Starting phenix.real_space_refine on Sat Aug 23 01:04:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzi_38797/08_2025/8xzi_38797.map" } resolution = 2.7 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= 0.002 sd= 0.006 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 73 5.16 5 C 5758 2.51 5 N 1528 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9041 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2473 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2553 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 327} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} 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: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'A1D5N': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.16 Number of scatterers: 9041 At special positions: 0 Unit cell: (101.352, 131.016, 115.36, 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 73 16.00 O 1682 8.00 N 1528 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.08 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.12 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 338.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 16 sheets defined 40.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 26 through 56 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.170A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.095A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.535A pdb=" N VAL R 117 " --> pdb=" O MET R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.058A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.707A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 193 No H-bonds generated for 'chain 'R' and resid 191 through 193' Processing helix chain 'R' and resid 194 through 210 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 277 Proline residue: R 263 - end of helix removed outlier: 3.548A pdb=" N SER R 275 " --> pdb=" O TYR R 271 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 310 removed outlier: 3.640A pdb=" N CYS R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.907A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.525A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.799A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.139A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.602A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.737A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.745A 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: 3.867A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.157A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.800A 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 153 removed outlier: 6.611A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.926A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.627A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.628A 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 5 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.715A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.338A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.752A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.540A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1332 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: 1.34 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1510 1.30 - 1.43: 2567 1.43 - 1.56: 5024 1.56 - 1.69: 35 1.69 - 1.82: 101 Bond restraints: 9237 Sorted by residual: bond pdb=" C28 A1D5N R 401 " pdb=" S01 A1D5N R 401 " ideal model delta sigma weight residual 1.722 1.545 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C16 A1D5N R 401 " pdb=" C21 A1D5N R 401 " ideal model delta sigma weight residual 1.389 1.566 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C11 A1D5N R 401 " pdb=" C18 A1D5N R 401 " ideal model delta sigma weight residual 1.393 1.565 -0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C30 A1D5N R 401 " pdb=" C31 A1D5N R 401 " ideal model delta sigma weight residual 1.422 1.593 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C32 A1D5N R 401 " pdb=" S01 A1D5N R 401 " ideal model delta sigma weight residual 1.714 1.551 0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 11561 3.09 - 6.19: 880 6.19 - 9.28: 61 9.28 - 12.37: 4 12.37 - 15.47: 5 Bond angle restraints: 12511 Sorted by residual: angle pdb=" N ARG R 91 " pdb=" CA ARG R 91 " pdb=" C ARG R 91 " ideal model delta sigma weight residual 110.53 97.92 12.61 1.32e+00 5.74e-01 9.12e+01 angle pdb=" C SER S 106 " pdb=" N PRO S 107 " pdb=" CA PRO S 107 " ideal model delta sigma weight residual 119.78 128.74 -8.96 1.03e+00 9.43e-01 7.56e+01 angle pdb=" N ARG S 179 " pdb=" CA ARG S 179 " pdb=" C ARG S 179 " ideal model delta sigma weight residual 110.14 96.83 13.31 1.55e+00 4.16e-01 7.37e+01 angle pdb=" C ASP G 48 " pdb=" N PRO G 49 " pdb=" CA PRO G 49 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" CA PHE B 199 " pdb=" CB PHE B 199 " pdb=" CG PHE B 199 " ideal model delta sigma weight residual 113.80 121.86 -8.06 1.00e+00 1.00e+00 6.50e+01 ... (remaining 12506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5304 17.23 - 34.46: 131 34.46 - 51.69: 17 51.69 - 68.92: 14 68.92 - 86.14: 4 Dihedral angle restraints: 5470 sinusoidal: 2137 harmonic: 3333 Sorted by residual: dihedral pdb=" C PHE B 241 " pdb=" N PHE B 241 " pdb=" CA PHE B 241 " pdb=" CB PHE B 241 " ideal model delta harmonic sigma weight residual -122.60 -106.76 -15.84 0 2.50e+00 1.60e-01 4.01e+01 dihedral pdb=" C PHE B 199 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " pdb=" CB PHE B 199 " ideal model delta harmonic sigma weight residual -122.60 -107.20 -15.40 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" C TRP B 82 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " ideal model delta harmonic sigma weight residual -122.60 -114.04 -8.56 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 899 0.081 - 0.161: 395 0.161 - 0.242: 88 0.242 - 0.322: 25 0.322 - 0.403: 1 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA ASN R 112 " pdb=" N ASN R 112 " pdb=" C ASN R 112 " pdb=" CB ASN R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA TYR R 221 " pdb=" N TYR R 221 " pdb=" C TYR R 221 " pdb=" CB TYR R 221 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB THR R 170 " pdb=" CA THR R 170 " pdb=" OG1 THR R 170 " pdb=" CG2 THR R 170 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1405 not shown) Planarity restraints: 1573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.059 2.00e-02 2.50e+03 3.00e-02 1.80e+01 pdb=" CG TYR B 105 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 50 " -0.053 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR S 50 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR S 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR S 50 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR S 50 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR S 50 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR S 50 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR S 50 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 40 " 0.048 2.00e-02 2.50e+03 2.69e-02 1.45e+01 pdb=" CG TYR G 40 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR G 40 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR G 40 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 40 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR G 40 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR G 40 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 40 " 0.044 2.00e-02 2.50e+03 ... (remaining 1570 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.96: 1 1.96 - 2.70: 544 2.70 - 3.43: 12384 3.43 - 4.17: 23553 4.17 - 4.90: 40949 Nonbonded interactions: 77431 Sorted by model distance: nonbonded pdb=" O ASP R 23 " pdb=" N LYS R 25 " model vdw 1.226 3.120 nonbonded pdb=" C ASP R 23 " pdb=" N LYS R 25 " model vdw 2.118 3.350 nonbonded pdb=" O ASP R 23 " pdb=" CA LYS R 25 " model vdw 2.126 3.470 nonbonded pdb=" O ASP R 23 " pdb=" C TRP R 24 " model vdw 2.300 3.270 nonbonded pdb=" N ARG S 179 " pdb=" O ARG S 179 " model vdw 2.313 2.496 ... (remaining 77426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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 : 0.021 0.181 9241 Z= 1.076 Angle : 1.726 15.465 12519 Z= 1.157 Chirality : 0.093 0.403 1408 Planarity : 0.009 0.041 1573 Dihedral : 9.398 86.144 3310 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1131 helix: 0.55 (0.24), residues: 400 sheet: 1.25 (0.31), residues: 268 loop : 1.03 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 98 TYR 0.059 0.007 TYR B 105 PHE 0.039 0.006 PHE A 199 TRP 0.046 0.009 TRP B 99 HIS 0.011 0.003 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.02074 ( 9237) covalent geometry : angle 1.72255 (12511) SS BOND : bond 0.04884 ( 4) SS BOND : angle 4.67163 ( 8) hydrogen bonds : bond 0.15503 ( 477) hydrogen bonds : angle 6.87520 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: R 62 ARG cc_start: 0.6894 (ptt180) cc_final: 0.6639 (mtt90) REVERT: R 271 TYR cc_start: 0.8235 (t80) cc_final: 0.7949 (t80) REVERT: A 195 HIS cc_start: 0.7655 (t70) cc_final: 0.7423 (t70) REVERT: A 271 LYS cc_start: 0.6732 (pttp) cc_final: 0.6530 (pttp) REVERT: B 129 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7513 (mmm-85) REVERT: B 199 PHE cc_start: 0.5958 (m-10) cc_final: 0.5609 (m-80) REVERT: S 23 SER cc_start: 0.8188 (t) cc_final: 0.7985 (m) REVERT: S 77 ASN cc_start: 0.8283 (m-40) cc_final: 0.8043 (m110) REVERT: S 113 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7728 (mm110) REVERT: S 207 LEU cc_start: 0.7344 (tp) cc_final: 0.6691 (tt) REVERT: S 212 VAL cc_start: 0.8049 (p) cc_final: 0.7722 (t) outliers start: 2 outliers final: 1 residues processed: 210 average time/residue: 0.5384 time to fit residues: 119.2065 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102954 restraints weight = 12710.756| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.88 r_work: 0.3184 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9241 Z= 0.201 Angle : 0.709 9.190 12519 Z= 0.382 Chirality : 0.047 0.189 1408 Planarity : 0.005 0.039 1573 Dihedral : 5.873 42.933 1277 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 2.75 % Allowed : 7.02 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1131 helix: 1.51 (0.25), residues: 415 sheet: 1.24 (0.31), residues: 255 loop : 0.22 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.017 0.002 TYR R 88 PHE 0.021 0.002 PHE B 151 TRP 0.028 0.002 TRP R 51 HIS 0.005 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9237) covalent geometry : angle 0.70613 (12511) SS BOND : bond 0.00481 ( 4) SS BOND : angle 2.61355 ( 8) hydrogen bonds : bond 0.05013 ( 477) hydrogen bonds : angle 4.89222 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.306 Fit side-chains REVERT: R 30 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7958 (mm) REVERT: R 62 ARG cc_start: 0.7335 (ptt180) cc_final: 0.6776 (mtt90) REVERT: R 170 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7063 (p) REVERT: R 204 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8225 (m) REVERT: R 285 LEU cc_start: 0.8042 (mt) cc_final: 0.7821 (mm) REVERT: A 24 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7368 (ttp-110) REVERT: A 33 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: A 186 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 192 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7236 (mptt) REVERT: A 247 MET cc_start: 0.7878 (mtp) cc_final: 0.7640 (mtm) REVERT: B 325 MET cc_start: 0.8499 (mmm) cc_final: 0.8071 (tpp) REVERT: S 23 SER cc_start: 0.8318 (t) cc_final: 0.7923 (m) REVERT: S 132 THR cc_start: 0.7232 (m) cc_final: 0.7005 (t) REVERT: S 207 LEU cc_start: 0.7891 (tp) cc_final: 0.7660 (tt) outliers start: 27 outliers final: 7 residues processed: 172 average time/residue: 0.5131 time to fit residues: 93.4732 Evaluate side-chains 146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101067 restraints weight = 12763.786| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.90 r_work: 0.3147 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9241 Z= 0.237 Angle : 0.703 11.012 12519 Z= 0.374 Chirality : 0.047 0.196 1408 Planarity : 0.005 0.041 1573 Dihedral : 5.881 46.445 1277 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.56 % Allowed : 9.05 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1131 helix: 1.34 (0.25), residues: 424 sheet: 0.82 (0.30), residues: 279 loop : 0.01 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.018 0.002 TYR S 178 PHE 0.023 0.003 PHE B 151 TRP 0.023 0.002 TRP R 51 HIS 0.007 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9237) covalent geometry : angle 0.70044 (12511) SS BOND : bond 0.01062 ( 4) SS BOND : angle 2.40128 ( 8) hydrogen bonds : bond 0.05132 ( 477) hydrogen bonds : angle 4.77225 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.367 Fit side-chains REVERT: R 30 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8045 (mp) REVERT: R 62 ARG cc_start: 0.7313 (ptt180) cc_final: 0.6930 (mtt90) REVERT: A 24 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7403 (ttp-110) REVERT: A 33 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: A 246 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7187 (m) REVERT: A 247 MET cc_start: 0.7977 (mtp) cc_final: 0.7709 (mtm) REVERT: B 219 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7392 (mtt180) REVERT: S 23 SER cc_start: 0.8204 (t) cc_final: 0.7880 (m) REVERT: S 132 THR cc_start: 0.7229 (m) cc_final: 0.7016 (t) outliers start: 35 outliers final: 16 residues processed: 157 average time/residue: 0.5376 time to fit residues: 89.2175 Evaluate side-chains 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 242 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 87 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104009 restraints weight = 13002.589| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.07 r_work: 0.3188 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9241 Z= 0.127 Angle : 0.564 9.747 12519 Z= 0.301 Chirality : 0.042 0.155 1408 Planarity : 0.004 0.043 1573 Dihedral : 5.286 40.605 1277 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.34 % Allowed : 11.19 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.25), residues: 1131 helix: 1.82 (0.26), residues: 420 sheet: 0.86 (0.31), residues: 260 loop : -0.00 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 190 TYR 0.016 0.001 TYR S 178 PHE 0.015 0.002 PHE B 151 TRP 0.017 0.002 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9237) covalent geometry : angle 0.56252 (12511) SS BOND : bond 0.00508 ( 4) SS BOND : angle 1.83656 ( 8) hydrogen bonds : bond 0.03927 ( 477) hydrogen bonds : angle 4.46881 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.336 Fit side-chains REVERT: R 62 ARG cc_start: 0.7407 (ptt180) cc_final: 0.6874 (mpt180) REVERT: R 204 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8172 (m) REVERT: R 285 LEU cc_start: 0.8127 (mt) cc_final: 0.7893 (mm) REVERT: A 24 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: A 33 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: A 246 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7150 (m) REVERT: A 247 MET cc_start: 0.7892 (mtp) cc_final: 0.7678 (mtm) REVERT: B 42 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6945 (tpp-160) REVERT: B 111 TYR cc_start: 0.8856 (m-80) cc_final: 0.8632 (m-80) REVERT: S 76 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7464 (mptt) outliers start: 23 outliers final: 9 residues processed: 159 average time/residue: 0.5368 time to fit residues: 90.2295 Evaluate side-chains 144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105324 restraints weight = 12770.633| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.91 r_work: 0.3210 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9241 Z= 0.119 Angle : 0.549 9.228 12519 Z= 0.292 Chirality : 0.042 0.170 1408 Planarity : 0.004 0.045 1573 Dihedral : 4.962 40.822 1275 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.93 % Allowed : 11.80 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1131 helix: 1.97 (0.26), residues: 420 sheet: 0.80 (0.31), residues: 269 loop : -0.02 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9237) covalent geometry : angle 0.54621 (12511) SS BOND : bond 0.00356 ( 4) SS BOND : angle 2.30290 ( 8) hydrogen bonds : bond 0.03753 ( 477) hydrogen bonds : angle 4.34678 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.220 Fit side-chains REVERT: R 62 ARG cc_start: 0.7367 (ptt180) cc_final: 0.6924 (mtt90) REVERT: R 204 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8158 (m) REVERT: R 285 LEU cc_start: 0.8081 (mt) cc_final: 0.7871 (mm) REVERT: A 24 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7364 (ttp-110) REVERT: A 33 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: A 247 MET cc_start: 0.7917 (mtp) cc_final: 0.7704 (mtm) REVERT: B 42 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6918 (tpp-160) REVERT: B 111 TYR cc_start: 0.8837 (m-80) cc_final: 0.8611 (m-80) REVERT: S 76 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7535 (mptt) outliers start: 19 outliers final: 10 residues processed: 147 average time/residue: 0.5371 time to fit residues: 83.3625 Evaluate side-chains 145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101842 restraints weight = 12857.029| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.93 r_work: 0.3161 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9241 Z= 0.182 Angle : 0.615 9.685 12519 Z= 0.326 Chirality : 0.044 0.165 1408 Planarity : 0.004 0.044 1573 Dihedral : 5.314 45.563 1275 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.95 % Allowed : 12.31 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1131 helix: 1.80 (0.26), residues: 420 sheet: 0.81 (0.31), residues: 267 loop : -0.09 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 148 TYR 0.020 0.002 TYR S 178 PHE 0.017 0.002 PHE B 151 TRP 0.013 0.002 TRP R 51 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9237) covalent geometry : angle 0.61366 (12511) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.77586 ( 8) hydrogen bonds : bond 0.04395 ( 477) hydrogen bonds : angle 4.50506 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.214 Fit side-chains REVERT: R 62 ARG cc_start: 0.7292 (ptt180) cc_final: 0.6883 (mpt180) REVERT: R 186 SER cc_start: 0.7475 (OUTLIER) cc_final: 0.7204 (m) REVERT: R 204 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 24 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7391 (ttp-110) REVERT: A 33 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: A 186 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 226 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: S 76 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7529 (mptt) REVERT: S 207 LEU cc_start: 0.7907 (tt) cc_final: 0.7045 (pp) outliers start: 29 outliers final: 15 residues processed: 151 average time/residue: 0.5374 time to fit residues: 85.5124 Evaluate side-chains 149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103754 restraints weight = 12834.087| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.80 r_work: 0.3209 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9241 Z= 0.123 Angle : 0.548 7.879 12519 Z= 0.293 Chirality : 0.042 0.164 1408 Planarity : 0.004 0.045 1573 Dihedral : 4.957 41.080 1275 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 13.63 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.26), residues: 1131 helix: 1.94 (0.26), residues: 420 sheet: 0.78 (0.31), residues: 269 loop : -0.14 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.016 0.001 PHE B 199 TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9237) covalent geometry : angle 0.54392 (12511) SS BOND : bond 0.00166 ( 4) SS BOND : angle 2.61974 ( 8) hydrogen bonds : bond 0.03740 ( 477) hydrogen bonds : angle 4.36707 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.232 Fit side-chains REVERT: R 62 ARG cc_start: 0.7337 (ptt180) cc_final: 0.6887 (mtt90) REVERT: R 186 SER cc_start: 0.7500 (OUTLIER) cc_final: 0.7127 (m) REVERT: R 204 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8158 (m) REVERT: R 271 TYR cc_start: 0.8672 (t80) cc_final: 0.8401 (t80) REVERT: R 323 MET cc_start: 0.4651 (mtt) cc_final: 0.4380 (ttp) REVERT: A 24 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7321 (ttp-110) REVERT: A 33 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: A 186 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7478 (mt-10) REVERT: B 42 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6882 (tpp-160) REVERT: S 207 LEU cc_start: 0.7927 (tt) cc_final: 0.7080 (pp) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 0.5739 time to fit residues: 92.0857 Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.0980 chunk 3 optimal weight: 0.0010 chunk 46 optimal weight: 0.9990 chunk 111 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105926 restraints weight = 12888.007| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.80 r_work: 0.3238 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9241 Z= 0.106 Angle : 0.528 8.207 12519 Z= 0.279 Chirality : 0.042 0.256 1408 Planarity : 0.004 0.046 1573 Dihedral : 4.662 36.970 1275 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 14.24 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1131 helix: 2.09 (0.26), residues: 420 sheet: 0.82 (0.31), residues: 267 loop : -0.17 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 148 TYR 0.014 0.001 TYR S 178 PHE 0.014 0.001 PHE B 151 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9237) covalent geometry : angle 0.52606 (12511) SS BOND : bond 0.00274 ( 4) SS BOND : angle 1.64164 ( 8) hydrogen bonds : bond 0.03385 ( 477) hydrogen bonds : angle 4.23810 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.268 Fit side-chains REVERT: R 62 ARG cc_start: 0.7263 (ptt180) cc_final: 0.6833 (mpt180) REVERT: R 186 SER cc_start: 0.7449 (OUTLIER) cc_final: 0.7022 (m) REVERT: R 204 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8114 (m) REVERT: R 271 TYR cc_start: 0.8623 (t80) cc_final: 0.8363 (t80) REVERT: R 323 MET cc_start: 0.4542 (mtt) cc_final: 0.4313 (ttp) REVERT: A 24 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7312 (ttp-110) REVERT: A 33 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: B 42 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6891 (tpp-160) REVERT: B 197 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7451 (mmt90) REVERT: S 207 LEU cc_start: 0.7937 (tt) cc_final: 0.7028 (pp) outliers start: 17 outliers final: 8 residues processed: 148 average time/residue: 0.5556 time to fit residues: 87.0667 Evaluate side-chains 142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103713 restraints weight = 12825.272| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.85 r_work: 0.3188 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9241 Z= 0.145 Angle : 0.581 8.383 12519 Z= 0.309 Chirality : 0.043 0.177 1408 Planarity : 0.004 0.045 1573 Dihedral : 4.983 43.013 1275 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.93 % Allowed : 15.16 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1131 helix: 1.95 (0.26), residues: 420 sheet: 0.77 (0.31), residues: 269 loop : -0.21 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 148 TYR 0.021 0.002 TYR R 90 PHE 0.034 0.002 PHE R 97 TRP 0.013 0.001 TRP R 95 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9237) covalent geometry : angle 0.57785 (12511) SS BOND : bond 0.00452 ( 4) SS BOND : angle 2.60685 ( 8) hydrogen bonds : bond 0.03897 ( 477) hydrogen bonds : angle 4.34209 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.286 Fit side-chains REVERT: R 62 ARG cc_start: 0.7344 (ptt180) cc_final: 0.6872 (mtt90) REVERT: R 186 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7049 (m) REVERT: R 204 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8174 (m) REVERT: R 271 TYR cc_start: 0.8674 (t80) cc_final: 0.8415 (t80) REVERT: R 323 MET cc_start: 0.4627 (mtt) cc_final: 0.4383 (ttm) REVERT: A 24 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7413 (ttp-110) REVERT: A 33 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: A 186 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 42 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6924 (tpp-160) REVERT: B 111 TYR cc_start: 0.8837 (m-80) cc_final: 0.8607 (m-80) REVERT: S 207 LEU cc_start: 0.7902 (tt) cc_final: 0.7014 (pp) outliers start: 19 outliers final: 10 residues processed: 145 average time/residue: 0.5874 time to fit residues: 90.0910 Evaluate side-chains 147 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104256 restraints weight = 12853.903| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.82 r_work: 0.3210 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9241 Z= 0.128 Angle : 0.564 8.766 12519 Z= 0.298 Chirality : 0.043 0.173 1408 Planarity : 0.004 0.045 1573 Dihedral : 4.918 41.285 1275 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.32 % Allowed : 15.56 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.26), residues: 1131 helix: 1.98 (0.26), residues: 420 sheet: 0.64 (0.30), residues: 279 loop : -0.20 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 148 TYR 0.022 0.001 TYR R 90 PHE 0.030 0.002 PHE R 97 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9237) covalent geometry : angle 0.56124 (12511) SS BOND : bond 0.00214 ( 4) SS BOND : angle 2.29376 ( 8) hydrogen bonds : bond 0.03680 ( 477) hydrogen bonds : angle 4.31009 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.367 Fit side-chains REVERT: R 62 ARG cc_start: 0.7301 (ptt180) cc_final: 0.6863 (mtt90) REVERT: R 186 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.6979 (m) REVERT: R 204 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8157 (m) REVERT: R 271 TYR cc_start: 0.8646 (t80) cc_final: 0.8365 (t80) REVERT: R 323 MET cc_start: 0.4565 (mtt) cc_final: 0.4314 (ttp) REVERT: A 24 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7326 (ttp-110) REVERT: A 33 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: A 186 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 42 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6878 (tpp-160) REVERT: B 111 TYR cc_start: 0.8820 (m-80) cc_final: 0.8595 (m-80) REVERT: S 207 LEU cc_start: 0.7897 (tt) cc_final: 0.6999 (pp) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 0.6038 time to fit residues: 91.9945 Evaluate side-chains 148 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102675 restraints weight = 12652.586| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.81 r_work: 0.3185 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9241 Z= 0.158 Angle : 0.607 8.664 12519 Z= 0.319 Chirality : 0.045 0.376 1408 Planarity : 0.004 0.045 1573 Dihedral : 5.122 44.375 1275 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.53 % Allowed : 15.36 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1131 helix: 1.88 (0.26), residues: 420 sheet: 0.65 (0.31), residues: 275 loop : -0.25 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 148 TYR 0.023 0.002 TYR R 90 PHE 0.029 0.002 PHE R 97 TRP 0.012 0.002 TRP R 95 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9237) covalent geometry : angle 0.60419 (12511) SS BOND : bond 0.00300 ( 4) SS BOND : angle 2.38339 ( 8) hydrogen bonds : bond 0.04055 ( 477) hydrogen bonds : angle 4.41599 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3460.25 seconds wall clock time: 59 minutes 9.08 seconds (3549.08 seconds total)