Starting phenix.real_space_refine on Tue Mar 3 21:14:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xji_22211/03_2026/6xji_22211_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xji_22211/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2026/6xji_22211_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2026/6xji_22211_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2026/6xji_22211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2026/6xji_22211.map" } 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-dev-5986/lib/python3.9/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: 2.31, per 1000 atoms: 0.26 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: 0.80 Conformation dependent library (CDL) restraints added in 316.7 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: 0.27 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: 1.31 Time building geometry restraints manager: 1.07 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: 11096 2.68 - 5.35: 855 5.35 - 8.03: 106 8.03 - 10.71: 14 10.71 - 13.39: 9 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 - 22.45: 5162 22.45 - 44.89: 134 44.89 - 67.34: 32 67.34 - 89.78: 12 89.78 - 112.23: 2 Dihedral angle restraints: 5342 sinusoidal: 2174 harmonic: 3168 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.50 -112.23 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O1A AGS D 301 " pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " pdb=" PB AGS D 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.46 -112.19 1 3.00e+01 1.11e-03 1.47e+01 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 ... (remaining 5339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 808 0.067 - 0.134: 420 0.134 - 0.201: 130 0.201 - 0.268: 40 0.268 - 0.335: 12 Chirality restraints: 1410 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 1407 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.140 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: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 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= 1.015 Angle : 1.602 13.386 12080 Z= 1.098 Chirality : 0.092 0.335 1410 Planarity : 0.008 0.044 1472 Dihedral : 12.076 112.230 3298 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 covalent geometry : bond 0.01825 ( 8934) covalent geometry : angle 1.60222 (12080) hydrogen bonds : bond 0.16130 ( 539) hydrogen bonds : angle 6.88848 ( 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 : 0.364 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: 0.1004 time to fit residues: 52.9924 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 : 0.318 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 237 ASN D 5 HIS D 35 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149621 restraints weight = 12021.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152418 restraints weight = 8137.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154016 restraints weight = 6114.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155512 restraints weight = 5069.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156549 restraints weight = 4360.227| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8934 Z= 0.170 Angle : 0.703 8.980 12080 Z= 0.378 Chirality : 0.048 0.325 1410 Planarity : 0.004 0.032 1472 Dihedral : 10.354 123.494 1205 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.51 % Allowed : 11.34 % 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: 1.55 (0.25), residues: 1074 helix: 2.00 (0.20), residues: 602 sheet: 0.91 (0.59), residues: 86 loop : -0.50 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 224 TYR 0.030 0.002 TYR C 228 PHE 0.036 0.002 PHE C 107 TRP 0.030 0.002 TRP A 223 HIS 0.007 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8934) covalent geometry : angle 0.70330 (12080) hydrogen bonds : bond 0.05848 ( 539) hydrogen bonds : angle 5.17953 ( 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 289 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.6998 (m-80) cc_final: 0.6771 (m-80) REVERT: A 166 MET cc_start: 0.6008 (mmp) cc_final: 0.4782 (ttm) REVERT: B 68 MET cc_start: 0.8205 (mmm) cc_final: 0.7856 (mmp) REVERT: B 116 TYR cc_start: 0.7192 (t80) cc_final: 0.6594 (t80) REVERT: B 144 LEU cc_start: 0.8600 (mt) cc_final: 0.8397 (tt) REVERT: B 222 GLN cc_start: 0.7485 (tt0) cc_final: 0.6976 (mt0) REVERT: B 239 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8362 (tt) REVERT: C 5 HIS cc_start: 0.5024 (m-70) cc_final: 0.4606 (m90) REVERT: C 37 VAL cc_start: 0.8912 (p) cc_final: 0.8609 (m) REVERT: C 43 MET cc_start: 0.6931 (mtm) cc_final: 0.6714 (mtm) REVERT: C 77 ASN cc_start: 0.7731 (m110) cc_final: 0.7401 (m110) REVERT: C 89 GLN cc_start: 0.8004 (mt0) cc_final: 0.7508 (mt0) REVERT: C 124 MET cc_start: 0.8283 (mtm) cc_final: 0.8018 (mtm) REVERT: D 5 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6384 (m170) REVERT: D 37 VAL cc_start: 0.8843 (p) cc_final: 0.8629 (p) REVERT: D 77 ASN cc_start: 0.7171 (p0) cc_final: 0.6584 (m-40) REVERT: D 165 LEU cc_start: 0.8395 (mt) cc_final: 0.8160 (mt) outliers start: 34 outliers final: 21 residues processed: 275 average time/residue: 0.0884 time to fit residues: 34.3280 Evaluate side-chains 218 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 161 SER 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 C residue 214 ILE 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: 3.9990 chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 89 GLN D 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.162533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138393 restraints weight = 12344.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.140885 restraints weight = 8576.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142352 restraints weight = 6591.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143745 restraints weight = 5522.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144481 restraints weight = 4801.152| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8934 Z= 0.173 Angle : 0.646 10.983 12080 Z= 0.343 Chirality : 0.045 0.226 1410 Planarity : 0.004 0.036 1472 Dihedral : 9.929 115.467 1201 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.85 % Allowed : 15.46 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1074 helix: 1.94 (0.20), residues: 602 sheet: -0.25 (0.53), residues: 100 loop : -0.58 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 110 TYR 0.021 0.002 TYR B 51 PHE 0.023 0.002 PHE C 107 TRP 0.021 0.002 TRP B 223 HIS 0.006 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8934) covalent geometry : angle 0.64582 (12080) hydrogen bonds : bond 0.05281 ( 539) hydrogen bonds : angle 4.87733 ( 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 255 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7179 (m-80) cc_final: 0.6815 (m-80) REVERT: A 166 MET cc_start: 0.6256 (mmp) cc_final: 0.5185 (ttm) REVERT: B 11 LEU cc_start: 0.8942 (mt) cc_final: 0.8676 (mt) REVERT: B 63 LEU cc_start: 0.8692 (mt) cc_final: 0.8331 (tp) REVERT: B 101 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (m) REVERT: B 110 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8046 (tt) REVERT: B 116 TYR cc_start: 0.7382 (t80) cc_final: 0.6866 (t80) REVERT: B 239 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8370 (tp) REVERT: C 37 VAL cc_start: 0.8959 (p) cc_final: 0.8652 (m) REVERT: C 82 TYR cc_start: 0.6880 (t80) cc_final: 0.6663 (t80) REVERT: C 89 GLN cc_start: 0.8208 (mt0) cc_final: 0.7930 (mt0) REVERT: C 99 TYR cc_start: 0.7156 (t80) cc_final: 0.6917 (t80) REVERT: C 246 MET cc_start: 0.6525 (mpp) cc_final: 0.6209 (mmp) REVERT: D 35 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7488 (p0) REVERT: D 194 ARG cc_start: 0.7603 (tmt170) cc_final: 0.7069 (tmt170) REVERT: D 200 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6949 (tm-30) REVERT: D 263 LEU cc_start: 0.5257 (tp) cc_final: 0.5010 (mp) outliers start: 47 outliers final: 32 residues processed: 237 average time/residue: 0.0823 time to fit residues: 28.1715 Evaluate side-chains 218 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 210 LYS 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 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 101 THR Chi-restraints excluded: chain B residue 110 LEU 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 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 124 MET 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 47 ASN C 148 ASN C 197 HIS C 234 GLN C 254 GLN D 5 HIS D 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143775 restraints weight = 12320.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146308 restraints weight = 8476.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148105 restraints weight = 6442.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149111 restraints weight = 5281.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.150024 restraints weight = 4646.437| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4796 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= 0.140 Angle : 0.611 10.320 12080 Z= 0.320 Chirality : 0.044 0.379 1410 Planarity : 0.003 0.036 1472 Dihedral : 9.324 115.391 1198 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.74 % Allowed : 16.91 % Favored : 78.35 % 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: 1.15 (0.25), residues: 1074 helix: 1.84 (0.20), residues: 603 sheet: -0.37 (0.52), residues: 100 loop : -0.70 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.022 0.001 TYR A 206 PHE 0.031 0.002 PHE C 107 TRP 0.019 0.002 TRP A 223 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8934) covalent geometry : angle 0.61146 (12080) hydrogen bonds : bond 0.04707 ( 539) hydrogen bonds : angle 4.77437 ( 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 243 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7256 (m-80) cc_final: 0.6966 (m-80) REVERT: A 166 MET cc_start: 0.6072 (mmp) cc_final: 0.4850 (ttm) REVERT: B 11 LEU cc_start: 0.8844 (mt) cc_final: 0.8569 (mt) REVERT: B 63 LEU cc_start: 0.8673 (mt) cc_final: 0.8299 (tp) REVERT: B 80 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7809 (mm-40) REVERT: B 110 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8142 (tt) REVERT: B 116 TYR cc_start: 0.7345 (t80) cc_final: 0.6871 (t80) REVERT: B 239 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8370 (tp) REVERT: C 37 VAL cc_start: 0.9033 (p) cc_final: 0.8764 (m) REVERT: C 82 TYR cc_start: 0.7032 (t80) cc_final: 0.6757 (t80) REVERT: C 89 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: C 99 TYR cc_start: 0.7285 (t80) cc_final: 0.7075 (t80) REVERT: C 197 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.5663 (p-80) REVERT: D 135 MET cc_start: 0.7999 (mmm) cc_final: 0.7652 (mmt) REVERT: D 200 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7112 (tm-30) outliers start: 46 outliers final: 32 residues processed: 225 average time/residue: 0.0791 time to fit residues: 26.2832 Evaluate side-chains 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 VAL 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 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 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 197 HIS Chi-restraints excluded: chain C residue 214 ILE 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 176 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN C 285 ASN D 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.165376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142529 restraints weight = 12208.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144562 restraints weight = 9515.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146389 restraints weight = 7201.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147309 restraints weight = 5570.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147682 restraints weight = 5002.232| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8934 Z= 0.157 Angle : 0.609 9.463 12080 Z= 0.323 Chirality : 0.044 0.305 1410 Planarity : 0.004 0.039 1472 Dihedral : 9.142 115.708 1198 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.15 % Allowed : 18.35 % Favored : 76.49 % 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: 0.98 (0.25), residues: 1074 helix: 1.80 (0.20), residues: 601 sheet: -0.56 (0.51), residues: 100 loop : -0.89 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.020 0.002 TYR A 206 PHE 0.017 0.002 PHE C 107 TRP 0.017 0.001 TRP A 223 HIS 0.022 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8934) covalent geometry : angle 0.60908 (12080) hydrogen bonds : bond 0.04593 ( 539) hydrogen bonds : angle 4.71047 ( 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 250 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8057 (m-80) cc_final: 0.7676 (t80) REVERT: A 38 MET cc_start: 0.6495 (mpp) cc_final: 0.6066 (mmp) REVERT: A 51 TYR cc_start: 0.7129 (m-80) cc_final: 0.6913 (m-80) REVERT: A 166 MET cc_start: 0.6051 (mmp) cc_final: 0.4910 (ttm) REVERT: B 11 LEU cc_start: 0.8830 (mt) cc_final: 0.8538 (mt) REVERT: B 38 MET cc_start: 0.5167 (tpt) cc_final: 0.4735 (tpt) REVERT: B 63 LEU cc_start: 0.8591 (mt) cc_final: 0.8178 (tp) REVERT: B 110 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8047 (tt) REVERT: B 116 TYR cc_start: 0.7471 (t80) cc_final: 0.6972 (t80) REVERT: B 239 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 37 VAL cc_start: 0.9096 (p) cc_final: 0.8824 (m) REVERT: C 82 TYR cc_start: 0.7208 (t80) cc_final: 0.6863 (t80) REVERT: C 89 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: C 99 TYR cc_start: 0.7395 (t80) cc_final: 0.7140 (t80) REVERT: C 135 MET cc_start: 0.6955 (mmp) cc_final: 0.6656 (mmp) REVERT: C 213 THR cc_start: 0.7193 (m) cc_final: 0.6811 (p) REVERT: C 270 ILE cc_start: 0.6691 (tt) cc_final: 0.6383 (mt) REVERT: D 35 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7359 (p0) REVERT: D 135 MET cc_start: 0.8159 (mmm) cc_final: 0.7853 (mmt) REVERT: D 150 MET cc_start: 0.7701 (mmm) cc_final: 0.7061 (mmm) REVERT: D 165 LEU cc_start: 0.8035 (mt) cc_final: 0.7750 (mm) REVERT: D 200 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7099 (tm-30) REVERT: D 246 MET cc_start: 0.6242 (mpp) cc_final: 0.5269 (mpp) REVERT: D 278 ARG cc_start: 0.7409 (ttt90) cc_final: 0.6782 (ttm-80) outliers start: 50 outliers final: 36 residues processed: 228 average time/residue: 0.0806 time to fit residues: 26.6435 Evaluate side-chains 218 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 235 ILE 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 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 D residue 14 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL 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 216 THR 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: 0.6980 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 237 ASN C 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144571 restraints weight = 12186.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.146303 restraints weight = 9444.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148064 restraints weight = 7249.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.149483 restraints weight = 5612.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149895 restraints weight = 4885.035| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8934 Z= 0.131 Angle : 0.613 14.183 12080 Z= 0.318 Chirality : 0.043 0.159 1410 Planarity : 0.003 0.035 1472 Dihedral : 8.915 114.773 1198 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.74 % Allowed : 18.76 % Favored : 76.49 % 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: 1.00 (0.25), residues: 1074 helix: 1.79 (0.20), residues: 609 sheet: -0.49 (0.51), residues: 100 loop : -0.91 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 172 TYR 0.021 0.001 TYR A 206 PHE 0.020 0.002 PHE A 187 TRP 0.017 0.001 TRP A 223 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8934) covalent geometry : angle 0.61267 (12080) hydrogen bonds : bond 0.04342 ( 539) hydrogen bonds : angle 4.62587 ( 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 246 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8043 (m-80) cc_final: 0.7650 (t80) REVERT: A 166 MET cc_start: 0.6201 (mmp) cc_final: 0.4891 (ttm) REVERT: B 11 LEU cc_start: 0.8790 (mt) cc_final: 0.8478 (mt) REVERT: B 38 MET cc_start: 0.5887 (tpt) cc_final: 0.5322 (tpt) REVERT: B 68 MET cc_start: 0.8602 (mmp) cc_final: 0.8324 (mmt) REVERT: B 110 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (tt) REVERT: B 116 TYR cc_start: 0.7394 (t80) cc_final: 0.6758 (t80) REVERT: B 239 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8373 (tp) REVERT: C 37 VAL cc_start: 0.9121 (p) cc_final: 0.8859 (m) REVERT: C 82 TYR cc_start: 0.7037 (t80) cc_final: 0.6727 (t80) REVERT: C 89 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: C 99 TYR cc_start: 0.7318 (t80) cc_final: 0.6895 (t80) REVERT: C 135 MET cc_start: 0.7150 (mmp) cc_final: 0.6850 (mmp) REVERT: C 189 ARG cc_start: 0.7729 (ptt180) cc_final: 0.7306 (ptt180) REVERT: C 213 THR cc_start: 0.7106 (m) cc_final: 0.6661 (p) REVERT: C 234 GLN cc_start: 0.7108 (mt0) cc_final: 0.6827 (mt0) REVERT: C 270 ILE cc_start: 0.6695 (tt) cc_final: 0.6393 (mt) REVERT: D 135 MET cc_start: 0.7925 (mmm) cc_final: 0.7677 (mmt) REVERT: D 165 LEU cc_start: 0.8202 (mt) cc_final: 0.7843 (mm) REVERT: D 200 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 246 MET cc_start: 0.6217 (mpp) cc_final: 0.5445 (mpp) REVERT: D 263 LEU cc_start: 0.5431 (tt) cc_final: 0.4671 (mp) REVERT: D 278 ARG cc_start: 0.7467 (ttt90) cc_final: 0.6636 (ttm-80) outliers start: 46 outliers final: 33 residues processed: 230 average time/residue: 0.0800 time to fit residues: 27.0953 Evaluate side-chains 218 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 117 VAL 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 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 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 20 ASP 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 186 ILE 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 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=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: 0.9990 chunk 88 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.159830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137865 restraints weight = 12633.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140232 restraints weight = 8544.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141610 restraints weight = 6408.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142930 restraints weight = 5303.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143604 restraints weight = 4551.083| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8934 Z= 0.131 Angle : 0.608 12.816 12080 Z= 0.318 Chirality : 0.042 0.146 1410 Planarity : 0.003 0.035 1472 Dihedral : 8.736 114.073 1198 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.74 % Allowed : 20.10 % Favored : 75.15 % 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: 1.05 (0.25), residues: 1074 helix: 1.84 (0.20), residues: 608 sheet: -0.37 (0.51), residues: 100 loop : -0.95 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 172 TYR 0.019 0.002 TYR A 206 PHE 0.012 0.001 PHE A 153 TRP 0.019 0.002 TRP A 223 HIS 0.005 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8934) covalent geometry : angle 0.60835 (12080) hydrogen bonds : bond 0.04265 ( 539) hydrogen bonds : angle 4.63828 ( 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 237 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 12 TYR cc_start: 0.8035 (m-80) cc_final: 0.7709 (t80) REVERT: A 166 MET cc_start: 0.6382 (mmp) cc_final: 0.4494 (ttm) REVERT: A 170 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 11 LEU cc_start: 0.8672 (mt) cc_final: 0.8209 (mt) REVERT: B 38 MET cc_start: 0.6124 (tpt) cc_final: 0.5781 (tpt) REVERT: B 110 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 116 TYR cc_start: 0.7395 (t80) cc_final: 0.6743 (t80) REVERT: B 239 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8308 (tp) REVERT: C 43 MET cc_start: 0.7130 (mpp) cc_final: 0.6845 (mpp) REVERT: C 89 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: C 99 TYR cc_start: 0.7462 (t80) cc_final: 0.7121 (t80) REVERT: C 135 MET cc_start: 0.7146 (mmp) cc_final: 0.6793 (mmp) REVERT: C 189 ARG cc_start: 0.7706 (ptt180) cc_final: 0.7199 (ptt180) REVERT: C 213 THR cc_start: 0.7057 (m) cc_final: 0.6610 (p) REVERT: C 234 GLN cc_start: 0.7174 (mt0) cc_final: 0.6866 (mt0) REVERT: C 270 ILE cc_start: 0.6649 (tt) cc_final: 0.6343 (mt) REVERT: D 150 MET cc_start: 0.7419 (mmm) cc_final: 0.7070 (mmm) REVERT: D 165 LEU cc_start: 0.8202 (mt) cc_final: 0.7898 (mm) REVERT: D 200 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7106 (tm-30) REVERT: D 246 MET cc_start: 0.5861 (mpp) cc_final: 0.5574 (mpp) REVERT: D 263 LEU cc_start: 0.5393 (tt) cc_final: 0.4681 (mp) REVERT: D 278 ARG cc_start: 0.7169 (ttt90) cc_final: 0.6635 (ttm-80) outliers start: 46 outliers final: 33 residues processed: 219 average time/residue: 0.0836 time to fit residues: 26.6238 Evaluate side-chains 219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 202 ILE 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 110 LEU 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 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 157 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136101 restraints weight = 12571.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138338 restraints weight = 8605.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139904 restraints weight = 6546.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141091 restraints weight = 5355.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141656 restraints weight = 4613.291| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8934 Z= 0.149 Angle : 0.643 12.610 12080 Z= 0.334 Chirality : 0.044 0.266 1410 Planarity : 0.004 0.035 1472 Dihedral : 8.651 110.707 1198 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.43 % Allowed : 21.44 % Favored : 74.12 % 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: 0.94 (0.25), residues: 1074 helix: 1.74 (0.20), residues: 610 sheet: -0.39 (0.51), residues: 100 loop : -0.99 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.017 0.002 TYR A 206 PHE 0.021 0.002 PHE A 187 TRP 0.019 0.002 TRP A 223 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8934) covalent geometry : angle 0.64308 (12080) hydrogen bonds : bond 0.04284 ( 539) hydrogen bonds : angle 4.67744 ( 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 231 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.6363 (mmp) cc_final: 0.4790 (ttm) REVERT: B 2 ARG cc_start: 0.6548 (mtm-85) cc_final: 0.6066 (tmt170) REVERT: B 38 MET cc_start: 0.6142 (tpt) cc_final: 0.5873 (tpt) REVERT: B 116 TYR cc_start: 0.7437 (t80) cc_final: 0.6818 (t80) REVERT: B 166 MET cc_start: 0.6829 (mmm) cc_final: 0.5872 (mmt) REVERT: B 239 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8383 (tp) REVERT: C 43 MET cc_start: 0.7210 (mpp) cc_final: 0.6688 (mpp) REVERT: C 89 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: C 99 TYR cc_start: 0.7520 (t80) cc_final: 0.7307 (t80) REVERT: C 189 ARG cc_start: 0.7701 (ptt180) cc_final: 0.7208 (ptt180) REVERT: C 213 THR cc_start: 0.7021 (m) cc_final: 0.6726 (p) REVERT: C 221 ASP cc_start: 0.5036 (m-30) cc_final: 0.3988 (p0) REVERT: C 234 GLN cc_start: 0.7305 (mt0) cc_final: 0.6995 (mt0) REVERT: C 270 ILE cc_start: 0.6644 (tt) cc_final: 0.6350 (mt) REVERT: D 150 MET cc_start: 0.7313 (mmm) cc_final: 0.6964 (mmm) REVERT: D 165 LEU cc_start: 0.8162 (mt) cc_final: 0.7823 (mm) REVERT: D 200 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 246 MET cc_start: 0.5982 (mpp) cc_final: 0.5750 (mpp) REVERT: D 263 LEU cc_start: 0.5328 (tt) cc_final: 0.4706 (mp) REVERT: D 278 ARG cc_start: 0.7293 (ttt90) cc_final: 0.6624 (ttm-80) outliers start: 43 outliers final: 33 residues processed: 215 average time/residue: 0.0812 time to fit residues: 25.5407 Evaluate side-chains 216 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 VAL 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 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 172 VAL 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 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 217 VAL 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: 4.9990 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135730 restraints weight = 12658.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137988 restraints weight = 8694.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139613 restraints weight = 6605.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140562 restraints weight = 5385.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141457 restraints weight = 4737.182| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8934 Z= 0.149 Angle : 0.654 12.539 12080 Z= 0.336 Chirality : 0.043 0.243 1410 Planarity : 0.003 0.034 1472 Dihedral : 8.594 109.814 1198 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.64 % Allowed : 22.06 % Favored : 73.30 % 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: 0.92 (0.25), residues: 1074 helix: 1.73 (0.20), residues: 610 sheet: -0.44 (0.51), residues: 100 loop : -0.99 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 110 TYR 0.050 0.002 TYR A 206 PHE 0.014 0.001 PHE C 198 TRP 0.019 0.002 TRP A 223 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8934) covalent geometry : angle 0.65353 (12080) hydrogen bonds : bond 0.04247 ( 539) hydrogen bonds : angle 4.67306 ( 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: 45 poor density : 192 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 166 MET cc_start: 0.6386 (mmp) cc_final: 0.4795 (ttm) REVERT: A 222 GLN cc_start: 0.6513 (tt0) cc_final: 0.6201 (mt0) REVERT: B 2 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.6050 (tmt170) REVERT: B 38 MET cc_start: 0.6180 (tpt) cc_final: 0.5937 (tpt) REVERT: B 116 TYR cc_start: 0.7446 (t80) cc_final: 0.6822 (t80) REVERT: B 239 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 89 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: C 99 TYR cc_start: 0.7633 (t80) cc_final: 0.7358 (t80) REVERT: C 189 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7224 (ptt180) REVERT: C 213 THR cc_start: 0.6999 (m) cc_final: 0.6733 (p) REVERT: C 221 ASP cc_start: 0.5054 (m-30) cc_final: 0.3965 (p0) REVERT: C 234 GLN cc_start: 0.7329 (mt0) cc_final: 0.7012 (mt0) REVERT: D 165 LEU cc_start: 0.8141 (mt) cc_final: 0.7827 (mm) REVERT: D 200 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7216 (tm-30) REVERT: D 263 LEU cc_start: 0.5318 (tt) cc_final: 0.4713 (mp) REVERT: D 278 ARG cc_start: 0.7302 (ttt90) cc_final: 0.6617 (ttm-80) outliers start: 45 outliers final: 37 residues processed: 217 average time/residue: 0.0809 time to fit residues: 25.3675 Evaluate side-chains 223 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 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 82 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 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 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 47 ASN 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 217 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.158923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136785 restraints weight = 12590.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139076 restraints weight = 8581.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140582 restraints weight = 6492.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141738 restraints weight = 5343.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142289 restraints weight = 4637.196| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.6133 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= 0.138 Angle : 0.644 12.330 12080 Z= 0.334 Chirality : 0.043 0.258 1410 Planarity : 0.003 0.034 1472 Dihedral : 8.473 107.924 1198 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.81 % Allowed : 22.99 % Favored : 73.20 % 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: 0.94 (0.25), residues: 1074 helix: 1.76 (0.20), residues: 610 sheet: -0.45 (0.51), residues: 100 loop : -1.01 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 110 TYR 0.052 0.002 TYR A 206 PHE 0.024 0.002 PHE A 187 TRP 0.018 0.002 TRP A 223 HIS 0.007 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8934) covalent geometry : angle 0.64357 (12080) hydrogen bonds : bond 0.04090 ( 539) hydrogen bonds : angle 4.64763 ( 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 231 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.337 Fit side-chains REVERT: A 166 MET cc_start: 0.6417 (mmp) cc_final: 0.4802 (ttm) REVERT: A 222 GLN cc_start: 0.6397 (tt0) cc_final: 0.6093 (mt0) REVERT: B 2 ARG cc_start: 0.6473 (mtm-85) cc_final: 0.5940 (tmt170) REVERT: B 116 TYR cc_start: 0.7451 (t80) cc_final: 0.6812 (t80) REVERT: B 166 MET cc_start: 0.6745 (mmm) cc_final: 0.5736 (mmt) REVERT: B 239 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 89 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: C 99 TYR cc_start: 0.7622 (t80) cc_final: 0.7336 (t80) REVERT: C 189 ARG cc_start: 0.7679 (ptt180) cc_final: 0.7235 (ptt180) REVERT: C 213 THR cc_start: 0.6972 (m) cc_final: 0.6708 (p) REVERT: C 221 ASP cc_start: 0.5046 (m-30) cc_final: 0.3970 (p0) REVERT: C 234 GLN cc_start: 0.7371 (mt0) cc_final: 0.7074 (mt0) REVERT: D 165 LEU cc_start: 0.8084 (mt) cc_final: 0.7793 (mm) REVERT: D 200 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7214 (tm-30) REVERT: D 246 MET cc_start: 0.6672 (mpp) cc_final: 0.6288 (mpp) REVERT: D 263 LEU cc_start: 0.5154 (tt) cc_final: 0.4580 (mp) REVERT: D 278 ARG cc_start: 0.7328 (ttt90) cc_final: 0.6613 (ttm-80) outliers start: 37 outliers final: 33 residues processed: 213 average time/residue: 0.0709 time to fit residues: 22.3847 Evaluate side-chains 222 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 82 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 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 49 ILE Chi-restraints excluded: chain B residue 70 VAL 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 47 ASN 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 191 VAL Chi-restraints excluded: chain D residue 217 VAL 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: 2.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134847 restraints weight = 12764.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137138 restraints weight = 8709.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138728 restraints weight = 6560.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139659 restraints weight = 5373.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140524 restraints weight = 4709.138| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.6246 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= 0.146 Angle : 0.665 12.306 12080 Z= 0.343 Chirality : 0.044 0.249 1410 Planarity : 0.004 0.035 1472 Dihedral : 8.388 105.795 1198 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.12 % Allowed : 23.09 % 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: 0.93 (0.25), residues: 1074 helix: 1.75 (0.20), residues: 608 sheet: -0.34 (0.50), residues: 105 loop : -1.06 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 110 TYR 0.051 0.002 TYR A 206 PHE 0.015 0.001 PHE C 198 TRP 0.019 0.002 TRP A 223 HIS 0.006 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8934) covalent geometry : angle 0.66473 (12080) hydrogen bonds : bond 0.04133 ( 539) hydrogen bonds : angle 4.63990 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1418.81 seconds wall clock time: 25 minutes 17.84 seconds (1517.84 seconds total)