Starting phenix.real_space_refine on Sat May 2 21:56:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijb_35484/05_2026/8ijb_35484_neut.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 66 5.16 5 C 5632 2.51 5 N 1506 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2301 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1712 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8842 At special positions: 0 Unit cell: (91.8, 121.55, 133.45, 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 66 16.00 O 1638 8.00 N 1506 7.00 C 5632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=1.91 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 291.0 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 35.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.575A pdb=" N LYS A 15 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 60 through 89 removed outlier: 3.823A pdb=" N PHE A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 140 through 161 removed outlier: 4.532A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 4.043A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.788A pdb=" N VAL A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.818A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.966A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.902A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.713A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 352 removed outlier: 3.783A pdb=" N PHE C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.806A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.119A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.509A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.631A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.927A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.218A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.660A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.477A 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: 6.970A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.912A 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: 4.295A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.387A 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: 6.603A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 188 through 190 removed outlier: 6.865A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.838A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.838A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.941A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 146 413 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2300 1.33 - 1.45: 1880 1.45 - 1.58: 4758 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9033 Sorted by residual: bond pdb=" N04 OJX A 401 " pdb=" O01 OJX A 401 " ideal model delta sigma weight residual 1.371 1.245 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" N PRO A 168 " pdb=" CD PRO A 168 " ideal model delta sigma weight residual 1.473 1.560 -0.087 1.40e-02 5.10e+03 3.89e+01 bond pdb=" CG ASN A 45 " pdb=" OD1 ASN A 45 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.59e+01 bond pdb=" CG ASN A 68 " pdb=" OD1 ASN A 68 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CG ASN A 68 " pdb=" ND2 ASN A 68 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.21e+01 ... (remaining 9028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.59: 12175 7.59 - 15.18: 39 15.18 - 22.77: 20 22.77 - 30.36: 6 30.36 - 37.95: 3 Bond angle restraints: 12243 Sorted by residual: angle pdb=" N TYR A 294 " pdb=" CA TYR A 294 " pdb=" C TYR A 294 " ideal model delta sigma weight residual 111.40 145.47 -34.07 1.22e+00 6.72e-01 7.80e+02 angle pdb=" N SER A 297 " pdb=" CA SER A 297 " pdb=" CB SER A 297 " ideal model delta sigma weight residual 114.17 139.03 -24.86 1.14e+00 7.69e-01 4.76e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 110.41 85.44 24.97 1.23e+00 6.61e-01 4.12e+02 angle pdb=" C ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta sigma weight residual 110.42 148.37 -37.95 1.99e+00 2.53e-01 3.64e+02 angle pdb=" N PHE C 323 " pdb=" CA PHE C 323 " pdb=" C PHE C 323 " ideal model delta sigma weight residual 108.75 77.24 31.51 1.71e+00 3.42e-01 3.40e+02 ... (remaining 12238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4462 18.00 - 35.99: 622 35.99 - 53.99: 199 53.99 - 71.98: 42 71.98 - 89.98: 16 Dihedral angle restraints: 5341 sinusoidal: 2050 harmonic: 3291 Sorted by residual: dihedral pdb=" C ASN A 171 " pdb=" N ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta harmonic sigma weight residual -122.60 -159.28 36.68 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" N TYR A 295 " pdb=" C TYR A 295 " pdb=" CA TYR A 295 " pdb=" CB TYR A 295 " ideal model delta harmonic sigma weight residual 122.80 92.90 29.90 0 2.50e+00 1.60e-01 1.43e+02 dihedral pdb=" N ASN B 35 " pdb=" C ASN B 35 " pdb=" CA ASN B 35 " pdb=" CB ASN B 35 " ideal model delta harmonic sigma weight residual 122.80 94.30 28.50 0 2.50e+00 1.60e-01 1.30e+02 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 1368 0.293 - 0.585: 10 0.585 - 0.878: 4 0.878 - 1.170: 2 1.170 - 1.463: 2 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR A 294 " pdb=" N TYR A 294 " pdb=" C TYR A 294 " pdb=" CB TYR A 294 " both_signs ideal model delta sigma weight residual False 2.51 1.05 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.37 2.00e-01 2.50e+01 4.72e+01 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 1.60 1.12 2.00e-01 2.50e+01 3.15e+01 ... (remaining 1383 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -1.102 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 128 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG A 228 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " -0.100 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 284 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.110 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 96 2.52 - 3.11: 6732 3.11 - 3.71: 13488 3.71 - 4.30: 18434 4.30 - 4.90: 31534 Nonbonded interactions: 70284 Sorted by model distance: nonbonded pdb=" O HIS A 259 " pdb=" CG HIS A 259 " model vdw 1.921 3.260 nonbonded pdb=" O ASN A 86 " pdb=" O ARG A 89 " model vdw 1.936 3.040 nonbonded pdb=" O SER A 297 " pdb=" OG SER A 297 " model vdw 1.966 3.040 nonbonded pdb=" N PHE C 323 " pdb=" O PHE C 323 " model vdw 1.998 2.496 nonbonded pdb=" N PHE A 296 " pdb=" O PHE A 296 " model vdw 2.067 2.496 ... (remaining 70279 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.006 0.126 9038 Z= 0.397 Angle : 1.540 37.949 12253 Z= 0.973 Chirality : 0.107 1.463 1386 Planarity : 0.021 0.494 1554 Dihedral : 19.074 89.979 3198 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.30 % Favored : 91.43 % Rotamer: Outliers : 8.31 % Allowed : 35.86 % Favored : 55.84 % Cbeta Deviations : 1.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1120 helix: 0.53 (0.30), residues: 357 sheet: -0.40 (0.33), residues: 270 loop : -2.16 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.110 0.002 TYR A 284 PHE 0.031 0.001 PHE A 193 TRP 0.029 0.001 TRP A 50 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 9033) covalent geometry : angle 1.53938 (12243) SS BOND : bond 0.05331 ( 5) SS BOND : angle 1.99011 ( 10) hydrogen bonds : bond 0.14156 ( 405) hydrogen bonds : angle 6.52451 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7458 (p0) REVERT: A 284 TYR cc_start: 0.7799 (m-80) cc_final: 0.7566 (m-80) REVERT: A 285 MET cc_start: 0.7792 (ptp) cc_final: 0.7385 (pmm) REVERT: A 290 ASP cc_start: 0.7957 (m-30) cc_final: 0.7733 (m-30) REVERT: B 130 GLU cc_start: 0.8940 (mp0) cc_final: 0.8635 (mp0) REVERT: C 197 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8312 (mttt) REVERT: S 18 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6452 (ttp80) outliers start: 79 outliers final: 40 residues processed: 234 average time/residue: 0.1010 time to fit residues: 31.9334 Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 130 GLN Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 210 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS B 35 ASN B 75 GLN C 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077645 restraints weight = 15912.778| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.21 r_work: 0.2915 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9038 Z= 0.188 Angle : 0.633 8.699 12253 Z= 0.335 Chirality : 0.044 0.230 1386 Planarity : 0.005 0.067 1554 Dihedral : 7.432 68.808 1292 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.94 % Allowed : 31.02 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1120 helix: 1.44 (0.28), residues: 365 sheet: -0.34 (0.32), residues: 269 loop : -1.92 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 228 TYR 0.023 0.001 TYR S 178 PHE 0.012 0.001 PHE C 189 TRP 0.014 0.001 TRP A 50 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9033) covalent geometry : angle 0.63256 (12243) SS BOND : bond 0.01148 ( 5) SS BOND : angle 0.82229 ( 10) hydrogen bonds : bond 0.04981 ( 405) hydrogen bonds : angle 4.62698 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 167 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.6242 (m-40) REVERT: A 264 GLN cc_start: 0.8843 (tp40) cc_final: 0.8507 (tp40) REVERT: A 290 ASP cc_start: 0.8846 (m-30) cc_final: 0.8504 (m-30) REVERT: B 134 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8706 (ptp90) REVERT: B 338 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9038 (mm) REVERT: C 243 MET cc_start: 0.8979 (mmm) cc_final: 0.8778 (tpp) REVERT: C 294 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.7982 (t0) REVERT: S 3 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8286 (mm110) REVERT: S 18 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7597 (tpp80) REVERT: S 190 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8935 (mtm-85) REVERT: S 208 GLU cc_start: 0.8611 (pm20) cc_final: 0.8363 (pm20) outliers start: 66 outliers final: 38 residues processed: 214 average time/residue: 0.1065 time to fit residues: 30.4901 Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080684 restraints weight = 15759.801| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.26 r_work: 0.2971 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9038 Z= 0.114 Angle : 0.579 7.569 12253 Z= 0.301 Chirality : 0.041 0.190 1386 Planarity : 0.004 0.058 1554 Dihedral : 5.564 55.510 1248 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.26 % Allowed : 31.76 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.26), residues: 1120 helix: 2.33 (0.28), residues: 365 sheet: -0.35 (0.32), residues: 272 loop : -1.68 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.010 0.001 PHE A 232 TRP 0.017 0.001 TRP A 50 HIS 0.009 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9033) covalent geometry : angle 0.57838 (12243) SS BOND : bond 0.00260 ( 5) SS BOND : angle 0.90016 ( 10) hydrogen bonds : bond 0.03901 ( 405) hydrogen bonds : angle 4.19375 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7169 (t0) REVERT: A 45 ASN cc_start: 0.8461 (m110) cc_final: 0.8230 (m110) REVERT: A 74 PHE cc_start: 0.8891 (t80) cc_final: 0.8621 (t80) REVERT: A 87 TYR cc_start: 0.8594 (m-80) cc_final: 0.8310 (m-80) REVERT: A 103 MET cc_start: 0.8226 (ttp) cc_final: 0.7697 (ttp) REVERT: A 106 MET cc_start: 0.8383 (tpt) cc_final: 0.8157 (tpt) REVERT: A 263 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7684 (p) REVERT: A 264 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8537 (tp40) REVERT: A 290 ASP cc_start: 0.8837 (m-30) cc_final: 0.8550 (m-30) REVERT: B 19 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8312 (ptt90) REVERT: B 134 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8521 (ptp90) REVERT: C 197 LYS cc_start: 0.8981 (mtpp) cc_final: 0.8750 (mttt) REVERT: C 242 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7290 (mpt-90) REVERT: C 243 MET cc_start: 0.8964 (mmm) cc_final: 0.8671 (tpp) REVERT: C 294 ASN cc_start: 0.8798 (m-40) cc_final: 0.8231 (t0) REVERT: G 42 GLU cc_start: 0.8958 (tt0) cc_final: 0.8575 (pp20) REVERT: S 3 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8273 (mm110) REVERT: S 18 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7564 (tpp80) REVERT: S 148 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7512 (ttp-170) REVERT: S 166 LEU cc_start: 0.9118 (tt) cc_final: 0.8915 (tt) outliers start: 50 outliers final: 25 residues processed: 212 average time/residue: 0.1159 time to fit residues: 32.4025 Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 96 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 340 ASN C 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078095 restraints weight = 15765.492| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.08 r_work: 0.2914 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9038 Z= 0.184 Angle : 0.612 8.589 12253 Z= 0.319 Chirality : 0.043 0.175 1386 Planarity : 0.004 0.055 1554 Dihedral : 5.367 58.690 1237 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 6.20 % Allowed : 30.81 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.26), residues: 1120 helix: 2.38 (0.28), residues: 364 sheet: -0.44 (0.32), residues: 281 loop : -1.68 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.022 0.001 TYR S 178 PHE 0.014 0.001 PHE S 29 TRP 0.018 0.001 TRP A 50 HIS 0.011 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9033) covalent geometry : angle 0.61203 (12243) SS BOND : bond 0.00425 ( 5) SS BOND : angle 0.88024 ( 10) hydrogen bonds : bond 0.04444 ( 405) hydrogen bonds : angle 4.27504 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7304 (t70) REVERT: A 165 LYS cc_start: 0.8067 (tptp) cc_final: 0.7517 (tptm) REVERT: A 264 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (tp40) REVERT: A 290 ASP cc_start: 0.8967 (m-30) cc_final: 0.8516 (m-30) REVERT: B 134 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8670 (ptp90) REVERT: C 243 MET cc_start: 0.9031 (mmm) cc_final: 0.8721 (tpp) REVERT: C 294 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8125 (t0) REVERT: G 42 GLU cc_start: 0.8981 (tt0) cc_final: 0.8581 (pp20) REVERT: S 3 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8290 (mm110) REVERT: S 18 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7925 (tpp80) REVERT: S 38 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8402 (ptp-170) REVERT: S 148 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7421 (ttp-170) REVERT: S 180 MET cc_start: 0.8741 (ptm) cc_final: 0.8322 (ptm) outliers start: 59 outliers final: 38 residues processed: 210 average time/residue: 0.1047 time to fit residues: 29.6541 Evaluate side-chains 204 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079161 restraints weight = 15588.465| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.08 r_work: 0.2933 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9038 Z= 0.150 Angle : 0.601 8.663 12253 Z= 0.313 Chirality : 0.042 0.187 1386 Planarity : 0.004 0.053 1554 Dihedral : 5.330 57.937 1237 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.78 % Allowed : 31.02 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1120 helix: 2.44 (0.28), residues: 364 sheet: -0.33 (0.32), residues: 279 loop : -1.67 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 32 TYR 0.021 0.001 TYR S 178 PHE 0.011 0.001 PHE C 189 TRP 0.019 0.001 TRP A 50 HIS 0.019 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9033) covalent geometry : angle 0.60108 (12243) SS BOND : bond 0.00391 ( 5) SS BOND : angle 0.79006 ( 10) hydrogen bonds : bond 0.04161 ( 405) hydrogen bonds : angle 4.17416 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.368 Fit side-chains REVERT: A 8 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7270 (t70) REVERT: A 103 MET cc_start: 0.8196 (ttp) cc_final: 0.7704 (ttp) REVERT: A 290 ASP cc_start: 0.8960 (m-30) cc_final: 0.8511 (m-30) REVERT: B 134 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8609 (ptp90) REVERT: C 243 MET cc_start: 0.9049 (mmm) cc_final: 0.8711 (tpp) REVERT: C 294 ASN cc_start: 0.8733 (m110) cc_final: 0.8192 (t0) REVERT: G 42 GLU cc_start: 0.9019 (tt0) cc_final: 0.8640 (pp20) REVERT: S 3 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8283 (mm110) REVERT: S 18 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7902 (tpp80) REVERT: S 148 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: S 180 MET cc_start: 0.8767 (ptm) cc_final: 0.8469 (ptm) REVERT: S 190 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8903 (mtm-85) outliers start: 55 outliers final: 40 residues processed: 204 average time/residue: 0.1055 time to fit residues: 29.1256 Evaluate side-chains 204 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.0770 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.116274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081059 restraints weight = 15711.605| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.20 r_work: 0.2979 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9038 Z= 0.111 Angle : 0.579 9.088 12253 Z= 0.299 Chirality : 0.041 0.187 1386 Planarity : 0.004 0.051 1554 Dihedral : 5.073 57.092 1237 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.36 % Allowed : 31.23 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1120 helix: 2.53 (0.28), residues: 365 sheet: -0.18 (0.33), residues: 272 loop : -1.63 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.010 0.001 PHE C 189 TRP 0.023 0.001 TRP A 50 HIS 0.014 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9033) covalent geometry : angle 0.57852 (12243) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.61273 ( 10) hydrogen bonds : bond 0.03580 ( 405) hydrogen bonds : angle 4.04079 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7211 (t70) REVERT: A 165 LYS cc_start: 0.8238 (tptp) cc_final: 0.7756 (tptm) REVERT: A 234 MET cc_start: 0.7725 (mmt) cc_final: 0.7451 (mmm) REVERT: A 264 GLN cc_start: 0.8706 (tp40) cc_final: 0.8335 (tp40) REVERT: A 290 ASP cc_start: 0.8873 (m-30) cc_final: 0.8520 (m-30) REVERT: B 19 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8331 (ptt90) REVERT: B 134 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8509 (ptp90) REVERT: C 197 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8704 (mttt) REVERT: C 243 MET cc_start: 0.9028 (mmm) cc_final: 0.8651 (tpp) REVERT: C 261 ASP cc_start: 0.8665 (t0) cc_final: 0.8463 (t0) REVERT: C 294 ASN cc_start: 0.8738 (m110) cc_final: 0.8214 (t0) REVERT: G 42 GLU cc_start: 0.8978 (tt0) cc_final: 0.8594 (pp20) REVERT: S 3 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8269 (mm110) REVERT: S 18 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7919 (tpp80) REVERT: S 148 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7496 (ttp-170) REVERT: S 180 MET cc_start: 0.8738 (ptm) cc_final: 0.8348 (ptm) REVERT: S 190 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8932 (mtm-85) outliers start: 51 outliers final: 31 residues processed: 215 average time/residue: 0.1001 time to fit residues: 29.0215 Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 184 HIS B 340 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077576 restraints weight = 16048.423| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.24 r_work: 0.2905 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9038 Z= 0.186 Angle : 0.624 10.275 12253 Z= 0.326 Chirality : 0.043 0.167 1386 Planarity : 0.004 0.057 1554 Dihedral : 5.290 59.038 1237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 6.10 % Allowed : 30.39 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1120 helix: 2.45 (0.28), residues: 364 sheet: -0.31 (0.32), residues: 281 loop : -1.63 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.022 0.001 TYR S 178 PHE 0.013 0.001 PHE C 196 TRP 0.022 0.001 TRP A 50 HIS 0.014 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9033) covalent geometry : angle 0.62348 (12243) SS BOND : bond 0.00496 ( 5) SS BOND : angle 0.88719 ( 10) hydrogen bonds : bond 0.04387 ( 405) hydrogen bonds : angle 4.25146 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7321 (t70) REVERT: A 165 LYS cc_start: 0.8257 (tptp) cc_final: 0.7854 (tptm) REVERT: A 234 MET cc_start: 0.7818 (mmt) cc_final: 0.7550 (mmm) REVERT: A 264 GLN cc_start: 0.8731 (tp40) cc_final: 0.8234 (tp40) REVERT: A 290 ASP cc_start: 0.8907 (m-30) cc_final: 0.8533 (m-30) REVERT: B 134 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8585 (ptp90) REVERT: C 243 MET cc_start: 0.9104 (mmm) cc_final: 0.8852 (tpp) REVERT: C 294 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8238 (t0) REVERT: S 3 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8250 (mm110) REVERT: S 18 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7888 (tpp80) REVERT: S 38 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8391 (ptp-170) REVERT: S 148 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7416 (ttp-170) REVERT: S 180 MET cc_start: 0.8844 (ptm) cc_final: 0.8595 (ptm) REVERT: S 190 ARG cc_start: 0.9185 (mtp180) cc_final: 0.8901 (mtm-85) outliers start: 58 outliers final: 43 residues processed: 208 average time/residue: 0.1079 time to fit residues: 29.9658 Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS C 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079580 restraints weight = 15874.411| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.20 r_work: 0.2953 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9038 Z= 0.129 Angle : 0.603 9.405 12253 Z= 0.313 Chirality : 0.042 0.158 1386 Planarity : 0.004 0.050 1554 Dihedral : 5.191 57.591 1237 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.36 % Allowed : 31.02 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1120 helix: 2.45 (0.28), residues: 364 sheet: -0.28 (0.32), residues: 284 loop : -1.63 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE C 189 TRP 0.024 0.001 TRP A 50 HIS 0.019 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9033) covalent geometry : angle 0.60299 (12243) SS BOND : bond 0.00340 ( 5) SS BOND : angle 0.72052 ( 10) hydrogen bonds : bond 0.03895 ( 405) hydrogen bonds : angle 4.13158 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7198 (t70) REVERT: A 165 LYS cc_start: 0.8283 (tptp) cc_final: 0.7826 (tptm) REVERT: A 234 MET cc_start: 0.7777 (mmt) cc_final: 0.7505 (mmm) REVERT: A 264 GLN cc_start: 0.8700 (tp40) cc_final: 0.8280 (tp40) REVERT: A 290 ASP cc_start: 0.8903 (m-30) cc_final: 0.8527 (m-30) REVERT: B 134 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8530 (ptp90) REVERT: C 197 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8711 (mttt) REVERT: C 243 MET cc_start: 0.9058 (mmm) cc_final: 0.8788 (tpp) REVERT: C 294 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8270 (t0) REVERT: S 3 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8221 (mm110) REVERT: S 18 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7880 (tpp80) REVERT: S 148 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7468 (ttp-170) REVERT: S 180 MET cc_start: 0.8793 (ptm) cc_final: 0.8514 (ptm) REVERT: S 190 ARG cc_start: 0.9202 (mtp180) cc_final: 0.8988 (mtm-85) outliers start: 51 outliers final: 39 residues processed: 209 average time/residue: 0.1139 time to fit residues: 31.5643 Evaluate side-chains 206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074946 restraints weight = 16073.964| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.23 r_work: 0.2868 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9038 Z= 0.293 Angle : 0.698 10.305 12253 Z= 0.367 Chirality : 0.046 0.175 1386 Planarity : 0.004 0.054 1554 Dihedral : 5.620 59.630 1237 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.68 % Favored : 92.23 % Rotamer: Outliers : 5.47 % Allowed : 31.13 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1120 helix: 2.22 (0.28), residues: 358 sheet: -0.50 (0.31), residues: 290 loop : -1.77 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.024 0.002 TYR S 178 PHE 0.017 0.002 PHE C 196 TRP 0.023 0.002 TRP A 50 HIS 0.016 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 9033) covalent geometry : angle 0.69737 (12243) SS BOND : bond 0.00558 ( 5) SS BOND : angle 0.95945 ( 10) hydrogen bonds : bond 0.05079 ( 405) hydrogen bonds : angle 4.47542 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7430 (t70) REVERT: A 234 MET cc_start: 0.7850 (mmt) cc_final: 0.7577 (mmm) REVERT: A 264 GLN cc_start: 0.8746 (tp40) cc_final: 0.8363 (tp40) REVERT: A 290 ASP cc_start: 0.8926 (m-30) cc_final: 0.8522 (m-30) REVERT: B 134 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8734 (ptp90) REVERT: C 242 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.8134 (mmt-90) REVERT: C 243 MET cc_start: 0.9128 (mmm) cc_final: 0.8873 (tpp) REVERT: C 294 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8244 (t0) REVERT: C 317 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8432 (ttmt) REVERT: C 325 CYS cc_start: 0.7849 (t) cc_final: 0.7565 (p) REVERT: S 148 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7394 (ttp-170) REVERT: S 154 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8911 (tm) REVERT: S 180 MET cc_start: 0.8856 (ptm) cc_final: 0.8566 (ptm) REVERT: S 190 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8930 (mtm-85) outliers start: 52 outliers final: 42 residues processed: 196 average time/residue: 0.1068 time to fit residues: 27.9110 Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 68 ASN A 184 HIS C 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076935 restraints weight = 15993.766| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.23 r_work: 0.2900 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9038 Z= 0.183 Angle : 0.663 9.918 12253 Z= 0.347 Chirality : 0.044 0.167 1386 Planarity : 0.004 0.051 1554 Dihedral : 5.485 59.675 1237 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.26 % Allowed : 32.28 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1120 helix: 2.27 (0.28), residues: 358 sheet: -0.42 (0.32), residues: 285 loop : -1.77 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.021 0.002 TYR S 178 PHE 0.012 0.001 PHE B 241 TRP 0.026 0.001 TRP A 50 HIS 0.011 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9033) covalent geometry : angle 0.66319 (12243) SS BOND : bond 0.00461 ( 5) SS BOND : angle 0.79718 ( 10) hydrogen bonds : bond 0.04517 ( 405) hydrogen bonds : angle 4.31451 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.217 Fit side-chains REVERT: A 8 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7347 (t70) REVERT: A 103 MET cc_start: 0.8259 (ttp) cc_final: 0.7887 (ttp) REVERT: A 234 MET cc_start: 0.7817 (mmt) cc_final: 0.7539 (mmm) REVERT: A 264 GLN cc_start: 0.8728 (tp40) cc_final: 0.8359 (tp40) REVERT: A 290 ASP cc_start: 0.8924 (m-30) cc_final: 0.8505 (m-30) REVERT: B 19 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8317 (ptt90) REVERT: B 134 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8565 (ptp90) REVERT: C 243 MET cc_start: 0.9073 (mmm) cc_final: 0.8793 (tpp) REVERT: C 294 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8176 (t0) REVERT: C 317 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8381 (ttmt) REVERT: C 325 CYS cc_start: 0.7790 (t) cc_final: 0.7522 (p) REVERT: S 3 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8222 (mm110) REVERT: S 148 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7379 (ttp-170) REVERT: S 180 MET cc_start: 0.8843 (ptm) cc_final: 0.8552 (ptm) REVERT: S 190 ARG cc_start: 0.9235 (mtp180) cc_final: 0.8958 (mtm-85) outliers start: 50 outliers final: 42 residues processed: 195 average time/residue: 0.1059 time to fit residues: 27.3968 Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS A 184 HIS C 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079579 restraints weight = 15611.982| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.17 r_work: 0.2951 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9038 Z= 0.132 Angle : 0.629 9.829 12253 Z= 0.327 Chirality : 0.043 0.167 1386 Planarity : 0.004 0.050 1554 Dihedral : 5.291 58.599 1237 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.94 % Allowed : 32.81 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1120 helix: 2.34 (0.28), residues: 364 sheet: -0.29 (0.32), residues: 286 loop : -1.71 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE C 189 TRP 0.028 0.001 TRP A 50 HIS 0.011 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9033) covalent geometry : angle 0.62853 (12243) SS BOND : bond 0.00427 ( 5) SS BOND : angle 0.74416 ( 10) hydrogen bonds : bond 0.03960 ( 405) hydrogen bonds : angle 4.18676 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2458.62 seconds wall clock time: 42 minutes 52.48 seconds (2572.48 seconds total)