Starting phenix.real_space_refine on Thu Mar 13 02:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vvl_32143/03_2025/7vvl_32143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vvl_32143/03_2025/7vvl_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_2025/7vvl_32143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2025/7vvl_32143.map" model { file = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2025/7vvl_32143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vvl_32143/03_2025/7vvl_32143.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 2, 'ARG:plan': 4, '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: {'GLU:plan': 1, 'ARG: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: {'PHE%COO:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} 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: 5.25, per 1000 atoms: 0.60 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.03 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: 2.45 Time building geometry restraints manager: 2.65 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- 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 8910 Z= 0.932 Angle : 1.688 9.035 12090 Z= 1.233 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 : 4.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), 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 TRP 0.019 0.004 TRP A 271 HIS 0.006 0.001 HIS B 311 PHE 0.012 0.003 PHE R 378 TYR 0.016 0.003 TYR R 134 ARG 0.005 0.001 ARG B 49 *********************** 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 : 1.005 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: 1.2883 time to fit residues: 293.0773 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 : 0.891 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.151723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115741 restraints weight = 10251.670| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.99 r_work: 0.3202 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8910 Z= 0.195 Angle : 0.539 6.768 12090 Z= 0.300 Chirality : 0.042 0.165 1361 Planarity : 0.004 0.046 1545 Dihedral : 8.876 76.549 1291 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.46 % Allowed : 21.94 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1104 helix: 1.33 (0.24), residues: 444 sheet: -0.07 (0.34), residues: 212 loop : -0.69 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.005 0.001 ARG N 72 *********************** 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 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6386 (pt0) REVERT: A 27 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6557 (mm-30) REVERT: A 28 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6718 (mtpt) REVERT: A 49 ASP cc_start: 0.7030 (m-30) cc_final: 0.6554 (t0) REVERT: A 58 LYS cc_start: 0.6638 (mtpp) cc_final: 0.6289 (mmtp) REVERT: A 208 PHE cc_start: 0.7744 (m-80) cc_final: 0.7505 (m-80) REVERT: A 289 GLU cc_start: 0.7517 (pp20) cc_final: 0.7004 (tp30) REVERT: A 307 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7480 (mtm180) REVERT: A 346 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6502 (mtm-85) REVERT: B 27 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.5883 (p0) REVERT: B 32 GLN cc_start: 0.6298 (pt0) cc_final: 0.5795 (tp40) REVERT: B 66 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7110 (p0) REVERT: B 70 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8473 (pp) REVERT: B 96 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7169 (ttm-80) REVERT: B 101 MET cc_start: 0.8797 (mtp) cc_final: 0.8270 (mtp) REVERT: B 124 TYR cc_start: 0.8504 (m-80) cc_final: 0.8120 (m-80) REVERT: B 137 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7220 (ttm110) REVERT: B 138 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 146 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 156 GLN cc_start: 0.7638 (mt0) cc_final: 0.7350 (mt0) REVERT: B 175 GLN cc_start: 0.7628 (pt0) cc_final: 0.7402 (pt0) REVERT: B 176 GLN cc_start: 0.8255 (tt0) cc_final: 0.7978 (tt0) REVERT: B 220 GLN cc_start: 0.8020 (mt0) cc_final: 0.7783 (mt0) REVERT: G 44 HIS cc_start: 0.7880 (m90) cc_final: 0.7606 (m-70) REVERT: N 3 GLN cc_start: 0.6988 (tt0) cc_final: 0.6369 (tt0) REVERT: N 39 GLN cc_start: 0.8482 (tt0) cc_final: 0.8062 (tt0) REVERT: N 53 GLN cc_start: 0.7340 (mp10) cc_final: 0.6863 (mp10) REVERT: N 80 TYR cc_start: 0.7878 (m-80) cc_final: 0.6319 (m-80) REVERT: N 83 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7074 (mtt) REVERT: N 95 TYR cc_start: 0.8682 (m-80) cc_final: 0.8278 (m-80) REVERT: N 104 THR cc_start: 0.8113 (p) cc_final: 0.7757 (p) REVERT: N 105 ARG cc_start: 0.6669 (ttt180) cc_final: 0.6298 (mmm-85) REVERT: N 106 ASP cc_start: 0.8585 (p0) cc_final: 0.8351 (p0) REVERT: N 123 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6674 (tp-100) REVERT: P 19 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6342 (pt0) REVERT: R 182 GLU cc_start: 0.7507 (tt0) cc_final: 0.7252 (tt0) REVERT: R 189 MET cc_start: 0.7754 (tpt) cc_final: 0.7473 (tpp) REVERT: R 224 MET cc_start: 0.7554 (mtt) cc_final: 0.7338 (mtm) REVERT: R 305 TYR cc_start: 0.8348 (t80) cc_final: 0.7708 (t80) REVERT: R 318 LYS cc_start: 0.6156 (mppt) cc_final: 0.5796 (mmtt) REVERT: R 346 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7219 (mm) REVERT: R 390 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6982 (ttp-110) REVERT: R 404 ARG cc_start: 0.6207 (tmm160) cc_final: 0.5302 (tmt-80) outliers start: 49 outliers final: 22 residues processed: 184 average time/residue: 1.4531 time to fit residues: 284.0259 Evaluate side-chains 167 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 135 VAL 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 P residue 19 GLU 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 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 30 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112399 restraints weight = 10563.134| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.01 r_work: 0.3168 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8910 Z= 0.423 Angle : 0.646 9.599 12090 Z= 0.351 Chirality : 0.047 0.187 1361 Planarity : 0.005 0.059 1545 Dihedral : 8.305 77.456 1258 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 7.57 % Allowed : 21.49 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1104 helix: 1.21 (0.25), residues: 439 sheet: -0.38 (0.33), residues: 222 loop : -0.80 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.017 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.005 0.001 ARG A 255 *********************** 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 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: A 27 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 28 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7138 (ptpp) REVERT: A 35 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6463 (mt0) REVERT: A 289 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: B 27 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.5985 (p0) REVERT: B 32 GLN cc_start: 0.6161 (pt0) cc_final: 0.5903 (tp40) REVERT: B 38 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6867 (p0) REVERT: B 66 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7297 (p0) REVERT: B 96 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7089 (ttm-80) REVERT: B 101 MET cc_start: 0.8804 (mtp) cc_final: 0.8358 (mtp) REVERT: B 124 TYR cc_start: 0.8466 (m-80) cc_final: 0.7994 (m-80) REVERT: B 130 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5327 (tt0) REVERT: B 137 ARG cc_start: 0.7449 (ttm110) cc_final: 0.6975 (tpp80) REVERT: B 146 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8750 (tt) REVERT: B 156 GLN cc_start: 0.7765 (mt0) cc_final: 0.7470 (mt0) REVERT: G 36 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: G 44 HIS cc_start: 0.8019 (m90) cc_final: 0.7738 (m-70) REVERT: N 3 GLN cc_start: 0.7094 (tt0) cc_final: 0.6393 (tt0) REVERT: N 39 GLN cc_start: 0.8518 (tt0) cc_final: 0.8087 (tt0) REVERT: N 53 GLN cc_start: 0.7385 (mp10) cc_final: 0.6931 (mp10) REVERT: N 76 LYS cc_start: 0.7483 (mppt) cc_final: 0.7149 (mmtm) REVERT: N 83 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7303 (mtp) REVERT: N 86 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7249 (mp) REVERT: N 105 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6286 (mmm-85) REVERT: R 34 LYS cc_start: 0.5772 (tttt) cc_final: 0.5259 (tttp) REVERT: R 224 MET cc_start: 0.7617 (mtt) cc_final: 0.7414 (mtm) REVERT: R 305 TYR cc_start: 0.8473 (t80) cc_final: 0.8248 (t80) REVERT: R 425 MET cc_start: 0.8765 (pp-130) cc_final: 0.8339 (ptm) outliers start: 68 outliers final: 40 residues processed: 188 average time/residue: 1.6860 time to fit residues: 338.8606 Evaluate side-chains 183 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 38 ASP Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL 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 217 MET 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 25 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 83 MET 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 197 VAL Chi-restraints excluded: chain R residue 203 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 349 THR Chi-restraints excluded: chain R residue 359 LYS 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 33 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 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 = 0.3798 r_free = 0.3798 target = 0.154798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119528 restraints weight = 10169.314| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.93 r_work: 0.3284 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8910 Z= 0.158 Angle : 0.477 5.505 12090 Z= 0.265 Chirality : 0.040 0.156 1361 Planarity : 0.004 0.055 1545 Dihedral : 7.443 74.224 1258 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 6.35 % Allowed : 23.61 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1104 helix: 1.78 (0.25), residues: 438 sheet: -0.28 (0.32), residues: 218 loop : -0.77 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG R 213 *********************** 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 202 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6585 (pt0) REVERT: A 27 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6695 (mm-30) REVERT: A 49 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6706 (t0) REVERT: A 58 LYS cc_start: 0.6602 (mtpp) cc_final: 0.6276 (mmtp) REVERT: A 208 PHE cc_start: 0.7865 (m-80) cc_final: 0.7615 (m-80) REVERT: A 273 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7440 (ptm160) REVERT: A 289 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: A 304 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: B 27 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.5727 (p0) REVERT: B 38 ASP cc_start: 0.7157 (p0) cc_final: 0.6874 (p0) REVERT: B 66 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7268 (p0) REVERT: B 70 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8441 (pp) REVERT: B 76 ASP cc_start: 0.8130 (p0) cc_final: 0.7885 (p0) REVERT: B 96 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7080 (ttm-80) REVERT: B 101 MET cc_start: 0.8766 (mtp) cc_final: 0.8360 (mtp) REVERT: B 130 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: B 137 ARG cc_start: 0.7524 (ttm110) cc_final: 0.7103 (ttm110) REVERT: B 138 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 146 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (tt) REVERT: B 156 GLN cc_start: 0.7632 (mt0) cc_final: 0.7342 (mt0) REVERT: G 44 HIS cc_start: 0.7930 (m90) cc_final: 0.7660 (m-70) REVERT: N 3 GLN cc_start: 0.7009 (tt0) cc_final: 0.6397 (tt0) REVERT: N 39 GLN cc_start: 0.8486 (tt0) cc_final: 0.8084 (tt0) REVERT: N 53 GLN cc_start: 0.7296 (mp10) cc_final: 0.6853 (mp10) REVERT: N 80 TYR cc_start: 0.7779 (m-80) cc_final: 0.6113 (m-80) REVERT: N 83 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.7125 (mtp) REVERT: N 86 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7272 (mp) REVERT: N 105 ARG cc_start: 0.6661 (ttt180) cc_final: 0.6185 (ttp-170) REVERT: N 125 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (p) REVERT: R 34 LYS cc_start: 0.5911 (tttt) cc_final: 0.5474 (tttp) REVERT: R 45 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.4809 (mt0) REVERT: R 240 LYS cc_start: 0.7400 (ttpt) cc_final: 0.6995 (ttpp) REVERT: R 305 TYR cc_start: 0.8466 (t80) cc_final: 0.8100 (t80) REVERT: R 308 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7725 (p) REVERT: R 390 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7194 (ttp-110) REVERT: R 469 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5695 (mm-30) outliers start: 57 outliers final: 21 residues processed: 184 average time/residue: 1.3186 time to fit residues: 257.1699 Evaluate side-chains 174 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU 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 273 ARG Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLU 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 97 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU 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 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 83 MET 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 125 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain R residue 45 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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** B 259 GLN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116031 restraints weight = 10247.947| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.94 r_work: 0.3239 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8910 Z= 0.322 Angle : 0.571 8.496 12090 Z= 0.312 Chirality : 0.044 0.177 1361 Planarity : 0.005 0.057 1545 Dihedral : 7.322 80.278 1250 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 6.46 % Allowed : 24.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1104 helix: 1.55 (0.25), residues: 439 sheet: -0.33 (0.33), residues: 218 loop : -0.81 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.004 0.001 ARG B 197 *********************** 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 193 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: A 27 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6888 (mm-30) REVERT: A 58 LYS cc_start: 0.6678 (mtpp) cc_final: 0.6329 (mmtp) REVERT: A 289 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7039 (tp30) REVERT: B 27 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.5809 (p0) REVERT: B 38 ASP cc_start: 0.6982 (p0) cc_final: 0.6712 (p0) REVERT: B 66 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 76 ASP cc_start: 0.8273 (p0) cc_final: 0.8047 (p0) REVERT: B 96 ARG cc_start: 0.7408 (mtm110) cc_final: 0.7058 (ttm-80) REVERT: B 101 MET cc_start: 0.8772 (mtp) cc_final: 0.8293 (mtp) REVERT: B 130 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5367 (tt0) REVERT: B 137 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7128 (ttm110) REVERT: B 138 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7585 (mt-10) REVERT: B 156 GLN cc_start: 0.7729 (mt0) cc_final: 0.7476 (mt0) REVERT: B 201 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8695 (p) REVERT: G 44 HIS cc_start: 0.7987 (m90) cc_final: 0.7723 (m-70) REVERT: N 3 GLN cc_start: 0.7030 (tt0) cc_final: 0.6376 (tt0) REVERT: N 6 GLU cc_start: 0.6634 (mp0) cc_final: 0.6408 (mp0) REVERT: N 39 GLN cc_start: 0.8506 (tt0) cc_final: 0.8146 (tt0) REVERT: N 53 GLN cc_start: 0.7391 (mp10) cc_final: 0.6935 (mp10) REVERT: N 80 TYR cc_start: 0.7858 (m-80) cc_final: 0.6463 (m-80) REVERT: N 86 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7258 (mp) REVERT: N 125 THR cc_start: 0.8062 (p) cc_final: 0.7817 (p) REVERT: R 34 LYS cc_start: 0.5829 (tttt) cc_final: 0.5447 (tttp) REVERT: R 305 TYR cc_start: 0.8463 (t80) cc_final: 0.8180 (t80) REVERT: R 317 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: R 383 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7855 (ttp-170) REVERT: R 390 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7188 (ttp-110) REVERT: R 469 GLU cc_start: 0.6056 (mm-30) cc_final: 0.5751 (mm-30) outliers start: 58 outliers final: 38 residues processed: 178 average time/residue: 1.3003 time to fit residues: 245.7200 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 : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU 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 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 153 ASP 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 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 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 P residue 13 LYS Chi-restraints excluded: chain P residue 19 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117508 restraints weight = 10220.002| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.94 r_work: 0.3274 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8910 Z= 0.247 Angle : 0.526 6.560 12090 Z= 0.289 Chirality : 0.042 0.168 1361 Planarity : 0.004 0.057 1545 Dihedral : 6.878 80.563 1244 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 6.68 % Allowed : 24.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1104 helix: 1.66 (0.25), residues: 439 sheet: -0.37 (0.33), residues: 218 loop : -0.83 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.002 PHE A 212 TYR 0.024 0.002 TYR R 191 ARG 0.003 0.000 ARG B 197 *********************** 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 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 140 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: A 27 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 273 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7463 (ptm160) REVERT: A 289 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: B 27 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5915 (p0) REVERT: B 38 ASP cc_start: 0.6978 (p0) cc_final: 0.6689 (p0) REVERT: B 66 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7435 (p0) REVERT: B 76 ASP cc_start: 0.8283 (p0) cc_final: 0.8015 (p0) REVERT: B 101 MET cc_start: 0.8826 (mtp) cc_final: 0.8391 (mtp) REVERT: B 124 TYR cc_start: 0.8527 (m-80) cc_final: 0.8004 (m-80) REVERT: B 130 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5338 (tt0) REVERT: B 137 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7270 (ttm110) REVERT: B 138 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 156 GLN cc_start: 0.7687 (mt0) cc_final: 0.7435 (mt0) REVERT: B 175 GLN cc_start: 0.7860 (pt0) cc_final: 0.7138 (mt0) REVERT: G 44 HIS cc_start: 0.8062 (m90) cc_final: 0.7794 (m-70) REVERT: N 3 GLN cc_start: 0.7018 (tt0) cc_final: 0.6334 (tt0) REVERT: N 39 GLN cc_start: 0.8509 (tt0) cc_final: 0.8184 (tt0) REVERT: N 53 GLN cc_start: 0.7392 (mp10) cc_final: 0.6981 (mp10) REVERT: N 77 ASN cc_start: 0.7191 (m-40) cc_final: 0.6926 (t0) REVERT: N 80 TYR cc_start: 0.7846 (m-80) cc_final: 0.6481 (m-80) REVERT: N 86 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7310 (mp) REVERT: N 125 THR cc_start: 0.8172 (p) cc_final: 0.7924 (p) REVERT: R 34 LYS cc_start: 0.5887 (tttt) cc_final: 0.5494 (tttp) REVERT: R 179 ARG cc_start: 0.5801 (mmt90) cc_final: 0.5595 (mmp80) REVERT: R 305 TYR cc_start: 0.8499 (t80) cc_final: 0.8170 (t80) REVERT: R 308 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.7937 (p) REVERT: R 317 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: R 383 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: R 390 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7315 (ttp-110) REVERT: R 404 ARG cc_start: 0.6390 (tmm160) cc_final: 0.5662 (tmt-80) REVERT: R 469 GLU cc_start: 0.6148 (mm-30) cc_final: 0.5893 (mm-30) outliers start: 60 outliers final: 37 residues processed: 186 average time/residue: 1.2488 time to fit residues: 247.7850 Evaluate side-chains 181 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU 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 273 ARG 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 66 ASP Chi-restraints excluded: chain B residue 67 SER 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 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 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 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 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 104 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 75 GLN B 142 HIS B 176 GLN P 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119072 restraints weight = 10343.752| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8910 Z= 0.187 Angle : 0.493 5.651 12090 Z= 0.272 Chirality : 0.041 0.161 1361 Planarity : 0.004 0.056 1545 Dihedral : 6.557 78.348 1244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.57 % Allowed : 25.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1104 helix: 1.87 (0.26), residues: 439 sheet: -0.32 (0.33), residues: 218 loop : -0.76 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG R 179 *********************** 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 188 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 273 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7493 (ptm160) REVERT: A 285 ASP cc_start: 0.7735 (t0) cc_final: 0.7408 (p0) REVERT: A 289 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6961 (tp30) REVERT: B 27 ASP cc_start: 0.6305 (OUTLIER) cc_final: 0.5757 (p0) REVERT: B 38 ASP cc_start: 0.6880 (p0) cc_final: 0.6570 (p0) REVERT: B 66 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 101 MET cc_start: 0.8838 (mtp) cc_final: 0.8450 (mtp) REVERT: B 124 TYR cc_start: 0.8453 (m-80) cc_final: 0.7972 (m-80) REVERT: B 130 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5359 (tt0) REVERT: B 137 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7237 (ttm110) REVERT: B 138 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 156 GLN cc_start: 0.7678 (mt0) cc_final: 0.7401 (mt0) REVERT: G 44 HIS cc_start: 0.8005 (m90) cc_final: 0.7758 (m-70) REVERT: G 62 ARG cc_start: 0.5227 (OUTLIER) cc_final: 0.4444 (ppt170) REVERT: N 3 GLN cc_start: 0.6928 (tt0) cc_final: 0.6301 (tt0) REVERT: N 39 GLN cc_start: 0.8506 (tt0) cc_final: 0.8146 (tt0) REVERT: N 53 GLN cc_start: 0.7332 (mp10) cc_final: 0.6910 (mp10) REVERT: N 77 ASN cc_start: 0.7166 (m-40) cc_final: 0.6901 (t0) REVERT: N 80 TYR cc_start: 0.7711 (m-80) cc_final: 0.6175 (m-80) REVERT: N 86 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7395 (mp) REVERT: N 105 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6238 (ttp-170) REVERT: N 125 THR cc_start: 0.8106 (p) cc_final: 0.7859 (p) REVERT: R 34 LYS cc_start: 0.5871 (tttt) cc_final: 0.5494 (tttp) REVERT: R 305 TYR cc_start: 0.8461 (t80) cc_final: 0.8085 (t80) REVERT: R 308 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7763 (p) REVERT: R 317 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: R 383 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7740 (ttp-170) REVERT: R 390 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7195 (ttp-110) REVERT: R 404 ARG cc_start: 0.6466 (tmm160) cc_final: 0.5764 (tmt-80) outliers start: 50 outliers final: 31 residues processed: 171 average time/residue: 1.3581 time to fit residues: 246.5315 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 359 LYS Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 P 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121450 restraints weight = 10364.392| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.89 r_work: 0.3314 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8910 Z= 0.150 Angle : 0.473 5.502 12090 Z= 0.261 Chirality : 0.040 0.154 1361 Planarity : 0.004 0.056 1545 Dihedral : 5.305 58.565 1238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.12 % Allowed : 26.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1104 helix: 2.21 (0.26), residues: 433 sheet: -0.24 (0.34), residues: 215 loop : -0.69 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.003 0.000 ARG B 197 *********************** 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 185 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 49 ASP cc_start: 0.7065 (m-30) cc_final: 0.6297 (t0) REVERT: A 273 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7567 (ptm160) REVERT: A 285 ASP cc_start: 0.7658 (t0) cc_final: 0.7396 (p0) REVERT: A 289 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: B 27 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5738 (p0) REVERT: B 38 ASP cc_start: 0.6974 (p0) cc_final: 0.6664 (p0) REVERT: B 70 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 101 MET cc_start: 0.8844 (mtp) cc_final: 0.8350 (mtp) REVERT: B 124 TYR cc_start: 0.8426 (m-80) cc_final: 0.7893 (m-80) REVERT: B 130 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5350 (tt0) REVERT: B 137 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7091 (ttm110) REVERT: B 138 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 156 GLN cc_start: 0.7641 (mt0) cc_final: 0.7364 (mt0) REVERT: G 44 HIS cc_start: 0.7968 (m90) cc_final: 0.7741 (m-70) REVERT: G 62 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.4856 (ppt170) REVERT: N 3 GLN cc_start: 0.6934 (tt0) cc_final: 0.6336 (tt0) REVERT: N 39 GLN cc_start: 0.8523 (tt0) cc_final: 0.8182 (tt0) REVERT: N 53 GLN cc_start: 0.7364 (mp10) cc_final: 0.6912 (mp10) REVERT: N 77 ASN cc_start: 0.7093 (m-40) cc_final: 0.6836 (t0) REVERT: N 80 TYR cc_start: 0.7588 (m-80) cc_final: 0.5891 (m-80) REVERT: N 86 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7331 (mp) REVERT: N 105 ARG cc_start: 0.6750 (ttt180) cc_final: 0.6253 (ttp-170) REVERT: N 125 THR cc_start: 0.8134 (p) cc_final: 0.7933 (p) REVERT: R 34 LYS cc_start: 0.5844 (tttt) cc_final: 0.5471 (tttp) REVERT: R 189 MET cc_start: 0.7909 (tpp) cc_final: 0.7491 (tpp) REVERT: R 305 TYR cc_start: 0.8375 (t80) cc_final: 0.7861 (t80) REVERT: R 308 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7751 (p) REVERT: R 317 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: R 383 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7721 (ttp-170) REVERT: R 390 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7224 (ttp-110) REVERT: R 404 ARG cc_start: 0.6380 (tmm160) cc_final: 0.5732 (tmt-80) outliers start: 46 outliers final: 25 residues processed: 172 average time/residue: 1.2820 time to fit residues: 234.0028 Evaluate side-chains 170 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR 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 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 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 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 359 LYS Chi-restraints excluded: chain R residue 408 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 G 11 GLN P 16 ASN R 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114592 restraints weight = 10458.324| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.95 r_work: 0.3216 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 8910 Z= 0.536 Angle : 0.711 9.791 12090 Z= 0.382 Chirality : 0.051 0.208 1361 Planarity : 0.006 0.061 1545 Dihedral : 6.300 59.444 1237 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.12 % Allowed : 25.72 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1104 helix: 1.17 (0.24), residues: 439 sheet: -0.63 (0.33), residues: 222 loop : -0.93 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 82 HIS 0.006 0.002 HIS A 347 PHE 0.017 0.003 PHE R 335 TYR 0.024 0.003 TYR R 191 ARG 0.007 0.001 ARG B 197 *********************** 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 192 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6962 (mm-30) REVERT: A 58 LYS cc_start: 0.6708 (mtpp) cc_final: 0.6327 (mmtp) REVERT: A 289 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: A 380 GLN cc_start: 0.7542 (mt0) cc_final: 0.7307 (mt0) REVERT: B 27 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.5948 (p0) REVERT: B 38 ASP cc_start: 0.6938 (p0) cc_final: 0.6682 (p0) REVERT: B 76 ASP cc_start: 0.7804 (p0) cc_final: 0.7496 (p0) REVERT: B 101 MET cc_start: 0.8713 (mtp) cc_final: 0.8486 (mtp) REVERT: B 124 TYR cc_start: 0.8567 (m-80) cc_final: 0.8070 (m-80) REVERT: B 130 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5070 (tt0) REVERT: B 137 ARG cc_start: 0.7569 (ttm110) cc_final: 0.7319 (ttm110) REVERT: B 138 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7653 (mt-10) REVERT: G 44 HIS cc_start: 0.7988 (m90) cc_final: 0.7783 (m-70) REVERT: N 39 GLN cc_start: 0.8564 (tt0) cc_final: 0.8004 (tt0) REVERT: N 53 GLN cc_start: 0.7301 (mp10) cc_final: 0.6894 (mp10) REVERT: N 79 LEU cc_start: 0.7877 (tp) cc_final: 0.7625 (tp) REVERT: N 86 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7405 (mp) REVERT: N 105 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6341 (mmm-85) REVERT: R 212 PHE cc_start: 0.6410 (m-80) cc_final: 0.6162 (m-10) REVERT: R 305 TYR cc_start: 0.8508 (t80) cc_final: 0.8294 (t80) REVERT: R 317 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: R 318 LYS cc_start: 0.6426 (mmpt) cc_final: 0.5833 (mptp) REVERT: R 383 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7856 (ttp-170) REVERT: R 390 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7255 (ttp-110) REVERT: R 404 ARG cc_start: 0.6306 (tmm160) cc_final: 0.5682 (tmt-80) REVERT: R 469 GLU cc_start: 0.6070 (mm-30) cc_final: 0.5803 (mm-30) outliers start: 55 outliers final: 36 residues processed: 178 average time/residue: 1.3349 time to fit residues: 251.7567 Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 67 SER 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 143 THR Chi-restraints excluded: chain B residue 153 ASP 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 86 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain R residue 197 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120785 restraints weight = 10270.882| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.95 r_work: 0.3297 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8910 Z= 0.149 Angle : 0.498 5.590 12090 Z= 0.275 Chirality : 0.041 0.158 1361 Planarity : 0.004 0.055 1545 Dihedral : 5.572 57.646 1237 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.79 % Allowed : 27.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1104 helix: 1.85 (0.25), residues: 439 sheet: -0.38 (0.33), residues: 217 loop : -0.83 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.004 0.000 ARG R 179 ********************** 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 172 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6790 (mm-30) REVERT: A 49 ASP cc_start: 0.7143 (m-30) cc_final: 0.6337 (t0) REVERT: A 289 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6944 (tp30) REVERT: B 27 ASP cc_start: 0.6296 (OUTLIER) cc_final: 0.5919 (p0) REVERT: B 38 ASP cc_start: 0.6916 (p0) cc_final: 0.6614 (p0) REVERT: B 70 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 101 MET cc_start: 0.8840 (mtp) cc_final: 0.8344 (mtp) REVERT: B 130 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5370 (tt0) REVERT: B 137 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7301 (ttm110) REVERT: B 138 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7664 (mt-10) REVERT: G 44 HIS cc_start: 0.7988 (m90) cc_final: 0.7724 (m-70) REVERT: G 62 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.5040 (ppt170) REVERT: N 3 GLN cc_start: 0.6868 (tt0) cc_final: 0.6286 (tt0) REVERT: N 39 GLN cc_start: 0.8506 (tt0) cc_final: 0.8115 (tt0) REVERT: N 53 GLN cc_start: 0.7410 (mp10) cc_final: 0.6994 (mp10) REVERT: N 77 ASN cc_start: 0.7396 (m-40) cc_final: 0.7186 (t0) REVERT: N 80 TYR cc_start: 0.7727 (m-80) cc_final: 0.6259 (m-80) REVERT: N 86 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7408 (mp) REVERT: R 34 LYS cc_start: 0.5776 (tttt) cc_final: 0.5370 (tttp) REVERT: R 305 TYR cc_start: 0.8469 (t80) cc_final: 0.8095 (t80) REVERT: R 308 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7774 (p) REVERT: R 383 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7693 (ttp-170) REVERT: R 390 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7185 (ttp-110) REVERT: R 404 ARG cc_start: 0.6322 (tmm160) cc_final: 0.5735 (tmt-80) outliers start: 34 outliers final: 22 residues processed: 163 average time/residue: 1.3195 time to fit residues: 228.1193 Evaluate side-chains 163 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 143 THR 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 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 70 ILE 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 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 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 77 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116839 restraints weight = 10371.771| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.95 r_work: 0.3246 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8910 Z= 0.346 Angle : 0.602 8.542 12090 Z= 0.327 Chirality : 0.045 0.178 1361 Planarity : 0.005 0.058 1545 Dihedral : 5.942 58.994 1237 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.23 % Allowed : 27.62 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1104 helix: 1.58 (0.25), residues: 439 sheet: -0.54 (0.33), residues: 220 loop : -0.89 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.002 HIS A 220 PHE 0.016 0.002 PHE A 212 TYR 0.023 0.002 TYR R 191 ARG 0.006 0.001 ARG R 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8115.31 seconds wall clock time: 140 minutes 19.68 seconds (8419.68 seconds total)