Starting phenix.real_space_refine on Sat Aug 23 01:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfx_37207/08_2025/8kfx_37207.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5762 2.51 5 N 1506 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9001 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OS9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 9001 At special positions: 0 Unit cell: (89.44, 121.68, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1667 8.00 N 1506 7.00 C 5762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 235.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.534A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.666A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.962A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.727A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.663A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.749A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix removed outlier: 3.777A pdb=" N VAL R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.537A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET R 202 " --> pdb=" O THR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.523A pdb=" N ARG R 227 " --> pdb=" O HIS R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 291 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.785A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.512A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.552A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.339A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.927A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.704A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.538A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.301A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.814A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.843A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1320 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: 1.04 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2861 1.34 - 1.46: 2235 1.46 - 1.58: 4001 1.58 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9193 Sorted by residual: bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.473 1.624 -0.151 1.40e-02 5.10e+03 1.17e+02 bond pdb=" N ARG S 67 " pdb=" CA ARG S 67 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.06e+00 bond pdb=" N PHE R 290 " pdb=" CA PHE R 290 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.31e-02 5.83e+03 7.05e+00 bond pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.29e-02 6.01e+03 6.69e+00 bond pdb=" N SER R 289 " pdb=" CA SER R 289 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.18e-02 7.18e+03 5.73e+00 ... (remaining 9188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12301 2.29 - 4.57: 119 4.57 - 6.86: 18 6.86 - 9.15: 5 9.15 - 11.43: 1 Bond angle restraints: 12444 Sorted by residual: angle pdb=" N THR R 291 " pdb=" CA THR R 291 " pdb=" C THR R 291 " ideal model delta sigma weight residual 112.34 107.46 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 121.80 113.02 8.78 2.44e+00 1.68e-01 1.29e+01 angle pdb=" CA PHE R 290 " pdb=" CB PHE R 290 " pdb=" CG PHE R 290 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA LEU R 205 " pdb=" CB LEU R 205 " pdb=" CG LEU R 205 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 ... (remaining 12439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4718 17.91 - 35.82: 558 35.82 - 53.73: 162 53.73 - 71.65: 22 71.65 - 89.56: 5 Dihedral angle restraints: 5465 sinusoidal: 2151 harmonic: 3314 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.057: 354 0.057 - 0.085: 154 0.085 - 0.114: 71 0.114 - 0.142: 14 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE S 70 " pdb=" CA ILE S 70 " pdb=" CG1 ILE S 70 " pdb=" CG2 ILE S 70 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA PHE R 41 " pdb=" N PHE R 41 " pdb=" C PHE R 41 " pdb=" CB PHE R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1411 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO S 224 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 186 " -0.011 2.00e-02 2.50e+03 1.64e-02 4.71e+00 pdb=" CG PHE R 186 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 186 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE R 186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 186 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 170 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" CG ASP B 170 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 170 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 170 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 8901 3.27 - 3.82: 15392 3.82 - 4.36: 18481 4.36 - 4.90: 31911 Nonbonded interactions: 75239 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 3.040 nonbonded pdb=" O LEU R 50 " pdb=" OG SER R 54 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.208 3.040 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.252 3.120 nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.267 3.120 ... (remaining 75234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.600 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 9196 Z= 0.207 Angle : 0.613 11.433 12450 Z= 0.329 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.058 1558 Dihedral : 16.545 89.558 3318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 30.16 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1125 helix: 2.18 (0.27), residues: 398 sheet: 0.30 (0.30), residues: 286 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 148 TYR 0.016 0.001 TYR R 94 PHE 0.037 0.002 PHE R 186 TRP 0.023 0.002 TRP R 251 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9193) covalent geometry : angle 0.61294 (12444) SS BOND : bond 0.00419 ( 3) SS BOND : angle 0.88224 ( 6) hydrogen bonds : bond 0.14760 ( 465) hydrogen bonds : angle 5.86794 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.217 Fit side-chains REVERT: A 231 ASP cc_start: 0.7629 (t0) cc_final: 0.7403 (t0) REVERT: A 340 THR cc_start: 0.8656 (m) cc_final: 0.8351 (t) REVERT: B 19 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7279 (mtm110) REVERT: B 61 MET cc_start: 0.8231 (tmm) cc_final: 0.7993 (ppp) REVERT: R 117 PHE cc_start: 0.8151 (t80) cc_final: 0.7919 (t80) REVERT: R 121 MET cc_start: 0.8187 (tpp) cc_final: 0.7617 (mpp) REVERT: R 216 PHE cc_start: 0.8045 (t80) cc_final: 0.7738 (t80) outliers start: 5 outliers final: 4 residues processed: 256 average time/residue: 0.4362 time to fit residues: 119.1487 Evaluate side-chains 246 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain S residue 130 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108384 restraints weight = 13164.881| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.99 r_work: 0.3277 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9196 Z= 0.163 Angle : 0.555 10.047 12450 Z= 0.295 Chirality : 0.042 0.176 1414 Planarity : 0.004 0.060 1558 Dihedral : 5.324 46.172 1276 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.15 % Allowed : 25.61 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1125 helix: 2.21 (0.26), residues: 405 sheet: 0.29 (0.30), residues: 293 loop : -0.61 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.024 0.002 PHE R 290 TRP 0.023 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9193) covalent geometry : angle 0.55468 (12444) SS BOND : bond 0.00343 ( 3) SS BOND : angle 0.65472 ( 6) hydrogen bonds : bond 0.04438 ( 465) hydrogen bonds : angle 4.68289 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.244 Fit side-chains REVERT: A 49 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.5995 (mp) REVERT: A 186 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 193 ASP cc_start: 0.8026 (m-30) cc_final: 0.7808 (t0) REVERT: A 231 ASP cc_start: 0.7913 (t0) cc_final: 0.7647 (t0) REVERT: B 19 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7175 (ttp80) REVERT: B 22 ARG cc_start: 0.7240 (mtt180) cc_final: 0.6983 (mtt180) REVERT: B 61 MET cc_start: 0.8196 (tmm) cc_final: 0.7982 (ppp) REVERT: B 197 ARG cc_start: 0.7840 (mpt-90) cc_final: 0.7609 (mtt-85) REVERT: B 258 ASP cc_start: 0.8015 (t0) cc_final: 0.7375 (t0) REVERT: R 37 LEU cc_start: 0.8487 (tp) cc_final: 0.7972 (tm) REVERT: R 41 PHE cc_start: 0.7809 (m-80) cc_final: 0.7293 (m-80) REVERT: R 46 PHE cc_start: 0.7645 (t80) cc_final: 0.7345 (t80) REVERT: R 55 LEU cc_start: 0.8240 (tm) cc_final: 0.7931 (tt) REVERT: R 95 LEU cc_start: 0.8661 (mt) cc_final: 0.8428 (mm) REVERT: R 101 PHE cc_start: 0.7754 (m-80) cc_final: 0.7396 (m-80) REVERT: R 105 MET cc_start: 0.7776 (mmm) cc_final: 0.7400 (tmm) REVERT: R 121 MET cc_start: 0.8127 (tpp) cc_final: 0.7543 (mpp) REVERT: S 39 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7980 (tp40) REVERT: S 69 THR cc_start: 0.8167 (p) cc_final: 0.7938 (t) REVERT: S 223 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7447 (t80) outliers start: 41 outliers final: 19 residues processed: 270 average time/residue: 0.4490 time to fit residues: 129.4971 Evaluate side-chains 266 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107875 restraints weight = 13092.743| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.99 r_work: 0.3270 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9196 Z= 0.202 Angle : 0.553 10.817 12450 Z= 0.293 Chirality : 0.042 0.149 1414 Planarity : 0.004 0.063 1558 Dihedral : 5.355 51.837 1271 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.15 % Allowed : 24.90 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1125 helix: 2.28 (0.26), residues: 400 sheet: 0.17 (0.29), residues: 297 loop : -0.65 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.015 0.002 TYR S 178 PHE 0.022 0.002 PHE R 290 TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9193) covalent geometry : angle 0.55328 (12444) SS BOND : bond 0.00340 ( 3) SS BOND : angle 0.83193 ( 6) hydrogen bonds : bond 0.04307 ( 465) hydrogen bonds : angle 4.62428 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 0.373 Fit side-chains REVERT: A 49 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.5744 (mp) REVERT: A 186 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 193 ASP cc_start: 0.8025 (m-30) cc_final: 0.7796 (t0) REVERT: A 231 ASP cc_start: 0.7946 (t0) cc_final: 0.7683 (t0) REVERT: A 269 ASN cc_start: 0.8466 (m-40) cc_final: 0.8222 (m110) REVERT: B 19 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7203 (ttp80) REVERT: B 22 ARG cc_start: 0.7271 (mtt180) cc_final: 0.7014 (mtp180) REVERT: B 61 MET cc_start: 0.8226 (tmm) cc_final: 0.8003 (ppp) REVERT: B 74 SER cc_start: 0.8271 (p) cc_final: 0.7910 (p) REVERT: B 76 ASP cc_start: 0.7714 (p0) cc_final: 0.7429 (p0) REVERT: B 197 ARG cc_start: 0.7901 (mpt-90) cc_final: 0.7591 (mtt-85) REVERT: B 214 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7533 (mmt180) REVERT: B 219 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7992 (mtt-85) REVERT: B 258 ASP cc_start: 0.8100 (t0) cc_final: 0.7200 (t0) REVERT: R 37 LEU cc_start: 0.8459 (tp) cc_final: 0.7977 (tm) REVERT: R 41 PHE cc_start: 0.7900 (m-80) cc_final: 0.7438 (m-80) REVERT: R 46 PHE cc_start: 0.7768 (t80) cc_final: 0.7410 (t80) REVERT: R 55 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7935 (tt) REVERT: R 95 LEU cc_start: 0.8656 (mt) cc_final: 0.8445 (mm) REVERT: R 105 MET cc_start: 0.7874 (mmm) cc_final: 0.7411 (tmm) REVERT: R 117 PHE cc_start: 0.8172 (t80) cc_final: 0.7941 (t80) REVERT: R 220 LYS cc_start: 0.8325 (mmmm) cc_final: 0.7998 (mmmm) REVERT: S 39 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: S 69 THR cc_start: 0.8197 (p) cc_final: 0.7955 (t) REVERT: S 110 PHE cc_start: 0.8647 (t80) cc_final: 0.8333 (t80) REVERT: S 205 SER cc_start: 0.7999 (m) cc_final: 0.7659 (p) REVERT: S 223 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7574 (t80) outliers start: 41 outliers final: 19 residues processed: 273 average time/residue: 0.4476 time to fit residues: 130.9593 Evaluate side-chains 266 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 105 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 75 GLN B 220 GLN B 259 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108922 restraints weight = 13200.027| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.00 r_work: 0.3278 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9196 Z= 0.153 Angle : 0.525 9.518 12450 Z= 0.277 Chirality : 0.041 0.142 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.290 54.512 1271 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.06 % Allowed : 25.00 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.25), residues: 1125 helix: 2.31 (0.26), residues: 406 sheet: 0.22 (0.29), residues: 297 loop : -0.63 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.023 0.002 PHE R 186 TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9193) covalent geometry : angle 0.52503 (12444) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.66250 ( 6) hydrogen bonds : bond 0.03969 ( 465) hydrogen bonds : angle 4.54900 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.218 Fit side-chains REVERT: A 49 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.5796 (mp) REVERT: A 186 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6713 (mm-30) REVERT: A 193 ASP cc_start: 0.8019 (m-30) cc_final: 0.7803 (t0) REVERT: A 231 ASP cc_start: 0.7948 (t0) cc_final: 0.7664 (t0) REVERT: A 269 ASN cc_start: 0.8473 (m-40) cc_final: 0.8228 (m110) REVERT: B 19 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7178 (ttp80) REVERT: B 22 ARG cc_start: 0.7267 (mtt180) cc_final: 0.7004 (mtp180) REVERT: B 61 MET cc_start: 0.8219 (tmm) cc_final: 0.7993 (ppp) REVERT: B 76 ASP cc_start: 0.7695 (p0) cc_final: 0.7431 (p0) REVERT: B 130 GLU cc_start: 0.8178 (mp0) cc_final: 0.7704 (mp0) REVERT: B 197 ARG cc_start: 0.7935 (mpt-90) cc_final: 0.7612 (mtt-85) REVERT: B 214 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7546 (mmt180) REVERT: B 219 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7969 (mtt-85) REVERT: B 258 ASP cc_start: 0.8105 (t0) cc_final: 0.7151 (t0) REVERT: R 37 LEU cc_start: 0.8427 (tp) cc_final: 0.8019 (tm) REVERT: R 41 PHE cc_start: 0.7938 (m-80) cc_final: 0.7499 (m-80) REVERT: R 46 PHE cc_start: 0.7744 (t80) cc_final: 0.7440 (t80) REVERT: R 55 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7955 (tt) REVERT: R 95 LEU cc_start: 0.8657 (mt) cc_final: 0.8432 (mm) REVERT: R 105 MET cc_start: 0.7859 (mmm) cc_final: 0.7426 (mmm) REVERT: R 168 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7610 (mp) REVERT: R 219 ILE cc_start: 0.8572 (mm) cc_final: 0.8360 (mt) REVERT: R 298 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8252 (t) REVERT: S 69 THR cc_start: 0.8223 (p) cc_final: 0.7982 (t) REVERT: S 110 PHE cc_start: 0.8622 (t80) cc_final: 0.8345 (t80) REVERT: S 205 SER cc_start: 0.7997 (m) cc_final: 0.7656 (p) REVERT: S 223 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7564 (t80) outliers start: 50 outliers final: 18 residues processed: 273 average time/residue: 0.4593 time to fit residues: 134.0934 Evaluate side-chains 268 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109209 restraints weight = 13001.009| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.99 r_work: 0.3287 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9196 Z= 0.126 Angle : 0.508 8.180 12450 Z= 0.267 Chirality : 0.040 0.143 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.177 59.361 1269 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.16 % Allowed : 24.60 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1125 helix: 2.42 (0.26), residues: 408 sheet: 0.21 (0.29), residues: 301 loop : -0.58 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.019 0.002 PHE R 216 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9193) covalent geometry : angle 0.50786 (12444) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.59091 ( 6) hydrogen bonds : bond 0.03726 ( 465) hydrogen bonds : angle 4.45072 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.334 Fit side-chains REVERT: A 49 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.5602 (mp) REVERT: A 186 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6669 (mm-30) REVERT: A 193 ASP cc_start: 0.8030 (m-30) cc_final: 0.7810 (t0) REVERT: A 231 ASP cc_start: 0.7943 (t0) cc_final: 0.7651 (t0) REVERT: A 269 ASN cc_start: 0.8471 (m-40) cc_final: 0.8215 (m110) REVERT: B 19 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7480 (ttp80) REVERT: B 22 ARG cc_start: 0.7252 (mtt180) cc_final: 0.7031 (mtp180) REVERT: B 61 MET cc_start: 0.8208 (tmm) cc_final: 0.7986 (ppp) REVERT: B 76 ASP cc_start: 0.7653 (p0) cc_final: 0.7423 (p0) REVERT: B 130 GLU cc_start: 0.8149 (mp0) cc_final: 0.7700 (mp0) REVERT: B 197 ARG cc_start: 0.7901 (mpt-90) cc_final: 0.7572 (mtt-85) REVERT: B 219 ARG cc_start: 0.8238 (mtp85) cc_final: 0.8000 (mtt-85) REVERT: B 258 ASP cc_start: 0.8075 (t0) cc_final: 0.7197 (t0) REVERT: R 37 LEU cc_start: 0.8400 (tp) cc_final: 0.7939 (tm) REVERT: R 41 PHE cc_start: 0.7934 (m-80) cc_final: 0.7519 (m-80) REVERT: R 46 PHE cc_start: 0.7721 (t80) cc_final: 0.7321 (t80) REVERT: R 49 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8324 (p) REVERT: R 55 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7939 (tt) REVERT: R 95 LEU cc_start: 0.8672 (mt) cc_final: 0.8461 (mm) REVERT: R 105 MET cc_start: 0.7873 (mmm) cc_final: 0.7461 (mmm) REVERT: R 121 MET cc_start: 0.8225 (tpp) cc_final: 0.7505 (mpp) REVERT: R 127 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: R 168 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7625 (mp) REVERT: R 258 LEU cc_start: 0.8321 (mt) cc_final: 0.8098 (tm) REVERT: R 298 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8229 (t) REVERT: S 39 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8004 (tp40) REVERT: S 69 THR cc_start: 0.8239 (p) cc_final: 0.7987 (t) REVERT: S 205 SER cc_start: 0.7990 (m) cc_final: 0.7590 (p) REVERT: S 223 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7553 (t80) outliers start: 51 outliers final: 21 residues processed: 280 average time/residue: 0.4547 time to fit residues: 136.4162 Evaluate side-chains 273 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 202 MET Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108939 restraints weight = 13011.447| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.00 r_work: 0.3288 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9196 Z= 0.144 Angle : 0.513 7.615 12450 Z= 0.270 Chirality : 0.040 0.142 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.039 50.948 1269 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.45 % Allowed : 26.62 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.26), residues: 1125 helix: 2.43 (0.26), residues: 408 sheet: 0.26 (0.29), residues: 299 loop : -0.57 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.015 0.001 TYR S 178 PHE 0.026 0.002 PHE R 186 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9193) covalent geometry : angle 0.51254 (12444) SS BOND : bond 0.00297 ( 3) SS BOND : angle 0.66885 ( 6) hydrogen bonds : bond 0.03764 ( 465) hydrogen bonds : angle 4.43751 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.325 Fit side-chains REVERT: A 186 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6713 (mm-30) REVERT: A 193 ASP cc_start: 0.8032 (m-30) cc_final: 0.7811 (t0) REVERT: A 231 ASP cc_start: 0.7930 (t0) cc_final: 0.7618 (t0) REVERT: A 269 ASN cc_start: 0.8492 (m-40) cc_final: 0.8210 (m110) REVERT: A 276 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 22 ARG cc_start: 0.7252 (mtt180) cc_final: 0.7047 (mtp180) REVERT: B 61 MET cc_start: 0.8193 (tmm) cc_final: 0.7980 (ppp) REVERT: B 76 ASP cc_start: 0.7659 (p0) cc_final: 0.7416 (p0) REVERT: B 130 GLU cc_start: 0.8172 (mp0) cc_final: 0.7734 (mp0) REVERT: B 197 ARG cc_start: 0.7891 (mpt-90) cc_final: 0.7570 (mtt-85) REVERT: B 214 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7560 (mmt180) REVERT: B 219 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7980 (mtt-85) REVERT: B 258 ASP cc_start: 0.8069 (t0) cc_final: 0.7246 (t0) REVERT: R 37 LEU cc_start: 0.8384 (tp) cc_final: 0.7954 (tm) REVERT: R 41 PHE cc_start: 0.7934 (m-80) cc_final: 0.7543 (m-80) REVERT: R 46 PHE cc_start: 0.7726 (t80) cc_final: 0.7432 (t80) REVERT: R 55 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7939 (tt) REVERT: R 95 LEU cc_start: 0.8639 (mt) cc_final: 0.8364 (mm) REVERT: R 105 MET cc_start: 0.7891 (mmm) cc_final: 0.7468 (mmm) REVERT: R 168 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7641 (mp) REVERT: R 219 ILE cc_start: 0.8573 (mm) cc_final: 0.8369 (mt) REVERT: R 235 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7369 (mmmm) REVERT: R 298 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8252 (t) REVERT: S 39 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8052 (tp40) REVERT: S 69 THR cc_start: 0.8190 (p) cc_final: 0.7953 (t) REVERT: S 205 SER cc_start: 0.7998 (m) cc_final: 0.7588 (p) REVERT: S 223 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7524 (t80) outliers start: 44 outliers final: 21 residues processed: 276 average time/residue: 0.4426 time to fit residues: 130.9234 Evaluate side-chains 273 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109249 restraints weight = 13099.160| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.99 r_work: 0.3297 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9196 Z= 0.132 Angle : 0.523 11.644 12450 Z= 0.271 Chirality : 0.040 0.140 1414 Planarity : 0.003 0.062 1558 Dihedral : 5.055 52.279 1269 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.45 % Allowed : 27.13 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.26), residues: 1125 helix: 2.41 (0.26), residues: 408 sheet: 0.22 (0.29), residues: 299 loop : -0.51 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.020 0.002 PHE R 117 TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9193) covalent geometry : angle 0.52244 (12444) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.64337 ( 6) hydrogen bonds : bond 0.03682 ( 465) hydrogen bonds : angle 4.41204 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.287 Fit side-chains REVERT: A 8 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6971 (mt-10) REVERT: A 53 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6045 (mtm) REVERT: A 186 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6691 (mm-30) REVERT: A 193 ASP cc_start: 0.8006 (m-30) cc_final: 0.7792 (t0) REVERT: A 231 ASP cc_start: 0.7887 (t0) cc_final: 0.7571 (t0) REVERT: A 269 ASN cc_start: 0.8484 (m-40) cc_final: 0.8200 (m110) REVERT: A 276 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 340 THR cc_start: 0.8645 (m) cc_final: 0.8311 (t) REVERT: B 19 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7300 (mtm-85) REVERT: B 22 ARG cc_start: 0.7274 (mtt180) cc_final: 0.7009 (mtp180) REVERT: B 76 ASP cc_start: 0.7635 (p0) cc_final: 0.7407 (p0) REVERT: B 130 GLU cc_start: 0.8160 (mp0) cc_final: 0.7744 (mp0) REVERT: B 197 ARG cc_start: 0.7868 (mpt-90) cc_final: 0.7533 (mtt-85) REVERT: B 214 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7541 (mmt180) REVERT: B 258 ASP cc_start: 0.8066 (t0) cc_final: 0.7340 (t0) REVERT: R 37 LEU cc_start: 0.8351 (tp) cc_final: 0.7916 (tm) REVERT: R 41 PHE cc_start: 0.7952 (m-80) cc_final: 0.7544 (m-80) REVERT: R 46 PHE cc_start: 0.7711 (t80) cc_final: 0.7327 (t80) REVERT: R 49 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (p) REVERT: R 55 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7919 (tt) REVERT: R 95 LEU cc_start: 0.8595 (mt) cc_final: 0.8371 (mm) REVERT: R 105 MET cc_start: 0.7902 (mmm) cc_final: 0.7490 (mmm) REVERT: R 168 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7670 (mp) REVERT: R 204 ILE cc_start: 0.8390 (pp) cc_final: 0.8189 (pt) REVERT: R 219 ILE cc_start: 0.8566 (mm) cc_final: 0.8339 (mt) REVERT: R 235 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7358 (mmmm) REVERT: R 298 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8257 (t) REVERT: S 39 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: S 69 THR cc_start: 0.8207 (p) cc_final: 0.7968 (t) REVERT: S 205 SER cc_start: 0.7997 (m) cc_final: 0.7613 (p) REVERT: S 223 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7511 (t80) outliers start: 44 outliers final: 20 residues processed: 272 average time/residue: 0.4222 time to fit residues: 123.0834 Evaluate side-chains 274 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108806 restraints weight = 13055.989| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.98 r_work: 0.3290 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.153 Angle : 0.533 11.280 12450 Z= 0.278 Chirality : 0.041 0.142 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.104 53.597 1269 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.55 % Allowed : 26.92 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1125 helix: 2.38 (0.26), residues: 408 sheet: 0.30 (0.29), residues: 297 loop : -0.51 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR S 178 PHE 0.023 0.002 PHE R 186 TRP 0.016 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9193) covalent geometry : angle 0.53318 (12444) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.68202 ( 6) hydrogen bonds : bond 0.03785 ( 465) hydrogen bonds : angle 4.46199 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 0.221 Fit side-chains REVERT: A 8 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7016 (mt-10) REVERT: A 53 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6189 (mtm) REVERT: A 186 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 193 ASP cc_start: 0.8007 (m-30) cc_final: 0.7792 (t0) REVERT: A 231 ASP cc_start: 0.7810 (t0) cc_final: 0.7500 (t0) REVERT: A 269 ASN cc_start: 0.8502 (m-40) cc_final: 0.8217 (m110) REVERT: A 340 THR cc_start: 0.8661 (m) cc_final: 0.8323 (t) REVERT: B 30 LEU cc_start: 0.7906 (tp) cc_final: 0.7585 (tt) REVERT: B 76 ASP cc_start: 0.7646 (p0) cc_final: 0.7405 (p0) REVERT: B 130 GLU cc_start: 0.8165 (mp0) cc_final: 0.7736 (mp0) REVERT: B 197 ARG cc_start: 0.7908 (mpt-90) cc_final: 0.7570 (mtt-85) REVERT: B 214 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7539 (mmt180) REVERT: B 258 ASP cc_start: 0.8057 (t0) cc_final: 0.7403 (t0) REVERT: R 37 LEU cc_start: 0.8341 (tp) cc_final: 0.7890 (tm) REVERT: R 41 PHE cc_start: 0.7947 (m-80) cc_final: 0.7532 (m-80) REVERT: R 46 PHE cc_start: 0.7728 (t80) cc_final: 0.7347 (t80) REVERT: R 49 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8353 (p) REVERT: R 55 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7950 (tt) REVERT: R 95 LEU cc_start: 0.8626 (mt) cc_final: 0.8389 (mm) REVERT: R 105 MET cc_start: 0.7915 (mmm) cc_final: 0.7479 (mmm) REVERT: R 121 MET cc_start: 0.8221 (tpp) cc_final: 0.7447 (mpp) REVERT: R 168 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 235 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7359 (mmmm) REVERT: R 298 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8272 (t) REVERT: S 39 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8050 (tp40) REVERT: S 69 THR cc_start: 0.8211 (p) cc_final: 0.7975 (t) REVERT: S 205 SER cc_start: 0.8017 (m) cc_final: 0.7603 (p) REVERT: S 223 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7526 (t80) outliers start: 45 outliers final: 23 residues processed: 274 average time/residue: 0.3962 time to fit residues: 116.2701 Evaluate side-chains 277 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110936 restraints weight = 13006.571| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.97 r_work: 0.3310 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9196 Z= 0.106 Angle : 0.517 10.544 12450 Z= 0.268 Chirality : 0.040 0.153 1414 Planarity : 0.003 0.061 1558 Dihedral : 4.974 53.721 1269 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.44 % Allowed : 28.54 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1125 helix: 2.47 (0.26), residues: 408 sheet: 0.33 (0.30), residues: 299 loop : -0.45 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 148 TYR 0.015 0.001 TYR S 178 PHE 0.022 0.001 PHE R 216 TRP 0.017 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9193) covalent geometry : angle 0.51657 (12444) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.58256 ( 6) hydrogen bonds : bond 0.03488 ( 465) hydrogen bonds : angle 4.40766 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.319 Fit side-chains REVERT: A 8 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6850 (mt-10) REVERT: A 53 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6242 (mtm) REVERT: A 186 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6653 (mm-30) REVERT: A 193 ASP cc_start: 0.8025 (m-30) cc_final: 0.7804 (t0) REVERT: A 231 ASP cc_start: 0.7793 (t0) cc_final: 0.7470 (t0) REVERT: A 269 ASN cc_start: 0.8480 (m-40) cc_final: 0.8188 (m110) REVERT: A 276 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 285 ILE cc_start: 0.8341 (tt) cc_final: 0.8125 (pp) REVERT: A 328 ASP cc_start: 0.7815 (m-30) cc_final: 0.7578 (m-30) REVERT: A 340 THR cc_start: 0.8645 (m) cc_final: 0.8276 (t) REVERT: B 19 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7320 (mtm-85) REVERT: B 22 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6703 (mtp85) REVERT: B 30 LEU cc_start: 0.7766 (tp) cc_final: 0.7433 (tt) REVERT: B 46 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7820 (mtt180) REVERT: B 61 MET cc_start: 0.8121 (ppp) cc_final: 0.7805 (pp-130) REVERT: B 76 ASP cc_start: 0.7631 (p0) cc_final: 0.7388 (p0) REVERT: B 130 GLU cc_start: 0.8146 (mp0) cc_final: 0.7741 (mp0) REVERT: B 197 ARG cc_start: 0.7871 (mpt-90) cc_final: 0.7524 (mtt-85) REVERT: B 214 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7535 (mmt180) REVERT: B 258 ASP cc_start: 0.8025 (t0) cc_final: 0.7368 (t0) REVERT: B 317 CYS cc_start: 0.8161 (p) cc_final: 0.7958 (p) REVERT: B 335 PHE cc_start: 0.8050 (m-80) cc_final: 0.7837 (m-80) REVERT: R 37 LEU cc_start: 0.8316 (tp) cc_final: 0.7862 (tm) REVERT: R 41 PHE cc_start: 0.7957 (m-80) cc_final: 0.7530 (m-80) REVERT: R 46 PHE cc_start: 0.7744 (t80) cc_final: 0.7528 (t80) REVERT: R 49 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8358 (p) REVERT: R 55 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7853 (tt) REVERT: R 105 MET cc_start: 0.7967 (mmm) cc_final: 0.7523 (mmm) REVERT: R 121 MET cc_start: 0.8150 (tpp) cc_final: 0.7423 (mpp) REVERT: R 168 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7672 (mp) REVERT: R 298 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (t) REVERT: S 39 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7988 (tp40) REVERT: S 69 THR cc_start: 0.8221 (p) cc_final: 0.7978 (t) REVERT: S 83 MET cc_start: 0.7037 (mtp) cc_final: 0.6793 (ptm) REVERT: S 205 SER cc_start: 0.7998 (m) cc_final: 0.7610 (p) REVERT: S 223 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7494 (t80) outliers start: 34 outliers final: 16 residues processed: 280 average time/residue: 0.3829 time to fit residues: 115.4115 Evaluate side-chains 277 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108566 restraints weight = 13063.873| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.96 r_work: 0.3288 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9196 Z= 0.191 Angle : 0.568 10.736 12450 Z= 0.296 Chirality : 0.043 0.256 1414 Planarity : 0.004 0.063 1558 Dihedral : 5.211 52.665 1269 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.24 % Allowed : 29.35 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.26), residues: 1125 helix: 2.41 (0.26), residues: 402 sheet: 0.32 (0.30), residues: 297 loop : -0.50 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 49 TYR 0.014 0.002 TYR R 114 PHE 0.024 0.002 PHE R 117 TRP 0.017 0.001 TRP R 251 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9193) covalent geometry : angle 0.56834 (12444) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.80202 ( 6) hydrogen bonds : bond 0.03970 ( 465) hydrogen bonds : angle 4.54547 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.213 Fit side-chains REVERT: A 8 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 53 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6601 (mtp) REVERT: A 186 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6726 (mm-30) REVERT: A 193 ASP cc_start: 0.7984 (m-30) cc_final: 0.7746 (t0) REVERT: A 231 ASP cc_start: 0.7832 (t0) cc_final: 0.7533 (t0) REVERT: A 269 ASN cc_start: 0.8490 (m-40) cc_final: 0.8192 (m110) REVERT: B 19 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7498 (mtm110) REVERT: B 22 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6691 (mtp85) REVERT: B 30 LEU cc_start: 0.7805 (tp) cc_final: 0.7516 (tt) REVERT: B 61 MET cc_start: 0.8079 (ppp) cc_final: 0.7829 (pp-130) REVERT: B 76 ASP cc_start: 0.7631 (p0) cc_final: 0.7391 (p0) REVERT: B 130 GLU cc_start: 0.8195 (mp0) cc_final: 0.7754 (mp0) REVERT: B 197 ARG cc_start: 0.7885 (mpt-90) cc_final: 0.7537 (mtt-85) REVERT: B 214 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7539 (mmt180) REVERT: B 228 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: B 258 ASP cc_start: 0.7949 (t0) cc_final: 0.7293 (t0) REVERT: R 37 LEU cc_start: 0.8346 (tp) cc_final: 0.7871 (tm) REVERT: R 41 PHE cc_start: 0.7948 (m-80) cc_final: 0.7542 (m-80) REVERT: R 46 PHE cc_start: 0.7771 (t80) cc_final: 0.7361 (t80) REVERT: R 49 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8390 (p) REVERT: R 55 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7945 (tt) REVERT: R 60 LEU cc_start: 0.7950 (mt) cc_final: 0.7720 (mt) REVERT: R 105 MET cc_start: 0.8021 (mmm) cc_final: 0.7600 (mmm) REVERT: R 168 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7715 (mp) REVERT: R 291 THR cc_start: 0.8588 (t) cc_final: 0.8305 (p) REVERT: R 298 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8293 (t) REVERT: S 39 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: S 69 THR cc_start: 0.8209 (p) cc_final: 0.7977 (t) REVERT: S 98 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8343 (ptm160) REVERT: S 110 PHE cc_start: 0.8410 (t80) cc_final: 0.8196 (t80) REVERT: S 205 SER cc_start: 0.8030 (m) cc_final: 0.7607 (p) REVERT: S 223 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7493 (t80) outliers start: 32 outliers final: 17 residues processed: 273 average time/residue: 0.3888 time to fit residues: 113.9842 Evaluate side-chains 274 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109344 restraints weight = 12838.289| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.90 r_work: 0.3300 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9196 Z= 0.162 Angle : 0.562 10.430 12450 Z= 0.291 Chirality : 0.042 0.256 1414 Planarity : 0.004 0.064 1558 Dihedral : 5.190 54.662 1268 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.54 % Allowed : 28.74 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1125 helix: 2.39 (0.26), residues: 402 sheet: 0.26 (0.29), residues: 297 loop : -0.51 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 49 TYR 0.014 0.001 TYR R 73 PHE 0.024 0.002 PHE R 216 TRP 0.022 0.002 TRP R 251 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9193) covalent geometry : angle 0.56125 (12444) SS BOND : bond 0.00342 ( 3) SS BOND : angle 1.12156 ( 6) hydrogen bonds : bond 0.03863 ( 465) hydrogen bonds : angle 4.53251 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.67 seconds wall clock time: 53 minutes 27.81 seconds (3207.81 seconds total)