVERT: R 469 GLU cc_start: 0.5881 (mm-30) cc_final: 0.5661 (mm-30) outliers start: 66 outliers final: 35 residues processed: 184 average time/residue: 0.6313 time to fit residues: 122.7219 Evaluate side-chains 178 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 175 GLN B 176 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN P 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118409 restraints weight = 10292.289| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3267 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8913 Z= 0.140 Angle : 0.510 7.205 12096 Z= 0.280 Chirality : 0.041 0.162 1361 Planarity : 0.004 0.057 1545 Dihedral : 6.496 59.715 1248 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 6.35 % Allowed : 24.94 % Favored : 68.71 % 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: 0.48 (0.26), residues: 1104 helix: 1.78 (0.25), residues: 439 sheet: -0.41 (0.33), residues: 220 loop : -0.74 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.023 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8910) covalent geometry : angle 0.51008 (12090) SS BOND : bond 0.00042 ( 3) SS BOND : angle 0.78623 ( 6) hydrogen bonds : bond 0.04484 ( 453) hydrogen bonds : angle 4.67972 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6698 (tm-30) REVERT: A 27 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 28 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6924 (mtpt) REVERT: A 208 PHE cc_start: 0.7786 (m-80) cc_final: 0.7515 (m-80) REVERT: A 273 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7521 (ptm160) REVERT: A 289 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: B 27 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.5732 (p0) REVERT: B 32 GLN cc_start: 0.6279 (pt0) cc_final: 0.6043 (tp40) REVERT: B 38 ASP cc_start: 0.6877 (p0) cc_final: 0.6569 (p0) REVERT: B 101 MET cc_start: 0.8799 (mtp) cc_final: 0.8352 (mtp) REVERT: B 124 TYR cc_start: 0.8495 (m-80) cc_final: 0.7966 (m-80) REVERT: B 130 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5370 (tt0) REVERT: B 137 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7149 (ttm110) REVERT: B 138 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 156 GLN cc_start: 0.7655 (mt0) cc_final: 0.7403 (mt0) REVERT: G 44 HIS cc_start: 0.7947 (m90) cc_final: 0.7674 (m-70) REVERT: N 3 GLN cc_start: 0.7010 (tt0) cc_final: 0.6319 (tt0) REVERT: N 6 GLU cc_start: 0.6587 (mp0) cc_final: 0.6383 (mp0) REVERT: N 39 GLN cc_start: 0.8504 (tt0) cc_final: 0.8056 (tt0) REVERT: N 53 GLN cc_start: 0.7351 (mp10) cc_final: 0.6919 (mp10) REVERT: N 77 ASN cc_start: 0.7306 (m-40) cc_final: 0.7095 (t0) REVERT: N 80 TYR cc_start: 0.7879 (m-80) cc_final: 0.6424 (m-80) REVERT: N 105 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6239 (ttp-170) REVERT: N 125 THR cc_start: 0.8081 (p) cc_final: 0.7855 (p) REVERT: R 34 LYS cc_start: 0.5872 (ttpm) cc_final: 0.5633 (tttm) REVERT: R 179 ARG cc_start: 0.5913 (mmt90) cc_final: 0.5042 (mmm-85) REVERT: R 212 PHE cc_start: 0.6365 (m-80) cc_final: 0.5933 (m-10) REVERT: R 305 TYR cc_start: 0.8460 (t80) cc_final: 0.8085 (t80) REVERT: R 308 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7871 (p) REVERT: R 317 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.6004 (mp0) REVERT: R 318 LYS cc_start: 0.6185 (mptp) cc_final: 0.5710 (mmpt) REVERT: R 390 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7162 (ttp-110) REVERT: R 404 ARG cc_start: 0.6344 (tmm160) cc_final: 0.5586 (tmt-80) REVERT: R 425 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8371 (ptm) REVERT: R 469 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5591 (mm-30) outliers start: 57 outliers final: 31 residues processed: 179 average time/residue: 0.6388 time to fit residues: 120.9491 Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN B 259 GLN P 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.154279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118478 restraints weight = 10340.163| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3258 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8913 Z= 0.144 Angle : 0.514 8.654 12096 Z= 0.280 Chirality : 0.042 0.162 1361 Planarity : 0.004 0.058 1545 Dihedral : 6.255 59.455 1245 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.68 % Allowed : 25.28 % Favored : 69.04 % 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: 0.54 (0.26), residues: 1104 helix: 1.86 (0.25), residues: 439 sheet: -0.40 (0.33), residues: 220 loop : -0.73 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.023 0.002 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8910) covalent geometry : angle 0.51376 (12090) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.81550 ( 6) hydrogen bonds : bond 0.04448 ( 453) hydrogen bonds : angle 4.60359 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6832 (mm-30) REVERT: A 28 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6912 (mtpt) REVERT: A 49 ASP cc_start: 0.7247 (m-30) cc_final: 0.6387 (t0) REVERT: A 208 PHE cc_start: 0.7772 (m-80) cc_final: 0.7545 (m-80) REVERT: A 273 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7611 (ptm160) REVERT: A 289 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: B 27 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.5814 (p0) REVERT: B 38 ASP cc_start: 0.6884 (p0) cc_final: 0.6594 (p0) REVERT: B 66 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7316 (p0) REVERT: B 101 MET cc_start: 0.8820 (mtp) cc_final: 0.8374 (mtp) REVERT: B 124 TYR cc_start: 0.8475 (m-80) cc_final: 0.8014 (m-80) REVERT: B 130 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5369 (tt0) REVERT: B 137 ARG cc_start: 0.7527 (ttm110) cc_final: 0.7125 (ttm110) REVERT: B 138 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 156 GLN cc_start: 0.7687 (mt0) cc_final: 0.7425 (mt0) REVERT: G 44 HIS cc_start: 0.8005 (m90) cc_final: 0.7765 (m-70) REVERT: N 3 GLN cc_start: 0.6993 (tt0) cc_final: 0.6274 (tt0) REVERT: N 6 GLU cc_start: 0.6701 (mp0) cc_final: 0.6487 (mp0) REVERT: N 39 GLN cc_start: 0.8526 (tt0) cc_final: 0.8097 (tt0) REVERT: N 46 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7396 (mt-10) REVERT: N 53 GLN cc_start: 0.7353 (mp10) cc_final: 0.6934 (mp10) REVERT: N 77 ASN cc_start: 0.7084 (m-40) cc_final: 0.6810 (t0) REVERT: N 80 TYR cc_start: 0.7757 (m-80) cc_final: 0.6320 (m-80) REVERT: N 105 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6267 (ttp-170) REVERT: N 125 THR cc_start: 0.8078 (p) cc_final: 0.7857 (p) REVERT: R 179 ARG cc_start: 0.5668 (mmt90) cc_final: 0.5005 (mmm-85) REVERT: R 305 TYR cc_start: 0.8462 (t80) cc_final: 0.8003 (t80) REVERT: R 308 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7748 (p) REVERT: R 317 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.5986 (mp0) REVERT: R 318 LYS cc_start: 0.6355 (mptp) cc_final: 0.5803 (mmpt) REVERT: R 390 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: R 404 ARG cc_start: 0.6463 (tmm160) cc_final: 0.5744 (tmt-80) REVERT: R 425 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8369 (ptm) outliers start: 51 outliers final: 36 residues processed: 171 average time/residue: 0.6663 time to fit residues: 120.1785 Evaluate side-chains 180 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 359 LYS Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119286 restraints weight = 10284.782| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.97 r_work: 0.3285 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8913 Z= 0.131 Angle : 0.499 9.322 12096 Z= 0.272 Chirality : 0.041 0.159 1361 Planarity : 0.004 0.057 1545 Dihedral : 5.671 58.984 1242 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.68 % Allowed : 25.72 % Favored : 68.60 % 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: 0.65 (0.26), residues: 1104 helix: 2.02 (0.25), residues: 439 sheet: -0.36 (0.33), residues: 219 loop : -0.73 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.023 0.001 TYR R 191 PHE 0.016 0.001 PHE R 335 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8910) covalent geometry : angle 0.49854 (12090) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.73095 ( 6) hydrogen bonds : bond 0.04319 ( 453) hydrogen bonds : angle 4.52917 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6849 (mm-30) REVERT: A 28 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6877 (mtpt) REVERT: A 49 ASP cc_start: 0.7078 (m-30) cc_final: 0.6297 (t0) REVERT: A 208 PHE cc_start: 0.7755 (m-80) cc_final: 0.7498 (m-80) REVERT: A 273 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7594 (ptm160) REVERT: A 285 ASP cc_start: 0.7718 (t0) cc_final: 0.7448 (p0) REVERT: A 289 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: B 27 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.5853 (p0) REVERT: B 38 ASP cc_start: 0.6892 (p0) cc_final: 0.6580 (p0) REVERT: B 66 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7292 (p0) REVERT: B 101 MET cc_start: 0.8832 (mtp) cc_final: 0.8404 (mtp) REVERT: B 124 TYR cc_start: 0.8440 (m-80) cc_final: 0.7820 (m-80) REVERT: B 130 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5362 (tt0) REVERT: B 137 ARG cc_start: 0.7530 (ttm110) cc_final: 0.7099 (ttm110) REVERT: B 138 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7476 (mt-10) REVERT: B 156 GLN cc_start: 0.7680 (mt0) cc_final: 0.7416 (mt0) REVERT: B 212 ASP cc_start: 0.7493 (t0) cc_final: 0.7203 (t70) REVERT: G 36 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: G 44 HIS cc_start: 0.7992 (m90) cc_final: 0.7744 (m-70) REVERT: G 62 ARG cc_start: 0.5159 (OUTLIER) cc_final: 0.4441 (ppt170) REVERT: N 3 GLN cc_start: 0.6924 (tt0) cc_final: 0.6242 (tt0) REVERT: N 6 GLU cc_start: 0.6633 (mp0) cc_final: 0.6405 (mp0) REVERT: N 39 GLN cc_start: 0.8529 (tt0) cc_final: 0.8149 (tt0) REVERT: N 46 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7455 (mt-10) REVERT: N 53 GLN cc_start: 0.7377 (mp10) cc_final: 0.6917 (mp10) REVERT: N 77 ASN cc_start: 0.7056 (m-40) cc_final: 0.6793 (t0) REVERT: N 80 TYR cc_start: 0.7729 (m-80) cc_final: 0.6200 (m-80) REVERT: N 105 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6279 (ttp-170) REVERT: N 125 THR cc_start: 0.7982 (p) cc_final: 0.7769 (p) REVERT: P 25 ARG cc_start: 0.5961 (ttp-110) cc_final: 0.5706 (ttp-110) REVERT: R 179 ARG cc_start: 0.5660 (mmt90) cc_final: 0.5035 (mmm-85) REVERT: R 212 PHE cc_start: 0.6401 (m-80) cc_final: 0.6196 (m-10) REVERT: R 305 TYR cc_start: 0.8465 (t80) cc_final: 0.8006 (t80) REVERT: R 308 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7744 (p) REVERT: R 317 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: R 318 LYS cc_start: 0.6525 (mptp) cc_final: 0.6315 (mmtp) REVERT: R 390 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7247 (ttp-110) REVERT: R 404 ARG cc_start: 0.6457 (tmm160) cc_final: 0.5788 (tmt-80) REVERT: R 425 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8369 (ptm) outliers start: 51 outliers final: 33 residues processed: 174 average time/residue: 0.6354 time to fit residues: 117.0072 Evaluate side-chains 182 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.0040 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.156199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120624 restraints weight = 10239.840| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.95 r_work: 0.3293 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8913 Z= 0.123 Angle : 0.498 11.015 12096 Z= 0.271 Chirality : 0.041 0.156 1361 Planarity : 0.004 0.057 1545 Dihedral : 5.531 57.936 1242 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.57 % Allowed : 25.61 % Favored : 68.82 % 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: 0.74 (0.26), residues: 1104 helix: 2.14 (0.25), residues: 433 sheet: -0.35 (0.33), residues: 219 loop : -0.68 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.023 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8910) covalent geometry : angle 0.49792 (12090) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.76629 ( 6) hydrogen bonds : bond 0.04219 ( 453) hydrogen bonds : angle 4.47133 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: A 27 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 28 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6995 (mtpt) REVERT: A 49 ASP cc_start: 0.7101 (m-30) cc_final: 0.6289 (t0) REVERT: A 208 PHE cc_start: 0.7721 (m-80) cc_final: 0.7459 (m-80) REVERT: A 273 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7510 (ptm160) REVERT: A 289 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: B 27 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.5856 (p0) REVERT: B 38 ASP cc_start: 0.6873 (p0) cc_final: 0.6560 (p0) REVERT: B 66 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7246 (p0) REVERT: B 70 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8255 (pp) REVERT: B 101 MET cc_start: 0.8844 (mtp) cc_final: 0.8448 (mtp) REVERT: B 124 TYR cc_start: 0.8446 (m-80) cc_final: 0.7810 (m-80) REVERT: B 130 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5360 (tt0) REVERT: B 137 ARG cc_start: 0.7556 (ttm110) cc_final: 0.7116 (ttm110) REVERT: B 138 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 156 GLN cc_start: 0.7682 (mt0) cc_final: 0.7426 (mt0) REVERT: G 44 HIS cc_start: 0.7980 (m90) cc_final: 0.7725 (m-70) REVERT: G 62 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4941 (ppt170) REVERT: N 3 GLN cc_start: 0.6853 (tt0) cc_final: 0.6293 (tt0) REVERT: N 6 GLU cc_start: 0.6646 (mp0) cc_final: 0.6415 (mp0) REVERT: N 39 GLN cc_start: 0.8541 (tt0) cc_final: 0.8215 (tt0) REVERT: N 46 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7499 (mt-10) REVERT: N 53 GLN cc_start: 0.7379 (mp10) cc_final: 0.6939 (mp10) REVERT: N 77 ASN cc_start: 0.7072 (m-40) cc_final: 0.6767 (t0) REVERT: N 80 TYR cc_start: 0.7721 (m-80) cc_final: 0.6153 (m-80) REVERT: N 105 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6238 (ttp-170) REVERT: N 125 THR cc_start: 0.7998 (p) cc_final: 0.7783 (p) REVERT: P 25 ARG cc_start: 0.5966 (ttp-110) cc_final: 0.5707 (ttp-110) REVERT: R 212 PHE cc_start: 0.6442 (m-80) cc_final: 0.6117 (m-10) REVERT: R 278 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.4275 (t80) REVERT: R 305 TYR cc_start: 0.8462 (t80) cc_final: 0.7960 (t80) REVERT: R 308 SER cc_start: 0.8087 (OUTLIER) cc_final: 0.7731 (p) REVERT: R 317 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: R 318 LYS cc_start: 0.6514 (mptp) cc_final: 0.6306 (mmtp) REVERT: R 390 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7239 (ttp-110) REVERT: R 404 ARG cc_start: 0.6339 (tmm160) cc_final: 0.5686 (tmt-80) REVERT: R 425 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8378 (ptm) outliers start: 50 outliers final: 28 residues processed: 174 average time/residue: 0.6240 time to fit residues: 114.7379 Evaluate side-chains 178 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN R 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120947 restraints weight = 10255.060| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.96 r_work: 0.3301 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8913 Z= 0.119 Angle : 0.497 11.267 12096 Z= 0.269 Chirality : 0.040 0.155 1361 Planarity : 0.004 0.057 1545 Dihedral : 5.371 57.579 1241 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.01 % Allowed : 26.61 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.26), residues: 1104 helix: 2.23 (0.25), residues: 433 sheet: -0.25 (0.33), residues: 217 loop : -0.69 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.024 0.001 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8910) covalent geometry : angle 0.49657 (12090) SS BOND : bond 0.00117 ( 3) SS BOND : angle 0.72534 ( 6) hydrogen bonds : bond 0.04172 ( 453) hydrogen bonds : angle 4.42553 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: A 27 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6914 (mm-30) REVERT: A 28 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6978 (mtpt) REVERT: A 49 ASP cc_start: 0.7144 (m-30) cc_final: 0.6317 (t0) REVERT: A 208 PHE cc_start: 0.7746 (m-80) cc_final: 0.7535 (m-80) REVERT: A 273 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7512 (ptm160) REVERT: A 285 ASP cc_start: 0.7713 (t0) cc_final: 0.7441 (p0) REVERT: A 289 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: B 27 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.5833 (p0) REVERT: B 38 ASP cc_start: 0.6888 (p0) cc_final: 0.6557 (p0) REVERT: B 66 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7317 (p0) REVERT: B 101 MET cc_start: 0.8848 (mtp) cc_final: 0.8458 (mtp) REVERT: B 124 TYR cc_start: 0.8439 (m-80) cc_final: 0.7968 (m-80) REVERT: B 130 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5363 (tt0) REVERT: B 137 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7114 (ttm110) REVERT: B 138 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 156 GLN cc_start: 0.7686 (mt0) cc_final: 0.7413 (mt0) REVERT: B 212 ASP cc_start: 0.7491 (t0) cc_final: 0.7207 (t70) REVERT: G 44 HIS cc_start: 0.7981 (m90) cc_final: 0.7758 (m-70) REVERT: N 3 GLN cc_start: 0.6867 (tt0) cc_final: 0.6303 (tt0) REVERT: N 6 GLU cc_start: 0.6655 (mp0) cc_final: 0.6414 (mp0) REVERT: N 39 GLN cc_start: 0.8526 (tt0) cc_final: 0.8204 (tt0) REVERT: N 46 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7488 (mt-10) REVERT: N 53 GLN cc_start: 0.7329 (mp10) cc_final: 0.7040 (mp10) REVERT: N 77 ASN cc_start: 0.7041 (m-40) cc_final: 0.6786 (t0) REVERT: N 80 TYR cc_start: 0.7676 (m-80) cc_final: 0.6148 (m-80) REVERT: N 105 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6286 (ttp-170) REVERT: N 125 THR cc_start: 0.7925 (p) cc_final: 0.7705 (p) REVERT: P 25 ARG cc_start: 0.5975 (ttp-110) cc_final: 0.5702 (ttp-110) REVERT: R 34 LYS cc_start: 0.5749 (tttt) cc_final: 0.5520 (tttp) REVERT: R 212 PHE cc_start: 0.6409 (m-80) cc_final: 0.6147 (m-10) REVERT: R 278 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.4284 (t80) REVERT: R 305 TYR cc_start: 0.8425 (t80) cc_final: 0.7906 (t80) REVERT: R 308 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7755 (p) REVERT: R 317 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: R 390 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7182 (ttp-110) REVERT: R 404 ARG cc_start: 0.6321 (tmm160) cc_final: 0.5686 (tmt-80) REVERT: R 425 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8388 (ptm) outliers start: 45 outliers final: 29 residues processed: 170 average time/residue: 0.5910 time to fit residues: 106.4500 Evaluate side-chains 176 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 278 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 317 GLU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 408 LYS Chi-restraints excluded: chain R residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118362 restraints weight = 10137.647| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.94 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8913 Z= 0.165 Angle : 0.550 11.337 12096 Z= 0.294 Chirality : 0.042 0.165 1361 Planarity : 0.004 0.057 1545 Dihedral : 5.271 58.384 1234 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.23 % Allowed : 26.39 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.26), residues: 1104 helix: 1.94 (0.25), residues: 439 sheet: -0.35 (0.33), residues: 220 loop : -0.73 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 383 TYR 0.023 0.002 TYR R 191 PHE 0.016 0.002 PHE R 335 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8910) covalent geometry : angle 0.54994 (12090) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.85589 ( 6) hydrogen bonds : bond 0.04540 ( 453) hydrogen bonds : angle 4.58016 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.17 seconds wall clock time: 65 minutes 29.26 seconds (3929.26 seconds total)