Starting phenix.real_space_refine on Fri Sep 11 08:57:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211.map" model { file = "/net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xji_22211/09_2026/6xji_22211_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 5738 2.51 5 N 1404 2.21 5 O 1566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8754 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2030 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "C" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain: "D" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 2.55, per 1000 atoms: 0.29 Number of scatterers: 8754 At special positions: 0 Unit cell: (75.98, 102.18, 132.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1566 8.00 N 1404 7.00 C 5738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 64.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid -4 through 15 Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 80 removed outlier: 3.562A pdb=" N VAL A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 132 through 162 Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.574A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Proline residue: A 179 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 191 through 200 removed outlier: 4.083A pdb=" N ASP A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 219 through 242 Processing helix chain 'B' and resid -3 through 15 Processing helix chain 'B' and resid 17 through 38 removed outlier: 3.705A pdb=" N TYR B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 80 removed outlier: 3.563A pdb=" N VAL B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 89 through 126 Processing helix chain 'B' and resid 132 through 162 Processing helix chain 'B' and resid 164 through 186 removed outlier: 3.575A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 191 through 200 removed outlier: 4.084A pdb=" N ASP B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 219 through 242 Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 121 through 135 Processing helix chain 'C' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 151 through 169 removed outlier: 4.068A pdb=" N ASN D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 276 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 21 removed outlier: 6.311A pdb=" N LYS C 8 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 6 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 19 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU C 4 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 21 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS C 2 " --> pdb=" O PHE C 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.437A pdb=" N LEU C 141 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER C 176 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU C 143 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 28 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL C 191 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY C 30 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 193 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 32 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 200 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG C 194 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N PHE C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 235 through 239 removed outlier: 6.940A pdb=" N MET C 246 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 238 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS C 244 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 13 through 21 removed outlier: 6.310A pdb=" N LYS D 8 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 6 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 19 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU D 4 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE D 21 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS D 2 " --> pdb=" O PHE D 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.436A pdb=" N LEU D 141 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N SER D 176 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU D 143 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 28 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL D 191 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY D 30 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU D 193 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE D 32 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA D 190 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP D 201 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE D 192 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 235 through 239 removed outlier: 8.510A pdb=" N LEU D 235 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN D 248 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 212 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 273 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 269 " --> pdb=" O THR D 216 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1545 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: 1.44 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1753 1.32 - 1.47: 3128 1.47 - 1.61: 3981 1.61 - 1.75: 16 1.75 - 1.90: 56 Bond restraints: 8934 Sorted by residual: bond pdb=" C VAL C 199 " pdb=" N GLN C 200 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.45e-02 4.76e+03 1.58e+02 bond pdb=" C TYR D 266 " pdb=" N PRO D 267 " ideal model delta sigma weight residual 1.332 1.234 0.098 1.30e-02 5.92e+03 5.67e+01 bond pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.331 1.411 -0.080 1.23e-02 6.61e+03 4.20e+01 bond pdb=" CB HIS B 115 " pdb=" CG HIS B 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.10e+01 ... (remaining 8929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 11082 2.68 - 5.35: 875 5.35 - 8.03: 110 8.03 - 10.71: 8 10.71 - 13.39: 5 Bond angle restraints: 12080 Sorted by residual: angle pdb=" O ILE C 270 " pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 123.00 111.71 11.29 1.10e+00 8.26e-01 1.05e+02 angle pdb=" O VAL C 215 " pdb=" C VAL C 215 " pdb=" N THR C 216 " ideal model delta sigma weight residual 123.10 112.21 10.89 1.17e+00 7.31e-01 8.67e+01 angle pdb=" CA ILE C 270 " pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 115.75 127.43 -11.68 1.28e+00 6.10e-01 8.33e+01 angle pdb=" CA VAL C 215 " pdb=" C VAL C 215 " pdb=" N THR C 216 " ideal model delta sigma weight residual 116.34 127.05 -10.71 1.28e+00 6.10e-01 7.00e+01 angle pdb=" C VAL C 215 " pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 123.00 133.79 -10.79 1.38e+00 5.25e-01 6.11e+01 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5102 17.78 - 35.56: 171 35.56 - 53.34: 52 53.34 - 71.12: 39 71.12 - 88.90: 14 Dihedral angle restraints: 5378 sinusoidal: 2210 harmonic: 3168 Sorted by residual: dihedral pdb=" C ILE B 188 " pdb=" N ILE B 188 " pdb=" CA ILE B 188 " pdb=" CB ILE B 188 " ideal model delta harmonic sigma weight residual -122.00 -130.51 8.51 0 2.50e+00 1.60e-01 1.16e+01 dihedral pdb=" C ILE A 188 " pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" CB ILE A 188 " ideal model delta harmonic sigma weight residual -122.00 -130.45 8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CA LYS C 251 " pdb=" C LYS C 251 " pdb=" N ASN C 252 " pdb=" CA ASN C 252 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 808 0.067 - 0.134: 416 0.134 - 0.201: 130 0.201 - 0.268: 40 0.268 - 0.335: 12 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CB VAL D 166 " pdb=" CA VAL D 166 " pdb=" CG1 VAL D 166 " pdb=" CG2 VAL D 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 1403 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " -0.069 2.00e-02 2.50e+03 3.63e-02 2.63e+01 pdb=" CG TYR B 206 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.068 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR A 206 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 212 " -0.021 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR D 212 " 0.076 2.00e-02 2.50e+03 pdb=" O THR D 212 " -0.029 2.00e-02 2.50e+03 pdb=" N THR D 213 " -0.026 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 851 2.72 - 3.26: 9261 3.26 - 3.81: 14509 3.81 - 4.35: 18585 4.35 - 4.90: 30145 Nonbonded interactions: 73351 Sorted by model distance: nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 2.173 2.170 nonbonded pdb=" O2G AGS C 301 " pdb="MG MG C 302 " model vdw 2.173 2.170 nonbonded pdb=" CG2 THR D 212 " pdb=" OE1 GLN D 236 " model vdw 2.188 3.460 nonbonded pdb=" N LYS D 39 " pdb=" O1B AGS D 301 " model vdw 2.257 3.120 nonbonded pdb=" N LYS C 39 " pdb=" O1B AGS C 301 " model vdw 2.258 3.120 ... (remaining 73346 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 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 : 0.018 0.182 8934 Z= 1.022 Angle : 1.584 13.386 12080 Z= 1.095 Chirality : 0.092 0.335 1406 Planarity : 0.008 0.044 1472 Dihedral : 13.050 88.897 3334 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.72 % Allowed : 1.86 % Favored : 97.42 % 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 are not related in a simple way. whole: 1.02 (0.24), residues: 1074 helix: 1.19 (0.19), residues: 606 sheet: 0.91 (0.57), residues: 87 loop : -0.06 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 189 TYR 0.069 0.008 TYR B 206 PHE 0.030 0.005 PHE B 55 TRP 0.023 0.007 TRP A 223 HIS 0.009 0.003 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.01840 / 1.02 ( 8934) covalent geometry : angle 1.58367 / 1.09 (12080) hydrogen bonds : bond 0.16130 / 10.72 ( 539) hydrogen bonds : angle 6.88848 / 5.10 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 385 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7717 (mttt) cc_final: 0.7006 (ttpp) REVERT: A 51 TYR cc_start: 0.7737 (m-80) cc_final: 0.7352 (m-80) REVERT: A 83 ILE cc_start: 0.7062 (tt) cc_final: 0.5955 (tt) REVERT: A 162 GLN cc_start: 0.7683 (mt0) cc_final: 0.7359 (pt0) REVERT: A 166 MET cc_start: 0.6175 (mmp) cc_final: 0.4575 (ttm) REVERT: B 16 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7080 (ttpt) REVERT: B 99 SER cc_start: 0.8640 (t) cc_final: 0.8337 (m) REVERT: B 116 TYR cc_start: 0.6612 (t80) cc_final: 0.5797 (t80) REVERT: B 122 VAL cc_start: 0.8149 (t) cc_final: 0.7745 (t) REVERT: B 142 PHE cc_start: 0.8493 (t80) cc_final: 0.8292 (t80) REVERT: B 166 MET cc_start: 0.6704 (mmp) cc_final: 0.6449 (mmm) REVERT: B 211 MET cc_start: 0.8622 (mtp) cc_final: 0.8338 (ptp) REVERT: C 5 HIS cc_start: 0.5984 (m-70) cc_final: 0.5358 (m90) REVERT: C 13 ASN cc_start: 0.6712 (t0) cc_final: 0.6454 (t0) REVERT: C 18 ASP cc_start: 0.7170 (t0) cc_final: 0.6829 (m-30) REVERT: C 20 ASP cc_start: 0.7347 (m-30) cc_final: 0.6757 (t70) REVERT: C 43 MET cc_start: 0.8065 (mtm) cc_final: 0.7744 (mtp) REVERT: C 58 ASP cc_start: 0.7313 (t0) cc_final: 0.6994 (m-30) REVERT: C 105 ASP cc_start: 0.8348 (m-30) cc_final: 0.7855 (p0) REVERT: C 118 LYS cc_start: 0.8294 (pttt) cc_final: 0.7880 (tptt) REVERT: C 135 MET cc_start: 0.7637 (mmm) cc_final: 0.7216 (mmt) REVERT: C 195 ASP cc_start: 0.6927 (m-30) cc_final: 0.6677 (m-30) REVERT: C 229 LEU cc_start: 0.5501 (mt) cc_final: 0.5121 (mp) REVERT: D 1 MET cc_start: 0.3952 (tpp) cc_final: 0.3700 (mmm) REVERT: D 56 LYS cc_start: 0.5901 (tttt) cc_final: 0.5668 (tptm) REVERT: D 77 ASN cc_start: 0.8150 (p0) cc_final: 0.7078 (m-40) REVERT: D 165 LEU cc_start: 0.8255 (mt) cc_final: 0.8034 (mt) REVERT: D 181 GLU cc_start: 0.7113 (mp0) cc_final: 0.6606 (tt0) REVERT: D 273 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6499 (ttm110) REVERT: D 281 TYR cc_start: 0.5233 (t80) cc_final: 0.4837 (t80) outliers start: 7 outliers final: 2 residues processed: 388 average time/residue: 0.0961 time to fit residues: 51.2730 Evaluate side-chains 216 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 HIS C 237 ASN D 5 HIS D 35 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 203 ASN D 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149316 restraints weight = 12024.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151910 restraints weight = 8129.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153929 restraints weight = 6170.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155056 restraints weight = 5029.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156032 restraints weight = 4406.961| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8934 Z= 0.172 Angle : 0.707 8.880 12080 Z= 0.379 Chirality : 0.047 0.300 1406 Planarity : 0.004 0.032 1472 Dihedral : 10.851 82.828 1241 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.30 % Allowed : 11.55 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1074 helix: 2.07 (0.20), residues: 603 sheet: 0.98 (0.59), residues: 86 loop : -0.41 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 224 TYR 0.029 0.002 TYR C 228 PHE 0.038 0.002 PHE C 107 TRP 0.029 0.003 TRP B 223 HIS 0.007 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 8934) covalent geometry : angle 0.70655 / 0.38 (12080) hydrogen bonds : bond 0.06015 / 4.07 ( 539) hydrogen bonds : angle 5.17969 / 3.77 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7077 (m-80) cc_final: 0.6823 (m-80) REVERT: A 166 MET cc_start: 0.6136 (mmp) cc_final: 0.4890 (ttm) REVERT: B 68 MET cc_start: 0.8356 (mmm) cc_final: 0.7962 (mmp) REVERT: B 116 TYR cc_start: 0.7207 (t80) cc_final: 0.6605 (t80) REVERT: B 144 LEU cc_start: 0.8602 (mt) cc_final: 0.8382 (tt) REVERT: B 239 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 5 HIS cc_start: 0.5129 (m-70) cc_final: 0.4742 (m90) REVERT: C 77 ASN cc_start: 0.7711 (m110) cc_final: 0.7399 (m110) REVERT: C 89 GLN cc_start: 0.7949 (mt0) cc_final: 0.7697 (mt0) REVERT: C 124 MET cc_start: 0.8321 (mtm) cc_final: 0.8034 (mtm) REVERT: C 135 MET cc_start: 0.7505 (mmm) cc_final: 0.7242 (mmt) REVERT: D 5 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6385 (m170) REVERT: D 37 VAL cc_start: 0.8792 (p) cc_final: 0.8569 (p) REVERT: D 77 ASN cc_start: 0.7189 (p0) cc_final: 0.6578 (m-40) REVERT: D 100 THR cc_start: 0.7375 (m) cc_final: 0.6907 (m) REVERT: D 165 LEU cc_start: 0.8390 (mt) cc_final: 0.8172 (mt) REVERT: D 194 ARG cc_start: 0.7612 (tmt170) cc_final: 0.7158 (tmt170) REVERT: D 200 GLN cc_start: 0.7084 (tm-30) cc_final: 0.6736 (tm-30) outliers start: 32 outliers final: 20 residues processed: 264 average time/residue: 0.0839 time to fit residues: 31.3601 Evaluate side-chains 211 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 5 HIS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN C 17 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS D 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.169966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146859 restraints weight = 11977.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149162 restraints weight = 8065.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151236 restraints weight = 6192.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152348 restraints weight = 5002.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153375 restraints weight = 4345.859| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8934 Z= 0.148 Angle : 0.626 10.925 12080 Z= 0.329 Chirality : 0.044 0.219 1406 Planarity : 0.003 0.035 1472 Dihedral : 9.170 77.230 1237 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.54 % Allowed : 15.46 % Favored : 80.00 % 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 are not related in a simple way. whole: 1.45 (0.25), residues: 1074 helix: 2.04 (0.20), residues: 604 sheet: 0.33 (0.55), residues: 91 loop : -0.65 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.022 0.001 TYR B 51 PHE 0.024 0.002 PHE C 107 TRP 0.020 0.002 TRP A 223 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 8934) covalent geometry : angle 0.62592 / 0.33 (12080) hydrogen bonds : bond 0.05111 / 3.45 ( 539) hydrogen bonds : angle 4.85774 / 3.54 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7077 (m-80) cc_final: 0.6770 (m-80) REVERT: A 166 MET cc_start: 0.6124 (mmp) cc_final: 0.4943 (ttm) REVERT: B 63 LEU cc_start: 0.8616 (mt) cc_final: 0.8272 (tp) REVERT: B 116 TYR cc_start: 0.7342 (t80) cc_final: 0.6833 (t80) REVERT: B 222 GLN cc_start: 0.7554 (tt0) cc_final: 0.7314 (mt0) REVERT: B 239 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 37 VAL cc_start: 0.8869 (p) cc_final: 0.8579 (m) REVERT: C 82 TYR cc_start: 0.7064 (t80) cc_final: 0.6783 (t80) REVERT: C 89 GLN cc_start: 0.8194 (mt0) cc_final: 0.7896 (mt0) REVERT: C 124 MET cc_start: 0.8275 (mtm) cc_final: 0.7976 (mtm) REVERT: C 197 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.5482 (p-80) REVERT: C 214 ILE cc_start: 0.6403 (OUTLIER) cc_final: 0.6090 (mt) REVERT: C 246 MET cc_start: 0.6469 (mpp) cc_final: 0.6170 (mmp) REVERT: D 35 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7339 (p0) REVERT: D 77 ASN cc_start: 0.7197 (p0) cc_final: 0.6817 (m-40) REVERT: D 135 MET cc_start: 0.8327 (mmt) cc_final: 0.8057 (mmm) REVERT: D 194 ARG cc_start: 0.7562 (tmt170) cc_final: 0.7106 (tmt170) REVERT: D 263 LEU cc_start: 0.5204 (tp) cc_final: 0.4943 (mp) outliers start: 44 outliers final: 25 residues processed: 234 average time/residue: 0.0735 time to fit residues: 25.1310 Evaluate side-chains 212 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 234 GLN C 254 GLN D 5 HIS D 35 ASN D 136 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148074 restraints weight = 12056.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151018 restraints weight = 8575.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152865 restraints weight = 6238.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.154182 restraints weight = 4749.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154586 restraints weight = 4172.753| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8934 Z= 0.132 Angle : 0.596 10.074 12080 Z= 0.313 Chirality : 0.044 0.345 1406 Planarity : 0.003 0.035 1472 Dihedral : 7.833 65.503 1234 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.43 % Allowed : 16.91 % Favored : 78.66 % 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 are not related in a simple way. whole: 1.19 (0.25), residues: 1074 helix: 1.92 (0.20), residues: 603 sheet: -0.18 (0.53), residues: 100 loop : -0.81 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.021 0.001 TYR A 206 PHE 0.024 0.002 PHE C 107 TRP 0.018 0.001 TRP A 223 HIS 0.018 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8934) covalent geometry : angle 0.59582 / 0.31 (12080) hydrogen bonds : bond 0.04617 / 3.16 ( 539) hydrogen bonds : angle 4.73575 / 3.44 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7949 (m-80) cc_final: 0.7695 (t80) REVERT: A 51 TYR cc_start: 0.7205 (m-80) cc_final: 0.6886 (m-80) REVERT: A 166 MET cc_start: 0.5981 (mmp) cc_final: 0.4798 (ttm) REVERT: B 63 LEU cc_start: 0.8656 (mt) cc_final: 0.8290 (tp) REVERT: B 68 MET cc_start: 0.8536 (mmp) cc_final: 0.8134 (mmt) REVERT: B 80 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7806 (mm-40) REVERT: B 110 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 116 TYR cc_start: 0.7345 (t80) cc_final: 0.6865 (t80) REVERT: B 239 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 37 VAL cc_start: 0.8965 (p) cc_final: 0.8749 (m) REVERT: C 82 TYR cc_start: 0.7127 (t80) cc_final: 0.6840 (t80) REVERT: C 89 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: C 99 TYR cc_start: 0.7140 (t80) cc_final: 0.6883 (t80) REVERT: C 135 MET cc_start: 0.7330 (mmt) cc_final: 0.7069 (mmp) REVERT: D 77 ASN cc_start: 0.7149 (p0) cc_final: 0.6947 (m-40) REVERT: D 165 LEU cc_start: 0.8193 (mt) cc_final: 0.7894 (mm) REVERT: D 195 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: D 200 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7098 (tm-30) outliers start: 43 outliers final: 31 residues processed: 232 average time/residue: 0.0748 time to fit residues: 25.6324 Evaluate side-chains 223 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144584 restraints weight = 12063.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147188 restraints weight = 8269.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.148962 restraints weight = 6224.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150080 restraints weight = 5070.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151067 restraints weight = 4399.401| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8934 Z= 0.144 Angle : 0.598 7.390 12080 Z= 0.314 Chirality : 0.044 0.295 1406 Planarity : 0.004 0.037 1472 Dihedral : 7.241 64.843 1234 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.05 % Allowed : 16.80 % Favored : 78.14 % 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 are not related in a simple way. whole: 1.05 (0.25), residues: 1074 helix: 1.76 (0.20), residues: 609 sheet: -0.24 (0.51), residues: 100 loop : -0.83 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.020 0.001 TYR A 206 PHE 0.011 0.001 PHE A 55 TRP 0.017 0.001 TRP A 223 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8934) covalent geometry : angle 0.59804 / 0.31 (12080) hydrogen bonds : bond 0.04400 / 2.99 ( 539) hydrogen bonds : angle 4.70631 / 3.42 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7978 (m-80) cc_final: 0.7685 (t80) REVERT: A 42 MET cc_start: 0.3462 (mmp) cc_final: 0.2979 (mmp) REVERT: A 51 TYR cc_start: 0.6978 (m-80) cc_final: 0.6720 (m-80) REVERT: A 166 MET cc_start: 0.6006 (mmp) cc_final: 0.4581 (ttm) REVERT: B 37 LEU cc_start: 0.6927 (mt) cc_final: 0.6724 (mt) REVERT: B 54 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8345 (m) REVERT: B 63 LEU cc_start: 0.8726 (mt) cc_final: 0.8319 (tp) REVERT: B 80 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7818 (mm-40) REVERT: B 110 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 116 TYR cc_start: 0.7386 (t80) cc_final: 0.6703 (t80) REVERT: B 239 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 37 VAL cc_start: 0.8837 (p) cc_final: 0.8607 (m) REVERT: C 82 TYR cc_start: 0.7221 (t80) cc_final: 0.6921 (t80) REVERT: C 89 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: C 99 TYR cc_start: 0.7316 (t80) cc_final: 0.7077 (t80) REVERT: C 135 MET cc_start: 0.7336 (mmt) cc_final: 0.7063 (mmp) REVERT: C 189 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7397 (ptt180) REVERT: C 270 ILE cc_start: 0.6757 (tt) cc_final: 0.6495 (mt) REVERT: D 13 ASN cc_start: 0.6316 (OUTLIER) cc_final: 0.6091 (t0) REVERT: D 35 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7253 (p0) REVERT: D 135 MET cc_start: 0.8109 (mmm) cc_final: 0.7829 (mmt) REVERT: D 150 MET cc_start: 0.7620 (mmm) cc_final: 0.7116 (mmm) REVERT: D 200 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 246 MET cc_start: 0.6147 (mpp) cc_final: 0.5399 (mpp) REVERT: D 263 LEU cc_start: 0.5910 (mp) cc_final: 0.5661 (tt) outliers start: 49 outliers final: 32 residues processed: 228 average time/residue: 0.0755 time to fit residues: 25.3911 Evaluate side-chains 220 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 283 ASN C 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140470 restraints weight = 12528.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142892 restraints weight = 8216.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144519 restraints weight = 6044.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145783 restraints weight = 4846.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.146319 restraints weight = 4112.246| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8934 Z= 0.123 Angle : 0.574 8.423 12080 Z= 0.305 Chirality : 0.042 0.181 1406 Planarity : 0.003 0.035 1472 Dihedral : 6.967 62.966 1234 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.23 % Allowed : 18.66 % Favored : 77.11 % 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 are not related in a simple way. whole: 1.04 (0.25), residues: 1074 helix: 1.76 (0.20), residues: 611 sheet: -0.19 (0.51), residues: 100 loop : -0.89 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.021 0.001 TYR A 206 PHE 0.020 0.002 PHE B 187 TRP 0.017 0.001 TRP A 223 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8934) covalent geometry : angle 0.57434 / 0.30 (12080) hydrogen bonds : bond 0.04223 / 2.87 ( 539) hydrogen bonds : angle 4.65993 / 3.40 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7990 (m-80) cc_final: 0.7577 (t80) REVERT: A 38 MET cc_start: 0.6467 (mpp) cc_final: 0.6203 (mmp) REVERT: A 51 TYR cc_start: 0.7056 (m-80) cc_final: 0.6766 (m-80) REVERT: A 166 MET cc_start: 0.6010 (mmp) cc_final: 0.4551 (ttm) REVERT: B 37 LEU cc_start: 0.6616 (mt) cc_final: 0.6338 (mt) REVERT: B 38 MET cc_start: 0.6069 (tpt) cc_final: 0.5573 (tpt) REVERT: B 54 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8322 (m) REVERT: B 63 LEU cc_start: 0.8700 (mt) cc_final: 0.8271 (tp) REVERT: B 68 MET cc_start: 0.8609 (mmp) cc_final: 0.8346 (mmt) REVERT: B 80 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7754 (mm-40) REVERT: B 110 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8077 (tt) REVERT: B 116 TYR cc_start: 0.7314 (t80) cc_final: 0.6676 (t80) REVERT: B 156 LEU cc_start: 0.7895 (tp) cc_final: 0.7626 (tp) REVERT: B 239 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 37 VAL cc_start: 0.8884 (p) cc_final: 0.8659 (m) REVERT: C 46 MET cc_start: 0.7390 (mtp) cc_final: 0.7101 (mtp) REVERT: C 89 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: C 99 TYR cc_start: 0.7287 (t80) cc_final: 0.6843 (t80) REVERT: C 135 MET cc_start: 0.7336 (mmt) cc_final: 0.7007 (mmp) REVERT: C 189 ARG cc_start: 0.7693 (ptt180) cc_final: 0.7404 (ptt180) REVERT: C 270 ILE cc_start: 0.6689 (tt) cc_final: 0.6434 (mt) REVERT: D 135 MET cc_start: 0.8037 (mmm) cc_final: 0.7778 (mmt) REVERT: D 165 LEU cc_start: 0.8133 (mm) cc_final: 0.7617 (mt) REVERT: D 169 LEU cc_start: 0.7510 (tt) cc_final: 0.7260 (mm) REVERT: D 200 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 232 HIS cc_start: 0.4528 (m90) cc_final: 0.3689 (m90) REVERT: D 246 MET cc_start: 0.5772 (mpp) cc_final: 0.5093 (mpp) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.0777 time to fit residues: 24.9619 Evaluate side-chains 212 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134956 restraints weight = 12732.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137239 restraints weight = 8660.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138842 restraints weight = 6502.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140063 restraints weight = 5278.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140581 restraints weight = 4527.716| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8934 Z= 0.180 Angle : 0.655 7.754 12080 Z= 0.341 Chirality : 0.045 0.198 1406 Planarity : 0.004 0.038 1472 Dihedral : 7.103 60.262 1234 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.67 % Allowed : 18.76 % Favored : 75.57 % 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 are not related in a simple way. whole: 0.85 (0.25), residues: 1074 helix: 1.61 (0.20), residues: 611 sheet: -0.33 (0.49), residues: 105 loop : -0.95 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.021 0.002 TYR B 206 PHE 0.017 0.002 PHE B 155 TRP 0.019 0.002 TRP A 223 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8934) covalent geometry : angle 0.65471 / 0.34 (12080) hydrogen bonds : bond 0.04578 / 3.08 ( 539) hydrogen bonds : angle 4.72641 / 3.45 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6546 (mpp) cc_final: 0.6300 (mmp) REVERT: A 166 MET cc_start: 0.6151 (mmp) cc_final: 0.4614 (ttm) REVERT: B 2 ARG cc_start: 0.6733 (mtm-85) cc_final: 0.6147 (tmt170) REVERT: B 38 MET cc_start: 0.6171 (tpt) cc_final: 0.5875 (tpt) REVERT: B 63 LEU cc_start: 0.8766 (mt) cc_final: 0.8302 (tp) REVERT: B 110 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8017 (tt) REVERT: B 116 TYR cc_start: 0.7429 (t80) cc_final: 0.6796 (t80) REVERT: B 239 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 89 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: C 99 TYR cc_start: 0.7531 (t80) cc_final: 0.7209 (t80) REVERT: C 213 THR cc_start: 0.7112 (m) cc_final: 0.6666 (p) REVERT: C 234 GLN cc_start: 0.7540 (mt0) cc_final: 0.7223 (mt0) REVERT: C 270 ILE cc_start: 0.6675 (tt) cc_final: 0.6379 (mt) REVERT: D 150 MET cc_start: 0.7425 (mmm) cc_final: 0.6533 (mmm) REVERT: D 165 LEU cc_start: 0.8141 (mm) cc_final: 0.7844 (mt) REVERT: D 195 ASP cc_start: 0.8190 (m-30) cc_final: 0.7976 (m-30) REVERT: D 200 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7244 (tm-30) REVERT: D 246 MET cc_start: 0.6117 (mpp) cc_final: 0.5492 (mpp) REVERT: D 263 LEU cc_start: 0.5949 (mp) cc_final: 0.5433 (tp) REVERT: D 278 ARG cc_start: 0.7450 (ttt90) cc_final: 0.6725 (ttm-80) outliers start: 55 outliers final: 40 residues processed: 224 average time/residue: 0.0776 time to fit residues: 25.2638 Evaluate side-chains 223 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134664 restraints weight = 12601.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136887 restraints weight = 8619.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138411 restraints weight = 6547.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139184 restraints weight = 5355.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140109 restraints weight = 4755.928| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8934 Z= 0.160 Angle : 0.639 8.506 12080 Z= 0.333 Chirality : 0.044 0.274 1406 Planarity : 0.004 0.036 1472 Dihedral : 6.988 59.938 1234 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.57 % Allowed : 20.82 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1074 helix: 1.61 (0.20), residues: 610 sheet: -0.26 (0.51), residues: 100 loop : -0.99 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 110 TYR 0.022 0.002 TYR B 51 PHE 0.021 0.002 PHE A 187 TRP 0.019 0.002 TRP A 223 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8934) covalent geometry : angle 0.63886 / 0.33 (12080) hydrogen bonds : bond 0.04437 / 2.98 ( 539) hydrogen bonds : angle 4.69001 / 3.42 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6096 (mpp) cc_final: 0.5765 (mmp) REVERT: A 51 TYR cc_start: 0.7362 (m-80) cc_final: 0.7077 (m-80) REVERT: A 166 MET cc_start: 0.6255 (mmp) cc_final: 0.4702 (ttm) REVERT: B 2 ARG cc_start: 0.6626 (mtm-85) cc_final: 0.6130 (tmt170) REVERT: B 63 LEU cc_start: 0.8772 (mt) cc_final: 0.8309 (tp) REVERT: B 116 TYR cc_start: 0.7518 (t80) cc_final: 0.6874 (t80) REVERT: B 166 MET cc_start: 0.6903 (mmm) cc_final: 0.5951 (mmt) REVERT: B 239 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8385 (tp) REVERT: C 89 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 99 TYR cc_start: 0.7616 (t80) cc_final: 0.7307 (t80) REVERT: C 189 ARG cc_start: 0.7764 (ptt180) cc_final: 0.7220 (ptt180) REVERT: C 213 THR cc_start: 0.7026 (m) cc_final: 0.6753 (p) REVERT: C 234 GLN cc_start: 0.7628 (mt0) cc_final: 0.7302 (mt0) REVERT: D 150 MET cc_start: 0.7462 (mmm) cc_final: 0.6790 (mmm) REVERT: D 165 LEU cc_start: 0.8116 (mm) cc_final: 0.7764 (mt) REVERT: D 195 ASP cc_start: 0.8109 (m-30) cc_final: 0.7857 (m-30) REVERT: D 200 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7310 (tm-30) REVERT: D 263 LEU cc_start: 0.6012 (mp) cc_final: 0.5664 (tt) REVERT: D 278 ARG cc_start: 0.7282 (ttt90) cc_final: 0.6724 (ttm-80) outliers start: 54 outliers final: 41 residues processed: 218 average time/residue: 0.0755 time to fit residues: 23.8734 Evaluate side-chains 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135558 restraints weight = 12719.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137870 restraints weight = 8698.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139455 restraints weight = 6558.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140476 restraints weight = 5356.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141275 restraints weight = 4646.375| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8934 Z= 0.135 Angle : 0.630 10.467 12080 Z= 0.328 Chirality : 0.044 0.257 1406 Planarity : 0.003 0.035 1472 Dihedral : 6.750 59.691 1234 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.33 % Allowed : 22.89 % Favored : 72.78 % 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 are not related in a simple way. whole: 0.90 (0.25), residues: 1074 helix: 1.67 (0.20), residues: 611 sheet: -0.53 (0.49), residues: 105 loop : -0.92 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 110 TYR 0.018 0.001 TYR D 99 PHE 0.015 0.001 PHE C 21 TRP 0.017 0.002 TRP A 223 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8934) covalent geometry : angle 0.63031 / 0.33 (12080) hydrogen bonds : bond 0.04161 / 2.80 ( 539) hydrogen bonds : angle 4.66817 / 3.40 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7385 (m-80) cc_final: 0.7119 (m-80) REVERT: A 166 MET cc_start: 0.6192 (mmp) cc_final: 0.4679 (ttm) REVERT: B 2 ARG cc_start: 0.6643 (mtm-85) cc_final: 0.6112 (tmt170) REVERT: B 63 LEU cc_start: 0.8653 (mt) cc_final: 0.8269 (tp) REVERT: B 116 TYR cc_start: 0.7489 (t80) cc_final: 0.6790 (t80) REVERT: B 129 LYS cc_start: 0.6838 (tptp) cc_final: 0.6527 (tptp) REVERT: B 239 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8341 (tp) REVERT: C 89 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: C 99 TYR cc_start: 0.7560 (t80) cc_final: 0.7261 (t80) REVERT: C 189 ARG cc_start: 0.7718 (ptt180) cc_final: 0.7178 (ptt180) REVERT: C 213 THR cc_start: 0.6986 (m) cc_final: 0.6713 (p) REVERT: C 234 GLN cc_start: 0.7633 (mt0) cc_final: 0.7356 (mt0) REVERT: D 150 MET cc_start: 0.7565 (mmm) cc_final: 0.7296 (mmm) REVERT: D 195 ASP cc_start: 0.8126 (m-30) cc_final: 0.7853 (m-30) REVERT: D 200 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7348 (tm-30) REVERT: D 246 MET cc_start: 0.6745 (mpp) cc_final: 0.6199 (mpp) REVERT: D 263 LEU cc_start: 0.5919 (mp) cc_final: 0.5563 (tt) REVERT: D 278 ARG cc_start: 0.7202 (ttt90) cc_final: 0.6611 (ttm-80) outliers start: 42 outliers final: 36 residues processed: 217 average time/residue: 0.0758 time to fit residues: 24.3719 Evaluate side-chains 221 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS B 84 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135525 restraints weight = 12691.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137841 restraints weight = 8662.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139260 restraints weight = 6544.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140462 restraints weight = 5407.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141146 restraints weight = 4671.386| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8934 Z= 0.139 Angle : 0.645 9.429 12080 Z= 0.335 Chirality : 0.044 0.251 1406 Planarity : 0.004 0.035 1472 Dihedral : 6.671 59.170 1234 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.33 % Allowed : 23.71 % Favored : 71.96 % 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 are not related in a simple way. whole: 0.90 (0.25), residues: 1074 helix: 1.67 (0.20), residues: 611 sheet: -0.46 (0.49), residues: 105 loop : -0.94 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 110 TYR 0.020 0.002 TYR D 112 PHE 0.022 0.002 PHE A 187 TRP 0.019 0.002 TRP B 60 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8934) covalent geometry : angle 0.64518 / 0.33 (12080) hydrogen bonds : bond 0.04174 / 2.82 ( 539) hydrogen bonds : angle 4.68397 / 3.43 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7416 (m-80) cc_final: 0.7157 (m-80) REVERT: A 166 MET cc_start: 0.6199 (mmp) cc_final: 0.4645 (ttm) REVERT: B 2 ARG cc_start: 0.6660 (mtm-85) cc_final: 0.5998 (tmt170) REVERT: B 9 TYR cc_start: 0.7813 (m-80) cc_final: 0.7469 (t80) REVERT: B 38 MET cc_start: 0.6055 (tpt) cc_final: 0.5787 (tpt) REVERT: B 63 LEU cc_start: 0.8726 (mt) cc_final: 0.8294 (tp) REVERT: B 116 TYR cc_start: 0.7491 (t80) cc_final: 0.6794 (t80) REVERT: B 129 LYS cc_start: 0.6825 (tptp) cc_final: 0.6527 (tptp) REVERT: B 239 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8219 (tp) REVERT: C 46 MET cc_start: 0.8072 (mtp) cc_final: 0.7664 (mtp) REVERT: C 89 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: C 99 TYR cc_start: 0.7553 (t80) cc_final: 0.7298 (t80) REVERT: C 189 ARG cc_start: 0.7748 (ptt180) cc_final: 0.7244 (ptt180) REVERT: C 213 THR cc_start: 0.6989 (m) cc_final: 0.6457 (p) REVERT: C 221 ASP cc_start: 0.4760 (m-30) cc_final: 0.3607 (p0) REVERT: C 234 GLN cc_start: 0.7674 (mt0) cc_final: 0.7377 (mt0) REVERT: C 246 MET cc_start: 0.6185 (mpp) cc_final: 0.5885 (mmp) REVERT: D 109 MET cc_start: 0.8101 (mtm) cc_final: 0.7547 (mtm) REVERT: D 200 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 246 MET cc_start: 0.6751 (mpp) cc_final: 0.6529 (mpp) REVERT: D 278 ARG cc_start: 0.7049 (ttt90) cc_final: 0.6473 (ttm-80) outliers start: 42 outliers final: 35 residues processed: 219 average time/residue: 0.0782 time to fit residues: 25.3151 Evaluate side-chains 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136131 restraints weight = 12662.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138484 restraints weight = 8644.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140093 restraints weight = 6535.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141256 restraints weight = 5326.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142054 restraints weight = 4604.917| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8934 Z= 0.131 Angle : 0.633 11.262 12080 Z= 0.329 Chirality : 0.044 0.256 1406 Planarity : 0.003 0.034 1472 Dihedral : 6.573 58.475 1234 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.61 % Allowed : 24.23 % Favored : 72.16 % 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 are not related in a simple way. whole: 0.93 (0.25), residues: 1074 helix: 1.68 (0.20), residues: 611 sheet: -0.37 (0.50), residues: 105 loop : -0.91 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.023 0.001 TYR D 112 PHE 0.021 0.002 PHE A 187 TRP 0.021 0.002 TRP A 223 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8934) covalent geometry : angle 0.63266 / 0.33 (12080) hydrogen bonds : bond 0.04068 / 2.75 ( 539) hydrogen bonds : angle 4.67985 / 3.43 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.73 seconds wall clock time: 25 minutes 1.44 seconds (1501.44 seconds total)