Starting phenix.real_space_refine on Wed Sep 17 13:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6l_62129/09_2025/9k6l_62129.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 63 5.16 5 C 5699 2.51 5 N 1499 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2240 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.27 Number of scatterers: 8914 At special positions: 0 Unit cell: (90.48, 119.6, 121.68, 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 63 16.00 O 1653 8.00 N 1499 7.00 C 5699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 385.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 39.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.431A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.148A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.551A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.694A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 4.149A pdb=" N GLN A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.805A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.814A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.892A 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 87 through 91 removed outlier: 3.653A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.884A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 40 Processing helix chain 'R' and resid 43 through 73 Processing helix chain 'R' and resid 81 through 108 Processing helix chain 'R' and resid 112 through 125 Processing helix chain 'R' and resid 125 through 155 Proline residue: R 143 - end of helix Processing helix chain 'R' and resid 172 through 210 Proline residue: R 188 - end of helix removed outlier: 3.772A pdb=" N LEU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS R 210 " --> pdb=" O GLN R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 248 Processing helix chain 'R' and resid 249 through 252 Processing helix chain 'R' and resid 257 through 279 Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.529A pdb=" N LYS R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.829A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.756A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.328A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.556A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.230A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.027A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.796A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.923A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 196 " --> pdb=" O ALA S 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.712A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1401 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: 1.62 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2369 1.33 - 1.45: 1783 1.45 - 1.57: 4863 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9108 Sorted by residual: bond pdb=" N LYS A 272 " pdb=" CA LYS A 272 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.04e+00 bond pdb=" CG LEU G 19 " pdb=" CD2 LEU G 19 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" C5 SA0 R 501 " pdb=" O5 SA0 R 501 " ideal model delta sigma weight residual 1.414 1.441 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB GLU A 25 " pdb=" CG GLU A 25 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 9103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12156 2.83 - 5.67: 151 5.67 - 8.50: 27 8.50 - 11.33: 4 11.33 - 14.17: 1 Bond angle restraints: 12339 Sorted by residual: angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 130.47 -14.17 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA GLU A 43 " pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA LYS R 254 " pdb=" CB LYS R 254 " pdb=" CG LYS R 254 " ideal model delta sigma weight residual 114.10 122.03 -7.93 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta sigma weight residual 122.54 116.13 6.41 1.65e+00 3.67e-01 1.51e+01 angle pdb=" CA MET S 93 " pdb=" CB MET S 93 " pdb=" CG MET S 93 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4635 17.27 - 34.54: 559 34.54 - 51.81: 158 51.81 - 69.08: 39 69.08 - 86.35: 6 Dihedral angle restraints: 5397 sinusoidal: 2122 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS R 69 " pdb=" SG CYS R 69 " pdb=" SG CYS R 79 " pdb=" CB CYS R 79 " ideal model delta sinusoidal sigma weight residual -86.00 0.35 -86.35 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CA THR S 160 " pdb=" C THR S 160 " pdb=" N TYR S 161 " pdb=" CA TYR S 161 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA MET A 53 " pdb=" C MET A 53 " pdb=" N LYS A 54 " pdb=" CA LYS A 54 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1095 0.049 - 0.099: 252 0.099 - 0.148: 51 0.148 - 0.197: 9 0.197 - 0.246: 3 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB ILE R 13 " pdb=" CA ILE R 13 " pdb=" CG1 ILE R 13 " pdb=" CG2 ILE R 13 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU R 123 " pdb=" CB LEU R 123 " pdb=" CD1 LEU R 123 " pdb=" CD2 LEU R 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE R 248 " pdb=" CA ILE R 248 " pdb=" CG1 ILE R 248 " pdb=" CG2 ILE R 248 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1407 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 88 " 0.025 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE R 88 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE R 88 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE R 88 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 88 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE R 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 117 " -0.020 2.00e-02 2.50e+03 1.85e-02 8.56e+00 pdb=" CG TRP R 117 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 117 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 117 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 117 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 117 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 117 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 117 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 117 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 117 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 120 " -0.025 2.00e-02 2.50e+03 1.70e-02 7.23e+00 pdb=" CG TRP R 120 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP R 120 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 120 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 120 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 120 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 120 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 120 " -0.007 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 150 2.65 - 3.21: 8568 3.21 - 3.78: 14646 3.78 - 4.34: 19390 4.34 - 4.90: 32174 Nonbonded interactions: 74928 Sorted by model distance: nonbonded pdb=" OG SER R 25 " pdb=" O GLY R 53 " model vdw 2.090 3.040 nonbonded pdb=" OD2 ASP R 46 " pdb=" OG1 THR R 282 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU R 262 " pdb=" O4 SA0 R 501 " model vdw 2.181 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.206 3.040 nonbonded pdb=" N GLN B 259 " pdb=" OE1 GLN B 259 " model vdw 2.251 3.120 ... (remaining 74923 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.044 9111 Z= 0.184 Angle : 0.774 14.168 12345 Z= 0.394 Chirality : 0.046 0.246 1410 Planarity : 0.005 0.056 1542 Dihedral : 16.438 79.200 3268 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.31 % Allowed : 32.86 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1111 helix: 1.91 (0.26), residues: 413 sheet: -0.05 (0.32), residues: 282 loop : -0.74 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 148 TYR 0.028 0.002 TYR S 223 PHE 0.056 0.002 PHE R 88 TRP 0.050 0.002 TRP R 117 HIS 0.006 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9108) covalent geometry : angle 0.77397 (12339) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.74877 ( 6) hydrogen bonds : bond 0.10971 ( 489) hydrogen bonds : angle 5.58845 ( 1401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8033 (t0) cc_final: 0.7512 (t0) REVERT: A 246 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7038 (tm-30) REVERT: A 344 ILE cc_start: 0.7808 (mm) cc_final: 0.7598 (mt) REVERT: B 49 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8240 (mtt-85) REVERT: B 71 VAL cc_start: 0.8189 (t) cc_final: 0.7893 (p) REVERT: B 134 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7195 (mtm180) REVERT: B 150 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8146 (mmp80) REVERT: B 161 SER cc_start: 0.8207 (p) cc_final: 0.7462 (p) REVERT: B 163 ASP cc_start: 0.7475 (m-30) cc_final: 0.7099 (m-30) REVERT: B 188 MET cc_start: 0.7953 (mmm) cc_final: 0.7584 (mmm) REVERT: B 219 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8042 (ttm110) REVERT: B 230 ASN cc_start: 0.8023 (m-40) cc_final: 0.7714 (m110) REVERT: B 265 SER cc_start: 0.7697 (p) cc_final: 0.7211 (t) REVERT: B 314 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7548 (ttm170) REVERT: G 21 MET cc_start: 0.7702 (mmm) cc_final: 0.7064 (mmm) REVERT: S 46 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6645 (mt-10) REVERT: S 127 VAL cc_start: 0.8326 (m) cc_final: 0.8024 (p) REVERT: S 191 PHE cc_start: 0.7423 (m-80) cc_final: 0.7088 (m-80) REVERT: S 208 GLU cc_start: 0.7460 (mp0) cc_final: 0.6934 (mp0) REVERT: R 11 MET cc_start: 0.7076 (tmm) cc_final: 0.6756 (tmm) REVERT: R 27 LEU cc_start: 0.7424 (tp) cc_final: 0.7147 (tm) REVERT: R 136 ILE cc_start: 0.7159 (tt) cc_final: 0.6892 (tp) REVERT: R 150 ILE cc_start: 0.6269 (pp) cc_final: 0.6020 (pt) outliers start: 3 outliers final: 3 residues processed: 217 average time/residue: 0.5368 time to fit residues: 124.9185 Evaluate side-chains 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 142 HIS B 156 GLN B 295 ASN S 39 GLN S 182 ASN R 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127056 restraints weight = 12890.799| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.05 r_work: 0.3644 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9111 Z= 0.190 Angle : 0.659 10.113 12345 Z= 0.340 Chirality : 0.045 0.203 1410 Planarity : 0.005 0.059 1542 Dihedral : 5.040 57.931 1242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.92 % Allowed : 29.29 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1111 helix: 1.95 (0.26), residues: 414 sheet: -0.20 (0.31), residues: 284 loop : -0.71 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 197 TYR 0.026 0.002 TYR R 266 PHE 0.031 0.002 PHE R 88 TRP 0.035 0.002 TRP R 120 HIS 0.005 0.001 HIS S 155 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9108) covalent geometry : angle 0.65851 (12339) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.10532 ( 6) hydrogen bonds : bond 0.04017 ( 489) hydrogen bonds : angle 4.82592 ( 1401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7231 (mtmp) REVERT: A 322 THR cc_start: 0.8510 (m) cc_final: 0.8285 (p) REVERT: B 37 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 161 SER cc_start: 0.8382 (p) cc_final: 0.7967 (p) REVERT: B 188 MET cc_start: 0.8298 (mmm) cc_final: 0.7945 (mmm) REVERT: B 230 ASN cc_start: 0.8175 (m-40) cc_final: 0.7842 (m110) REVERT: B 265 SER cc_start: 0.7732 (p) cc_final: 0.7410 (t) REVERT: B 318 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8177 (tp) REVERT: G 21 MET cc_start: 0.8023 (mmm) cc_final: 0.7621 (mmm) REVERT: S 46 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7289 (mt-10) REVERT: S 208 GLU cc_start: 0.7802 (mp0) cc_final: 0.7539 (mp0) REVERT: S 223 TYR cc_start: 0.6975 (OUTLIER) cc_final: 0.6485 (t80) REVERT: R 11 MET cc_start: 0.7324 (tmm) cc_final: 0.7031 (tmm) REVERT: R 27 LEU cc_start: 0.7566 (tp) cc_final: 0.7254 (tm) REVERT: R 136 ILE cc_start: 0.7644 (tt) cc_final: 0.7403 (tp) REVERT: R 200 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7572 (mtm) REVERT: R 260 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7828 (p) outliers start: 58 outliers final: 24 residues processed: 241 average time/residue: 0.4502 time to fit residues: 117.4423 Evaluate side-chains 226 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 200 MET Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN S 39 GLN S 182 ASN R 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126538 restraints weight = 12800.807| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.02 r_work: 0.3638 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9111 Z= 0.178 Angle : 0.608 8.439 12345 Z= 0.317 Chirality : 0.044 0.201 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.019 58.605 1240 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.92 % Allowed : 28.16 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1111 helix: 1.94 (0.26), residues: 412 sheet: -0.22 (0.32), residues: 269 loop : -0.61 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.026 0.002 TYR R 266 PHE 0.024 0.002 PHE R 88 TRP 0.030 0.002 TRP R 120 HIS 0.009 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9108) covalent geometry : angle 0.60750 (12339) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.04199 ( 6) hydrogen bonds : bond 0.03734 ( 489) hydrogen bonds : angle 4.62110 ( 1401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6564 (ttpp) cc_final: 0.6223 (ttpp) REVERT: A 201 ASP cc_start: 0.8054 (t0) cc_final: 0.7563 (t0) REVERT: A 243 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7335 (ttp-170) REVERT: A 322 THR cc_start: 0.8520 (m) cc_final: 0.8283 (p) REVERT: A 335 PHE cc_start: 0.8400 (t80) cc_final: 0.8195 (t80) REVERT: B 18 ILE cc_start: 0.8318 (pp) cc_final: 0.8097 (pt) REVERT: B 37 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7808 (tt) REVERT: B 114 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7672 (p) REVERT: B 128 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (p) REVERT: B 188 MET cc_start: 0.8351 (mmm) cc_final: 0.7987 (mmm) REVERT: B 230 ASN cc_start: 0.8177 (m-40) cc_final: 0.7863 (m-40) REVERT: B 246 ASP cc_start: 0.7858 (m-30) cc_final: 0.7420 (m-30) REVERT: B 265 SER cc_start: 0.7737 (p) cc_final: 0.7448 (t) REVERT: B 318 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8066 (tp) REVERT: G 21 MET cc_start: 0.8130 (mmm) cc_final: 0.7824 (mmm) REVERT: G 46 LYS cc_start: 0.8405 (mmmm) cc_final: 0.8186 (mmmm) REVERT: S 46 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7286 (mt-10) REVERT: S 108 PHE cc_start: 0.8513 (m-80) cc_final: 0.8243 (m-80) REVERT: S 208 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: S 223 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6529 (t80) REVERT: R 27 LEU cc_start: 0.7630 (tp) cc_final: 0.7390 (tm) REVERT: R 136 ILE cc_start: 0.7675 (tt) cc_final: 0.7424 (tp) REVERT: R 150 ILE cc_start: 0.6826 (pp) cc_final: 0.6546 (pt) outliers start: 58 outliers final: 32 residues processed: 235 average time/residue: 0.4661 time to fit residues: 118.3981 Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126302 restraints weight = 12988.791| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.03 r_work: 0.3633 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9111 Z= 0.186 Angle : 0.598 8.367 12345 Z= 0.312 Chirality : 0.043 0.196 1410 Planarity : 0.005 0.058 1542 Dihedral : 5.022 58.820 1240 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.53 % Allowed : 28.16 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1111 helix: 1.91 (0.26), residues: 412 sheet: -0.38 (0.31), residues: 271 loop : -0.57 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.026 0.002 TYR R 266 PHE 0.044 0.002 PHE R 88 TRP 0.028 0.002 TRP R 120 HIS 0.013 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9108) covalent geometry : angle 0.59747 (12339) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.96806 ( 6) hydrogen bonds : bond 0.03688 ( 489) hydrogen bonds : angle 4.58416 ( 1401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8242 (mtpp) REVERT: A 33 GLU cc_start: 0.7723 (pt0) cc_final: 0.7468 (pt0) REVERT: A 198 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7869 (mmmm) REVERT: A 322 THR cc_start: 0.8510 (m) cc_final: 0.8223 (p) REVERT: B 18 ILE cc_start: 0.8370 (pp) cc_final: 0.8138 (pt) REVERT: B 114 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7647 (p) REVERT: B 128 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8337 (p) REVERT: B 188 MET cc_start: 0.8313 (mmm) cc_final: 0.7892 (mmm) REVERT: B 262 MET cc_start: 0.7122 (mmm) cc_final: 0.6839 (mmm) REVERT: B 265 SER cc_start: 0.7724 (p) cc_final: 0.7449 (t) REVERT: G 21 MET cc_start: 0.8120 (mmm) cc_final: 0.7813 (mmm) REVERT: G 46 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8170 (mmmm) REVERT: G 50 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6868 (mt) REVERT: S 46 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7323 (mt-10) REVERT: S 108 PHE cc_start: 0.8514 (m-80) cc_final: 0.8312 (m-80) REVERT: S 208 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: S 223 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6501 (t80) REVERT: R 27 LEU cc_start: 0.7689 (tp) cc_final: 0.7442 (tm) REVERT: R 136 ILE cc_start: 0.7658 (tt) cc_final: 0.7417 (tp) REVERT: R 150 ILE cc_start: 0.6868 (pp) cc_final: 0.6622 (pt) outliers start: 64 outliers final: 36 residues processed: 235 average time/residue: 0.4835 time to fit residues: 122.8932 Evaluate side-chains 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127073 restraints weight = 12827.710| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.03 r_work: 0.3646 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9111 Z= 0.152 Angle : 0.585 8.227 12345 Z= 0.304 Chirality : 0.043 0.193 1410 Planarity : 0.005 0.057 1542 Dihedral : 4.978 59.624 1240 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.02 % Allowed : 29.29 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1111 helix: 1.99 (0.26), residues: 413 sheet: -0.31 (0.32), residues: 269 loop : -0.59 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.026 0.002 TYR R 266 PHE 0.031 0.002 PHE R 88 TRP 0.027 0.002 TRP R 120 HIS 0.007 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9108) covalent geometry : angle 0.58453 (12339) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.89527 ( 6) hydrogen bonds : bond 0.03528 ( 489) hydrogen bonds : angle 4.54013 ( 1401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: A 46 LYS cc_start: 0.6547 (ttmm) cc_final: 0.6187 (ttpp) REVERT: A 201 ASP cc_start: 0.8058 (t0) cc_final: 0.7527 (t0) REVERT: A 322 THR cc_start: 0.8501 (m) cc_final: 0.8293 (p) REVERT: B 18 ILE cc_start: 0.8380 (pp) cc_final: 0.8146 (pt) REVERT: B 114 CYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7628 (p) REVERT: B 128 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 188 MET cc_start: 0.8275 (mmm) cc_final: 0.7912 (mmm) REVERT: B 262 MET cc_start: 0.7026 (mmm) cc_final: 0.6773 (mmm) REVERT: B 265 SER cc_start: 0.7721 (p) cc_final: 0.7433 (t) REVERT: G 21 MET cc_start: 0.8102 (mmm) cc_final: 0.7803 (mmm) REVERT: G 46 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8175 (mmmm) REVERT: G 50 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6842 (mt) REVERT: S 46 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7288 (mt-10) REVERT: S 87 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: S 191 PHE cc_start: 0.8026 (m-80) cc_final: 0.7763 (m-80) REVERT: S 208 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: S 223 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6520 (t80) REVERT: R 27 LEU cc_start: 0.7673 (tp) cc_final: 0.7442 (tm) REVERT: R 28 ILE cc_start: 0.6647 (mm) cc_final: 0.6384 (mm) REVERT: R 136 ILE cc_start: 0.7649 (tt) cc_final: 0.7402 (tp) REVERT: R 190 ILE cc_start: 0.7942 (mm) cc_final: 0.7722 (tp) REVERT: R 219 MET cc_start: 0.6820 (mpp) cc_final: 0.6611 (mmm) outliers start: 59 outliers final: 33 residues processed: 228 average time/residue: 0.4801 time to fit residues: 118.4932 Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.143259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125490 restraints weight = 12721.646| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.02 r_work: 0.3622 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9111 Z= 0.210 Angle : 0.606 8.481 12345 Z= 0.315 Chirality : 0.044 0.202 1410 Planarity : 0.005 0.058 1542 Dihedral : 5.027 58.885 1240 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.53 % Allowed : 29.69 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1111 helix: 1.90 (0.25), residues: 412 sheet: -0.39 (0.31), residues: 271 loop : -0.57 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.027 0.002 TYR R 266 PHE 0.032 0.002 PHE R 88 TRP 0.026 0.002 TRP R 120 HIS 0.012 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9108) covalent geometry : angle 0.60549 (12339) SS BOND : bond 0.00302 ( 3) SS BOND : angle 0.86289 ( 6) hydrogen bonds : bond 0.03731 ( 489) hydrogen bonds : angle 4.56126 ( 1401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7424 (pm20) cc_final: 0.7204 (pt0) REVERT: A 33 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: A 46 LYS cc_start: 0.6566 (ttmm) cc_final: 0.6196 (ttpp) REVERT: A 198 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7953 (mmmm) REVERT: A 201 ASP cc_start: 0.8085 (t0) cc_final: 0.7542 (t0) REVERT: A 246 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 267 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 18 ILE cc_start: 0.8392 (pp) cc_final: 0.8147 (pt) REVERT: B 114 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 128 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8328 (p) REVERT: B 188 MET cc_start: 0.8331 (mmm) cc_final: 0.7907 (mmm) REVERT: B 262 MET cc_start: 0.7088 (mmm) cc_final: 0.6733 (mmm) REVERT: B 265 SER cc_start: 0.7733 (p) cc_final: 0.7458 (t) REVERT: G 21 MET cc_start: 0.8140 (mmm) cc_final: 0.7863 (mmm) REVERT: G 46 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8221 (mmmm) REVERT: G 50 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7288 (mt) REVERT: S 46 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7319 (mt-10) REVERT: S 87 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7273 (mtp180) REVERT: S 108 PHE cc_start: 0.8538 (m-80) cc_final: 0.8291 (m-80) REVERT: S 165 PHE cc_start: 0.8600 (m-80) cc_final: 0.8312 (m-80) REVERT: S 182 ASN cc_start: 0.8409 (m110) cc_final: 0.8202 (m110) REVERT: S 208 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: S 223 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6547 (t80) REVERT: R 27 LEU cc_start: 0.7750 (tp) cc_final: 0.7533 (tm) REVERT: R 136 ILE cc_start: 0.7781 (tt) cc_final: 0.7541 (tp) outliers start: 64 outliers final: 36 residues processed: 232 average time/residue: 0.4852 time to fit residues: 121.4266 Evaluate side-chains 234 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126550 restraints weight = 12855.355| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.05 r_work: 0.3638 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9111 Z= 0.159 Angle : 0.585 8.203 12345 Z= 0.304 Chirality : 0.043 0.193 1410 Planarity : 0.004 0.057 1542 Dihedral : 4.982 59.096 1240 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 6.22 % Allowed : 29.90 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1111 helix: 2.00 (0.25), residues: 413 sheet: -0.38 (0.31), residues: 271 loop : -0.61 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.027 0.002 TYR R 266 PHE 0.028 0.002 PHE R 88 TRP 0.028 0.002 TRP R 120 HIS 0.021 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9108) covalent geometry : angle 0.58498 (12339) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.82230 ( 6) hydrogen bonds : bond 0.03583 ( 489) hydrogen bonds : angle 4.53524 ( 1401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7411 (pm20) cc_final: 0.7183 (pt0) REVERT: A 33 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: A 198 LYS cc_start: 0.8256 (mmmm) cc_final: 0.7912 (mmmm) REVERT: A 246 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 258 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8143 (ptmm) REVERT: B 18 ILE cc_start: 0.8389 (pp) cc_final: 0.8139 (pt) REVERT: B 114 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 128 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 188 MET cc_start: 0.8269 (mmm) cc_final: 0.7901 (mmm) REVERT: B 262 MET cc_start: 0.7052 (mmm) cc_final: 0.6825 (mmm) REVERT: B 265 SER cc_start: 0.7719 (p) cc_final: 0.7448 (t) REVERT: G 21 MET cc_start: 0.8140 (mmm) cc_final: 0.7921 (mmp) REVERT: G 46 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8218 (mmmm) REVERT: G 50 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7253 (mt) REVERT: S 87 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7310 (mtp180) REVERT: S 108 PHE cc_start: 0.8503 (m-80) cc_final: 0.8292 (m-80) REVERT: S 208 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: S 223 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6535 (t80) REVERT: R 16 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7167 (pp) REVERT: R 27 LEU cc_start: 0.7712 (tp) cc_final: 0.7489 (tm) REVERT: R 136 ILE cc_start: 0.7754 (tt) cc_final: 0.7506 (tp) REVERT: R 190 ILE cc_start: 0.7948 (mm) cc_final: 0.7732 (tp) outliers start: 61 outliers final: 34 residues processed: 233 average time/residue: 0.4728 time to fit residues: 119.2788 Evaluate side-chains 235 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.0570 chunk 67 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127667 restraints weight = 12927.239| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.07 r_work: 0.3651 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9111 Z= 0.139 Angle : 0.581 8.410 12345 Z= 0.300 Chirality : 0.042 0.200 1410 Planarity : 0.004 0.059 1542 Dihedral : 4.936 59.760 1240 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.51 % Allowed : 30.41 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1111 helix: 2.12 (0.25), residues: 412 sheet: -0.39 (0.32), residues: 266 loop : -0.57 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 129 TYR 0.031 0.002 TYR R 266 PHE 0.026 0.001 PHE R 88 TRP 0.028 0.002 TRP R 120 HIS 0.011 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9108) covalent geometry : angle 0.58058 (12339) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.80881 ( 6) hydrogen bonds : bond 0.03499 ( 489) hydrogen bonds : angle 4.49756 ( 1401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7403 (pm20) cc_final: 0.7175 (pt0) REVERT: A 10 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8230 (mtpp) REVERT: A 33 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: A 198 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7859 (mmmm) REVERT: A 199 MET cc_start: 0.8155 (ttp) cc_final: 0.7929 (mtt) REVERT: A 246 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 258 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8123 (ptmm) REVERT: A 267 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8201 (mt) REVERT: B 18 ILE cc_start: 0.8371 (pp) cc_final: 0.8126 (pt) REVERT: B 114 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7618 (p) REVERT: B 128 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 188 MET cc_start: 0.8222 (mmm) cc_final: 0.7850 (mmm) REVERT: B 262 MET cc_start: 0.7000 (mmm) cc_final: 0.6782 (mmm) REVERT: B 265 SER cc_start: 0.7740 (p) cc_final: 0.7421 (t) REVERT: B 295 ASN cc_start: 0.8080 (m110) cc_final: 0.7873 (m-40) REVERT: G 21 MET cc_start: 0.8106 (mmm) cc_final: 0.7895 (mmp) REVERT: G 46 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8218 (mmmm) REVERT: G 50 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7056 (mt) REVERT: S 87 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7337 (mtp180) REVERT: S 108 PHE cc_start: 0.8485 (m-80) cc_final: 0.8273 (m-80) REVERT: S 165 PHE cc_start: 0.8594 (m-80) cc_final: 0.8263 (m-80) REVERT: S 182 ASN cc_start: 0.8439 (m-40) cc_final: 0.8230 (m-40) REVERT: S 208 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: S 223 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6480 (t80) REVERT: R 16 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7158 (pp) REVERT: R 27 LEU cc_start: 0.7674 (tp) cc_final: 0.7447 (tm) REVERT: R 136 ILE cc_start: 0.7610 (tt) cc_final: 0.7352 (tp) REVERT: R 277 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7188 (tmm) outliers start: 54 outliers final: 30 residues processed: 233 average time/residue: 0.4540 time to fit residues: 114.3431 Evaluate side-chains 237 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 277 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.0570 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN S 39 GLN R 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127690 restraints weight = 12765.889| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.04 r_work: 0.3652 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9111 Z= 0.159 Angle : 0.602 10.057 12345 Z= 0.309 Chirality : 0.043 0.203 1410 Planarity : 0.005 0.058 1542 Dihedral : 4.926 59.340 1240 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.80 % Allowed : 31.73 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1111 helix: 2.11 (0.25), residues: 413 sheet: -0.34 (0.31), residues: 279 loop : -0.63 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.028 0.002 TYR R 266 PHE 0.047 0.002 PHE S 68 TRP 0.029 0.002 TRP R 120 HIS 0.014 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9108) covalent geometry : angle 0.60151 (12339) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.84885 ( 6) hydrogen bonds : bond 0.03533 ( 489) hydrogen bonds : angle 4.50275 ( 1401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7450 (pm20) cc_final: 0.7220 (pt0) REVERT: A 10 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8261 (mtpp) REVERT: A 33 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: A 198 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7883 (mmmm) REVERT: A 246 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 258 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (ptmm) REVERT: A 267 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8206 (mt) REVERT: B 18 ILE cc_start: 0.8385 (pp) cc_final: 0.8141 (pt) REVERT: B 114 CYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 128 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 188 MET cc_start: 0.8240 (mmm) cc_final: 0.7863 (mmm) REVERT: B 262 MET cc_start: 0.7003 (mmm) cc_final: 0.6780 (mmm) REVERT: B 265 SER cc_start: 0.7737 (p) cc_final: 0.7447 (t) REVERT: B 266 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7561 (t-170) REVERT: G 21 MET cc_start: 0.8176 (mmm) cc_final: 0.7972 (mmp) REVERT: G 46 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8233 (mmmm) REVERT: G 50 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7107 (mt) REVERT: S 87 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7383 (mtp180) REVERT: S 108 PHE cc_start: 0.8489 (m-80) cc_final: 0.8278 (m-80) REVERT: S 182 ASN cc_start: 0.8444 (m-40) cc_final: 0.8227 (m-40) REVERT: S 189 ASP cc_start: 0.7684 (t0) cc_final: 0.7450 (t0) REVERT: S 208 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: S 223 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6499 (t80) REVERT: R 16 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7161 (pp) REVERT: R 27 LEU cc_start: 0.7647 (tp) cc_final: 0.7422 (tm) REVERT: R 136 ILE cc_start: 0.7620 (tt) cc_final: 0.7371 (tp) REVERT: R 190 ILE cc_start: 0.7982 (mm) cc_final: 0.7746 (tp) REVERT: R 277 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7230 (tmm) outliers start: 47 outliers final: 32 residues processed: 226 average time/residue: 0.4741 time to fit residues: 115.7925 Evaluate side-chains 239 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 277 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 266 HIS R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126926 restraints weight = 12759.574| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.03 r_work: 0.3645 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9111 Z= 0.176 Angle : 0.604 8.149 12345 Z= 0.314 Chirality : 0.043 0.216 1410 Planarity : 0.005 0.058 1542 Dihedral : 4.945 58.861 1240 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.10 % Allowed : 31.73 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1111 helix: 2.12 (0.25), residues: 413 sheet: -0.35 (0.31), residues: 279 loop : -0.61 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.028 0.002 TYR R 266 PHE 0.035 0.002 PHE S 200 TRP 0.029 0.002 TRP R 120 HIS 0.009 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9108) covalent geometry : angle 0.60383 (12339) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.87404 ( 6) hydrogen bonds : bond 0.03594 ( 489) hydrogen bonds : angle 4.51952 ( 1401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7472 (pm20) cc_final: 0.7235 (pt0) REVERT: A 10 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8274 (mtpp) REVERT: A 33 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: A 198 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7872 (mmmm) REVERT: A 246 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 258 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8111 (ptmm) REVERT: A 267 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8216 (mt) REVERT: B 18 ILE cc_start: 0.8389 (pp) cc_final: 0.8146 (pt) REVERT: B 114 CYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7741 (p) REVERT: B 128 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 188 MET cc_start: 0.8262 (mmm) cc_final: 0.7886 (mmm) REVERT: B 262 MET cc_start: 0.7023 (mmm) cc_final: 0.6818 (mmm) REVERT: B 265 SER cc_start: 0.7701 (p) cc_final: 0.7355 (t) REVERT: G 46 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8248 (mmmm) REVERT: G 50 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7182 (mt) REVERT: S 87 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7381 (mtp180) REVERT: S 208 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: S 223 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6505 (t80) REVERT: R 16 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7163 (pp) REVERT: R 27 LEU cc_start: 0.7665 (tp) cc_final: 0.7446 (tm) REVERT: R 136 ILE cc_start: 0.7645 (tt) cc_final: 0.7400 (tp) REVERT: R 190 ILE cc_start: 0.7995 (mm) cc_final: 0.7755 (tp) REVERT: R 277 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7377 (tmm) outliers start: 50 outliers final: 35 residues processed: 226 average time/residue: 0.4789 time to fit residues: 116.9466 Evaluate side-chains 244 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 277 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.145108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127556 restraints weight = 12737.776| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.04 r_work: 0.3654 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9111 Z= 0.150 Angle : 0.603 8.095 12345 Z= 0.311 Chirality : 0.043 0.203 1410 Planarity : 0.005 0.058 1542 Dihedral : 4.934 59.058 1240 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.80 % Allowed : 32.14 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1111 helix: 2.13 (0.25), residues: 413 sheet: -0.36 (0.31), residues: 279 loop : -0.62 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 129 TYR 0.027 0.002 TYR R 266 PHE 0.039 0.002 PHE S 200 TRP 0.030 0.002 TRP R 120 HIS 0.009 0.001 HIS R 210 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9108) covalent geometry : angle 0.60313 (12339) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.72625 ( 6) hydrogen bonds : bond 0.03529 ( 489) hydrogen bonds : angle 4.50940 ( 1401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3815.75 seconds wall clock time: 65 minutes 59.76 seconds (3959.76 seconds total)