Starting phenix.real_space_refine on Thu Feb 13 15:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.map" model { file = "/net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7euo_31323/02_2025/7euo_31323.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.072 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 64 5.16 5 C 5732 2.51 5 N 1511 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.30, per 1000 atoms: 0.59 Number of scatterers: 8950 At special positions: 0 Unit cell: (88.4, 124.95, 123.25, 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 64 16.00 O 1643 8.00 N 1511 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 removed outlier: 3.831A pdb=" N ASP R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.519A pdb=" N PHE R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.735A pdb=" N ASN R 135 " --> pdb=" O VAL R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 163 removed outlier: 4.514A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 removed outlier: 3.882A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 302 removed outlier: 3.821A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.010A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.542A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.106A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.602A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.845A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.711A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.854A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.555A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.768A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.187A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.894A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.804A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.942A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.659A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.477A 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: 5.980A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.624A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1444 1.32 - 1.44: 2509 1.44 - 1.57: 5095 1.57 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9144 Sorted by residual: bond pdb=" CA SER B 281 " pdb=" C SER B 281 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.31e-02 5.83e+03 1.29e+01 bond pdb=" C ILE R 204 " pdb=" O ILE R 204 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.60e-02 3.91e+03 1.13e+01 bond pdb=" N ILE R 207 " pdb=" CA ILE R 207 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.74e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12026 1.63 - 3.26: 298 3.26 - 4.89: 56 4.89 - 6.52: 12 6.52 - 8.15: 3 Bond angle restraints: 12395 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 111.14 107.05 4.09 1.08e+00 8.57e-01 1.44e+01 angle pdb=" O ILE R 203 " pdb=" C ILE R 203 " pdb=" N ILE R 204 " ideal model delta sigma weight residual 121.83 118.40 3.43 1.03e+00 9.43e-01 1.11e+01 angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 109.81 116.69 -6.88 2.21e+00 2.05e-01 9.68e+00 angle pdb=" CA PRO A 282 " pdb=" N PRO A 282 " pdb=" CD PRO A 282 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 angle pdb=" C ILE R 207 " pdb=" N ILE R 208 " pdb=" CA ILE R 208 " ideal model delta sigma weight residual 122.35 118.85 3.50 1.18e+00 7.18e-01 8.78e+00 ... (remaining 12390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4983 17.93 - 35.87: 430 35.87 - 53.80: 70 53.80 - 71.74: 11 71.74 - 89.67: 7 Dihedral angle restraints: 5501 sinusoidal: 2219 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1346 0.097 - 0.195: 66 0.195 - 0.292: 3 0.292 - 0.389: 2 0.389 - 0.486: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C9 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1416 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 203 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ILE R 203 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE R 203 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE R 204 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 280 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LYS B 280 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS B 280 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 281 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 282 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.032 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 706 2.74 - 3.28: 8682 3.28 - 3.82: 13883 3.82 - 4.36: 16034 4.36 - 4.90: 29453 Nonbonded interactions: 68758 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.270 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP R 186 " pdb=" NZ LYS R 188 " model vdw 2.282 3.120 ... (remaining 68753 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: 1.450 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.004 0.090 9144 Z= 0.258 Angle : 0.648 8.155 12395 Z= 0.355 Chirality : 0.051 0.486 1419 Planarity : 0.004 0.059 1550 Dihedral : 13.715 89.671 3374 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1119 helix: 1.83 (0.27), residues: 387 sheet: -0.53 (0.29), residues: 286 loop : -1.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.013 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8604 (m170) cc_final: 0.8366 (m-70) REVERT: A 193 ASP cc_start: 0.8488 (m-30) cc_final: 0.8254 (m-30) REVERT: A 242 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7757 (mmt90) REVERT: G 58 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8320 (mp0) REVERT: S 160 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7360 (ttm110) REVERT: S 234 GLU cc_start: 0.7925 (pt0) cc_final: 0.7262 (pp20) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 1.1661 time to fit residues: 209.8671 Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 overall best weight: 2.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN S 142 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084250 restraints weight = 11762.609| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.13 r_work: 0.2935 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9144 Z= 0.368 Angle : 0.639 7.190 12395 Z= 0.338 Chirality : 0.045 0.145 1419 Planarity : 0.004 0.038 1550 Dihedral : 5.884 79.935 1356 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.37 % Allowed : 10.84 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1119 helix: 1.95 (0.26), residues: 388 sheet: -0.46 (0.30), residues: 287 loop : -1.63 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS S 35 PHE 0.016 0.002 PHE B 235 TYR 0.018 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7676 (tp40) cc_final: 0.7467 (mm-40) REVERT: A 193 ASP cc_start: 0.8880 (m-30) cc_final: 0.8622 (m-30) REVERT: A 309 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 217 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6948 (ptp) REVERT: G 46 LYS cc_start: 0.9110 (mppt) cc_final: 0.8767 (mtmm) REVERT: G 47 GLU cc_start: 0.8327 (mp0) cc_final: 0.8051 (mp0) REVERT: G 58 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8306 (mp0) REVERT: S 160 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7403 (ttm110) REVERT: S 234 GLU cc_start: 0.8404 (pt0) cc_final: 0.7513 (pp20) outliers start: 23 outliers final: 12 residues processed: 126 average time/residue: 1.3083 time to fit residues: 175.6345 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090968 restraints weight = 11609.425| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.10 r_work: 0.2985 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9144 Z= 0.154 Angle : 0.529 6.717 12395 Z= 0.279 Chirality : 0.041 0.149 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.514 77.341 1356 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.96 % Allowed : 15.17 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1119 helix: 2.19 (0.27), residues: 389 sheet: -0.24 (0.30), residues: 285 loop : -1.51 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS S 35 PHE 0.012 0.001 PHE R 24 TYR 0.016 0.001 TYR S 190 ARG 0.008 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8583 (m170) cc_final: 0.8297 (m-70) REVERT: R 87 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6953 (mpt) REVERT: A 193 ASP cc_start: 0.8849 (m-30) cc_final: 0.8602 (m-30) REVERT: A 309 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: B 130 GLU cc_start: 0.8893 (mp0) cc_final: 0.8296 (mp0) REVERT: G 46 LYS cc_start: 0.8991 (mppt) cc_final: 0.8617 (mtmm) REVERT: G 47 GLU cc_start: 0.8097 (mp0) cc_final: 0.7734 (mp0) REVERT: G 58 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8246 (mp0) REVERT: S 160 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7293 (ttm110) REVERT: S 234 GLU cc_start: 0.8299 (pt0) cc_final: 0.7302 (pp20) outliers start: 19 outliers final: 10 residues processed: 135 average time/residue: 1.2571 time to fit residues: 181.0465 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086702 restraints weight = 11711.102| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.11 r_work: 0.2943 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9144 Z= 0.305 Angle : 0.586 8.149 12395 Z= 0.309 Chirality : 0.043 0.136 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.652 75.598 1356 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.30 % Allowed : 16.92 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1119 helix: 2.15 (0.27), residues: 388 sheet: -0.29 (0.30), residues: 289 loop : -1.45 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 PHE 0.015 0.001 PHE B 235 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6980 (mpt) REVERT: R 306 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7441 (mm-40) REVERT: A 193 ASP cc_start: 0.8873 (m-30) cc_final: 0.8615 (m-30) REVERT: A 309 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: B 215 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: B 217 MET cc_start: 0.8368 (ptt) cc_final: 0.7858 (ptm) REVERT: G 46 LYS cc_start: 0.9075 (mppt) cc_final: 0.8729 (mtmm) REVERT: G 47 GLU cc_start: 0.8226 (mp0) cc_final: 0.7922 (mp0) REVERT: S 140 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: S 160 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7431 (ttm110) REVERT: S 234 GLU cc_start: 0.8463 (pt0) cc_final: 0.7485 (pp20) outliers start: 32 outliers final: 13 residues processed: 132 average time/residue: 1.3567 time to fit residues: 190.7308 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN ** S 35 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083967 restraints weight = 11774.097| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.13 r_work: 0.2921 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9144 Z= 0.353 Angle : 0.612 7.352 12395 Z= 0.323 Chirality : 0.044 0.137 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.759 74.583 1356 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.92 % Allowed : 17.54 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1119 helix: 1.99 (0.27), residues: 392 sheet: -0.31 (0.30), residues: 286 loop : -1.48 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS S 35 PHE 0.016 0.002 PHE B 235 TYR 0.011 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6984 (mpt) REVERT: R 306 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7414 (mm-40) REVERT: A 193 ASP cc_start: 0.8856 (m-30) cc_final: 0.8603 (m-30) REVERT: A 309 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 215 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: B 217 MET cc_start: 0.8215 (ptt) cc_final: 0.7719 (ptm) REVERT: B 262 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: G 46 LYS cc_start: 0.9084 (mppt) cc_final: 0.8741 (mtmm) REVERT: G 47 GLU cc_start: 0.8240 (mp0) cc_final: 0.7919 (mp0) REVERT: S 140 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: S 160 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7434 (ttm110) REVERT: S 234 GLU cc_start: 0.8435 (pt0) cc_final: 0.7522 (pp20) outliers start: 38 outliers final: 22 residues processed: 135 average time/residue: 1.3371 time to fit residues: 192.6047 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086911 restraints weight = 11736.156| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.17 r_work: 0.2943 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9144 Z= 0.181 Angle : 0.539 6.990 12395 Z= 0.283 Chirality : 0.041 0.143 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.470 70.887 1356 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 19.09 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1119 helix: 2.13 (0.27), residues: 398 sheet: -0.23 (0.30), residues: 280 loop : -1.48 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 95 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6816 (mpt) REVERT: R 146 ILE cc_start: 0.8215 (tp) cc_final: 0.7991 (tp) REVERT: R 306 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7278 (mm-40) REVERT: A 193 ASP cc_start: 0.8840 (m-30) cc_final: 0.8600 (m-30) REVERT: A 309 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: B 215 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7778 (pp20) REVERT: B 217 MET cc_start: 0.8168 (ptt) cc_final: 0.7892 (ptm) REVERT: G 46 LYS cc_start: 0.8829 (mppt) cc_final: 0.8484 (mtmm) REVERT: G 47 GLU cc_start: 0.8016 (mp0) cc_final: 0.7659 (mp0) REVERT: S 140 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8243 (mmm) REVERT: S 160 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7272 (ttm110) REVERT: S 234 GLU cc_start: 0.8360 (pt0) cc_final: 0.7342 (pp20) outliers start: 29 outliers final: 14 residues processed: 132 average time/residue: 1.3261 time to fit residues: 186.4563 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN B 268 ASN 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 = 0.127271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083209 restraints weight = 11885.139| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.14 r_work: 0.2912 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9144 Z= 0.401 Angle : 0.637 7.258 12395 Z= 0.337 Chirality : 0.045 0.143 1419 Planarity : 0.004 0.040 1550 Dihedral : 5.779 69.916 1356 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.61 % Allowed : 19.20 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1119 helix: 1.92 (0.26), residues: 399 sheet: -0.29 (0.30), residues: 286 loop : -1.52 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.017 0.002 PHE B 235 TYR 0.010 0.001 TYR S 95 ARG 0.009 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6897 (mpt) REVERT: R 306 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7422 (mm-40) REVERT: A 193 ASP cc_start: 0.8849 (m-30) cc_final: 0.8603 (m-30) REVERT: A 240 MET cc_start: 0.5562 (pmt) cc_final: 0.5313 (pmt) REVERT: A 298 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 309 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 215 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: B 217 MET cc_start: 0.8242 (ptt) cc_final: 0.7356 (pp-130) REVERT: G 46 LYS cc_start: 0.9020 (mppt) cc_final: 0.8669 (mtmm) REVERT: G 47 GLU cc_start: 0.8159 (mp0) cc_final: 0.7779 (mp0) REVERT: S 160 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7409 (ttm110) REVERT: S 230 MET cc_start: 0.8696 (ttt) cc_final: 0.8372 (ttm) REVERT: S 234 GLU cc_start: 0.8450 (pt0) cc_final: 0.7536 (pp20) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 1.2394 time to fit residues: 177.1180 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087881 restraints weight = 11737.971| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.12 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9144 Z= 0.165 Angle : 0.555 11.455 12395 Z= 0.287 Chirality : 0.041 0.147 1419 Planarity : 0.003 0.040 1550 Dihedral : 5.430 65.208 1356 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.27 % Allowed : 20.85 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1119 helix: 2.06 (0.26), residues: 398 sheet: -0.16 (0.31), residues: 279 loop : -1.42 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 95 HIS 0.007 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.007 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6670 (mpt) REVERT: R 306 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7232 (mm-40) REVERT: A 193 ASP cc_start: 0.8834 (m-30) cc_final: 0.8597 (m-30) REVERT: A 298 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8030 (tm-30) REVERT: A 309 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: B 215 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7612 (pp20) REVERT: B 217 MET cc_start: 0.8182 (ptt) cc_final: 0.7689 (ptm) REVERT: G 46 LYS cc_start: 0.8912 (mppt) cc_final: 0.8561 (mtmm) REVERT: G 47 GLU cc_start: 0.7991 (mp0) cc_final: 0.7593 (mp0) REVERT: S 160 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7211 (ttm110) REVERT: S 234 GLU cc_start: 0.8367 (pt0) cc_final: 0.7361 (pp20) outliers start: 22 outliers final: 18 residues processed: 129 average time/residue: 1.3278 time to fit residues: 182.7585 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain C residue 2 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086967 restraints weight = 11756.175| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.29 r_work: 0.2948 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9144 Z= 0.193 Angle : 0.573 10.889 12395 Z= 0.298 Chirality : 0.041 0.148 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.348 59.987 1356 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.89 % Allowed : 20.85 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1119 helix: 2.08 (0.26), residues: 399 sheet: -0.10 (0.31), residues: 279 loop : -1.40 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7222 (mm-40) REVERT: A 193 ASP cc_start: 0.8816 (m-30) cc_final: 0.8579 (m-30) REVERT: A 298 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 309 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: B 215 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: B 217 MET cc_start: 0.8047 (ptt) cc_final: 0.7522 (ptm) REVERT: G 46 LYS cc_start: 0.8826 (mppt) cc_final: 0.8516 (mtmm) REVERT: G 47 GLU cc_start: 0.7786 (mp0) cc_final: 0.7329 (mp0) REVERT: S 160 ARG cc_start: 0.7600 (ttp80) cc_final: 0.7063 (ttm110) REVERT: S 192 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8131 (ptp) REVERT: S 234 GLU cc_start: 0.8303 (pt0) cc_final: 0.7284 (pp20) outliers start: 28 outliers final: 20 residues processed: 130 average time/residue: 1.2684 time to fit residues: 175.8286 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain C residue 2 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088229 restraints weight = 11824.431| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.33 r_work: 0.2966 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9144 Z= 0.175 Angle : 0.566 10.637 12395 Z= 0.294 Chirality : 0.041 0.145 1419 Planarity : 0.003 0.040 1550 Dihedral : 5.224 53.059 1356 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.37 % Allowed : 21.67 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1119 helix: 2.11 (0.26), residues: 399 sheet: -0.04 (0.31), residues: 279 loop : -1.36 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 95 HIS 0.007 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 306 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7219 (mm-40) REVERT: A 193 ASP cc_start: 0.8813 (m-30) cc_final: 0.8576 (m-30) REVERT: A 298 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 309 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: B 215 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: B 217 MET cc_start: 0.8048 (ptt) cc_final: 0.7542 (ptm) REVERT: G 46 LYS cc_start: 0.8790 (mppt) cc_final: 0.8537 (mtmm) REVERT: G 47 GLU cc_start: 0.7729 (mp0) cc_final: 0.7451 (mp0) REVERT: S 160 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7046 (ttm110) REVERT: S 192 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8038 (ptp) REVERT: S 234 GLU cc_start: 0.8274 (pt0) cc_final: 0.7259 (pp20) REVERT: C 2 LEU cc_start: 0.7430 (pp) cc_final: 0.7195 (pp) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 1.2460 time to fit residues: 177.3512 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 122 ASP Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN A 304 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085049 restraints weight = 11822.315| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.27 r_work: 0.2905 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9144 Z= 0.290 Angle : 0.616 11.744 12395 Z= 0.321 Chirality : 0.043 0.142 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.406 49.224 1356 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.37 % Allowed : 21.78 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1119 helix: 2.08 (0.26), residues: 396 sheet: -0.12 (0.31), residues: 279 loop : -1.42 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.025 0.001 PHE R 74 TYR 0.010 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6098.17 seconds wall clock time: 108 minutes 47.04 seconds (6527.04 seconds total)