Starting phenix.real_space_refine on Wed Mar 4 05:34:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o7f_12746/03_2026/7o7f_12746.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 75 5.16 5 C 7113 2.51 5 N 1882 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11170 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1767 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2440 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "I" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain: "F" Number of atoms: 1694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Conformer: "B" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} bond proxies already assigned to first conformer: 1700 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU F 148 " occ=0.73 ... (16 atoms not shown) pdb=" OE2BGLU F 148 " occ=0.27 Time building chain proxies: 2.81, per 1000 atoms: 0.25 Number of scatterers: 11170 At special positions: 0 Unit cell: (95.632, 136.776, 156.792, 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 75 16.00 O 2100 8.00 N 1882 7.00 C 7113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 34 " distance=2.03 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 113 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 219 " distance=2.04 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: 0.93 Conformation dependent library (CDL) restraints added in 496.4 milliseconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 20 sheets defined 34.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.868A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.811A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.702A 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 329 through 352 removed outlier: 3.699A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.927A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 58 Proline residue: C 34 - end of helix removed outlier: 3.637A pdb=" N GLY C 47 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 91 removed outlier: 3.702A pdb=" N ILE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.683A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 132 removed outlier: 3.541A pdb=" N HIS C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 140 removed outlier: 3.518A pdb=" N ALA C 136 " --> pdb=" O HIS C 132 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 139 " --> pdb=" O PHE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 165 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 183 through 201 removed outlier: 4.555A pdb=" N GLN C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 224 removed outlier: 3.641A pdb=" N ILE C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 260 Proline residue: C 250 - end of helix removed outlier: 3.595A pdb=" N PHE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 268 through 299 Proline residue: C 294 - end of helix Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.864A pdb=" N ASN C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 32 through 49 removed outlier: 3.615A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.524A pdb=" N LYS G 61 " --> pdb=" O PRO G 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 22 No H-bonds generated for 'chain 'I' and resid 20 through 22' Processing helix chain 'I' and resid 55 through 66 Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.548A pdb=" N PHE H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 75 removed outlier: 3.994A pdb=" N GLY H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 75' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'F' and resid 104 through 108 removed outlier: 4.049A pdb=" N VAL F 108 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 152 Processing helix chain 'F' and resid 208 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 8.577A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.540A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.989A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.795A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A 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: 6.878A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.617A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB1, first strand: chain 'I' and resid 24 through 29 removed outlier: 6.786A pdb=" N VAL I 42 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TYR I 27 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 40 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AB3, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.344A pdb=" N GLY H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.344A pdb=" N GLY H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE H 129 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 151 removed outlier: 5.760A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 147 through 151 removed outlier: 5.760A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 178 through 181 Processing sheet with id=AB8, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.729A pdb=" N ALA F 95 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.378A pdb=" N TRP F 60 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR F 74 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU F 58 " --> pdb=" O TYR F 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 139 through 143 removed outlier: 5.970A pdb=" N TYR F 198 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 178 through 180 removed outlier: 4.118A pdb=" N TRP F 173 " --> pdb=" O ARG F 180 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1554 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: 1.73 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1808 1.31 - 1.44: 3167 1.44 - 1.57: 6340 1.57 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 11420 Sorted by residual: bond pdb=" C VAL C 83 " pdb=" O VAL C 83 " ideal model delta sigma weight residual 1.238 1.181 0.057 8.50e-03 1.38e+04 4.58e+01 bond pdb=" N PCA I 0 " pdb=" CD PCA I 0 " ideal model delta sigma weight residual 1.345 1.467 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 1.237 1.177 0.060 1.17e-02 7.31e+03 2.60e+01 bond pdb=" C LEU C 80 " pdb=" O LEU C 80 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.29e-02 6.01e+03 1.50e+01 bond pdb=" N PRO I 3 " pdb=" CA PRO I 3 " ideal model delta sigma weight residual 1.469 1.424 0.044 1.28e-02 6.10e+03 1.20e+01 ... (remaining 11415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 15210 1.99 - 3.99: 231 3.99 - 5.98: 29 5.98 - 7.98: 5 7.98 - 9.97: 2 Bond angle restraints: 15477 Sorted by residual: angle pdb=" N MET C 287 " pdb=" CA MET C 287 " pdb=" C MET C 287 " ideal model delta sigma weight residual 111.28 104.25 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" CA THR C 288 " pdb=" C THR C 288 " pdb=" O THR C 288 " ideal model delta sigma weight residual 120.55 114.14 6.41 1.06e+00 8.90e-01 3.66e+01 angle pdb=" N THR C 284 " pdb=" CA THR C 284 " pdb=" C THR C 284 " ideal model delta sigma weight residual 111.28 105.08 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" CB THR C 288 " ideal model delta sigma weight residual 110.12 118.24 -8.12 1.47e+00 4.63e-01 3.05e+01 angle pdb=" CA PHE C 41 " pdb=" C PHE C 41 " pdb=" O PHE C 41 " ideal model delta sigma weight residual 120.70 115.27 5.43 1.03e+00 9.43e-01 2.78e+01 ... (remaining 15472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6169 17.93 - 35.87: 522 35.87 - 53.80: 80 53.80 - 71.73: 19 71.73 - 89.67: 16 Dihedral angle restraints: 6806 sinusoidal: 2676 harmonic: 4130 Sorted by residual: dihedral pdb=" CB CYS I 11 " pdb=" SG CYS I 11 " pdb=" SG CYS I 50 " pdb=" CB CYS I 50 " ideal model delta sinusoidal sigma weight residual 93.00 149.38 -56.38 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PHE H 51 " pdb=" C PHE H 51 " pdb=" N GLY H 52 " pdb=" CA GLY H 52 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1412 0.046 - 0.091: 234 0.091 - 0.137: 91 0.137 - 0.183: 7 0.183 - 0.228: 3 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CB THR C 288 " pdb=" CA THR C 288 " pdb=" OG1 THR C 288 " pdb=" CG2 THR C 288 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA HIS C 289 " pdb=" N HIS C 289 " pdb=" C HIS C 289 " pdb=" CB HIS C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 1744 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 78 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C PHE C 78 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE C 78 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE C 79 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 289 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C HIS C 289 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS C 289 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS C 290 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 80 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU C 80 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU C 80 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 81 " 0.014 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 87 2.53 - 3.12: 8740 3.12 - 3.71: 16834 3.71 - 4.31: 24341 4.31 - 4.90: 41735 Nonbonded interactions: 91737 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 1.932 3.040 nonbonded pdb=" OH TYR C 187 " pdb=" O CYS I 34 " model vdw 1.955 3.040 nonbonded pdb=" OG1 THR A 324 " pdb=" OD1 ASN A 331 " model vdw 1.970 3.040 nonbonded pdb=" OG1 THR C 65 " pdb=" OD2 ASP C 125 " model vdw 1.973 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 1.984 3.040 ... (remaining 91732 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=0.27 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.180 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 0.122 11428 Z= 0.210 Angle : 0.637 9.970 15493 Z= 0.401 Chirality : 0.042 0.228 1747 Planarity : 0.003 0.051 1959 Dihedral : 14.025 89.666 4120 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.16 % Allowed : 0.40 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1405 helix: 1.58 (0.25), residues: 425 sheet: 0.05 (0.27), residues: 378 loop : -0.32 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.017 0.001 TYR A 296 PHE 0.024 0.001 PHE C 41 TRP 0.012 0.001 TRP F 188 HIS 0.010 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00368 (11420) covalent geometry : angle 0.63676 (15477) SS BOND : bond 0.00432 ( 8) SS BOND : angle 1.08462 ( 16) hydrogen bonds : bond 0.12416 ( 540) hydrogen bonds : angle 5.72181 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6420 (tm-30) cc_final: 0.5940 (tm-30) REVERT: A 269 ASN cc_start: 0.8496 (m110) cc_final: 0.8292 (m-40) REVERT: C 54 ILE cc_start: 0.7939 (mm) cc_final: 0.7693 (mm) REVERT: C 182 PHE cc_start: 0.5716 (m-80) cc_final: 0.5345 (m-80) REVERT: C 198 ILE cc_start: 0.8489 (tt) cc_final: 0.8280 (tt) REVERT: C 273 ASN cc_start: 0.6768 (m-40) cc_final: 0.6468 (m-40) REVERT: C 274 ARG cc_start: 0.7667 (ttm110) cc_final: 0.6815 (ttp-170) REVERT: G 24 LYS cc_start: 0.8260 (ttmt) cc_final: 0.8058 (ttmt) REVERT: H 198 GLN cc_start: 0.6900 (tt0) cc_final: 0.6064 (pp30) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.1169 time to fit residues: 35.3262 Evaluate side-chains 181 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 55 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 241 ASN A 244 HIS B 237 ASN C 194 GLN C 293 ASN G 21 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157078 restraints weight = 24832.453| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 4.99 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11428 Z= 0.152 Angle : 0.585 8.495 15493 Z= 0.311 Chirality : 0.043 0.190 1747 Planarity : 0.004 0.055 1959 Dihedral : 4.460 29.576 1537 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.13 % Allowed : 7.33 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1405 helix: 1.74 (0.25), residues: 428 sheet: 0.23 (0.27), residues: 361 loop : -0.31 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 31 TYR 0.015 0.001 TYR B 59 PHE 0.019 0.002 PHE F 160 TRP 0.010 0.001 TRP B 211 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00353 (11420) covalent geometry : angle 0.58453 (15477) SS BOND : bond 0.00393 ( 8) SS BOND : angle 1.05796 ( 16) hydrogen bonds : bond 0.03983 ( 540) hydrogen bonds : angle 4.78133 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6169 (tm-30) REVERT: A 342 VAL cc_start: 0.8432 (t) cc_final: 0.8110 (t) REVERT: B 234 PHE cc_start: 0.5406 (p90) cc_final: 0.5115 (p90) REVERT: C 52 ILE cc_start: 0.7988 (pt) cc_final: 0.7664 (mt) REVERT: C 54 ILE cc_start: 0.7719 (mm) cc_final: 0.7285 (mm) REVERT: C 182 PHE cc_start: 0.5480 (m-80) cc_final: 0.5196 (m-80) REVERT: C 274 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6630 (ttp-170) REVERT: H 198 GLN cc_start: 0.6752 (tt0) cc_final: 0.6345 (pp30) REVERT: F 132 LYS cc_start: 0.8582 (ttpp) cc_final: 0.8359 (ttpp) REVERT: F 217 TYR cc_start: 0.6223 (m-80) cc_final: 0.5944 (m-80) outliers start: 14 outliers final: 10 residues processed: 209 average time/residue: 0.1197 time to fit residues: 34.0825 Evaluate side-chains 187 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.192425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141618 restraints weight = 38419.066| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.53 r_work: 0.3353 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11428 Z= 0.149 Angle : 0.566 7.349 15493 Z= 0.301 Chirality : 0.043 0.174 1747 Planarity : 0.004 0.052 1959 Dihedral : 4.408 29.858 1537 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.69 % Allowed : 10.23 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1405 helix: 1.62 (0.25), residues: 428 sheet: 0.18 (0.27), residues: 366 loop : -0.32 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 31 TYR 0.014 0.001 TYR C 187 PHE 0.024 0.002 PHE C 304 TRP 0.009 0.001 TRP I 57 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00348 (11420) covalent geometry : angle 0.56554 (15477) SS BOND : bond 0.00396 ( 8) SS BOND : angle 0.95834 ( 16) hydrogen bonds : bond 0.03814 ( 540) hydrogen bonds : angle 4.64006 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 234 PHE cc_start: 0.6222 (p90) cc_final: 0.5925 (p90) REVERT: C 52 ILE cc_start: 0.8346 (pt) cc_final: 0.8099 (mt) REVERT: C 120 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (mp) REVERT: C 182 PHE cc_start: 0.6090 (m-80) cc_final: 0.5564 (m-80) REVERT: C 274 ARG cc_start: 0.7920 (ttm110) cc_final: 0.6970 (ttp-170) REVERT: H 38 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7847 (ttpp) REVERT: H 198 GLN cc_start: 0.6945 (tt0) cc_final: 0.5955 (pp30) REVERT: F 44 ARG cc_start: 0.8670 (ptp-110) cc_final: 0.8375 (ptp-110) REVERT: F 217 TYR cc_start: 0.6407 (m-80) cc_final: 0.6007 (m-80) outliers start: 21 outliers final: 13 residues processed: 204 average time/residue: 0.1256 time to fit residues: 34.5828 Evaluate side-chains 191 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 67 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 110 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142480 restraints weight = 31511.792| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 4.30 r_work: 0.3362 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11428 Z= 0.124 Angle : 0.545 12.082 15493 Z= 0.287 Chirality : 0.042 0.157 1747 Planarity : 0.004 0.050 1959 Dihedral : 4.246 27.913 1537 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.10 % Allowed : 12.01 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1405 helix: 1.63 (0.25), residues: 428 sheet: 0.18 (0.27), residues: 370 loop : -0.30 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 31 TYR 0.021 0.001 TYR A 296 PHE 0.013 0.001 PHE F 160 TRP 0.009 0.001 TRP I 57 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00279 (11420) covalent geometry : angle 0.54469 (15477) SS BOND : bond 0.00349 ( 8) SS BOND : angle 0.90184 ( 16) hydrogen bonds : bond 0.03507 ( 540) hydrogen bonds : angle 4.49796 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6833 (tm-30) REVERT: A 342 VAL cc_start: 0.8358 (t) cc_final: 0.8154 (t) REVERT: B 234 PHE cc_start: 0.6127 (p90) cc_final: 0.5777 (p90) REVERT: C 52 ILE cc_start: 0.8426 (pt) cc_final: 0.8179 (mt) REVERT: C 120 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7797 (mp) REVERT: C 144 PHE cc_start: 0.6572 (t80) cc_final: 0.6265 (t80) REVERT: C 148 THR cc_start: 0.8501 (t) cc_final: 0.8272 (t) REVERT: C 182 PHE cc_start: 0.6104 (m-80) cc_final: 0.5661 (m-80) REVERT: C 274 ARG cc_start: 0.7964 (ttm110) cc_final: 0.6965 (mmt180) REVERT: G 38 GLU cc_start: 0.7875 (tp30) cc_final: 0.7653 (tp30) REVERT: H 38 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7950 (ttpp) REVERT: H 198 GLN cc_start: 0.6853 (tt0) cc_final: 0.5828 (pp30) REVERT: F 217 TYR cc_start: 0.6430 (m-80) cc_final: 0.6002 (m-80) outliers start: 26 outliers final: 15 residues processed: 207 average time/residue: 0.1199 time to fit residues: 34.0098 Evaluate side-chains 191 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.191894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158807 restraints weight = 26321.547| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 5.29 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11428 Z= 0.156 Angle : 0.570 11.143 15493 Z= 0.298 Chirality : 0.042 0.177 1747 Planarity : 0.004 0.052 1959 Dihedral : 4.346 30.198 1537 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 12.17 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1405 helix: 1.52 (0.25), residues: 435 sheet: 0.19 (0.26), residues: 379 loop : -0.36 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 44 TYR 0.014 0.002 TYR B 59 PHE 0.012 0.001 PHE F 160 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00367 (11420) covalent geometry : angle 0.56957 (15477) SS BOND : bond 0.00411 ( 8) SS BOND : angle 0.99723 ( 16) hydrogen bonds : bond 0.03644 ( 540) hydrogen bonds : angle 4.54555 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.356 Fit side-chains REVERT: A 245 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 198 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7584 (pp) REVERT: B 234 PHE cc_start: 0.5666 (p90) cc_final: 0.5299 (p90) REVERT: C 41 PHE cc_start: 0.5818 (t80) cc_final: 0.5527 (t80) REVERT: C 52 ILE cc_start: 0.7969 (pt) cc_final: 0.7666 (mt) REVERT: C 274 ARG cc_start: 0.7005 (ttm110) cc_final: 0.6793 (mmt180) outliers start: 29 outliers final: 17 residues processed: 201 average time/residue: 0.1219 time to fit residues: 33.4940 Evaluate side-chains 185 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.190057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142386 restraints weight = 22356.498| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.34 r_work: 0.3361 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11428 Z= 0.188 Angle : 0.595 9.685 15493 Z= 0.313 Chirality : 0.043 0.160 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.494 33.132 1537 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.18 % Allowed : 13.62 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1405 helix: 1.42 (0.25), residues: 435 sheet: 0.15 (0.26), residues: 375 loop : -0.44 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 44 TYR 0.021 0.002 TYR B 59 PHE 0.013 0.002 PHE A 189 TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00446 (11420) covalent geometry : angle 0.59362 (15477) SS BOND : bond 0.00366 ( 8) SS BOND : angle 1.42143 ( 16) hydrogen bonds : bond 0.03837 ( 540) hydrogen bonds : angle 4.66647 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.410 Fit side-chains REVERT: A 25 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 193 ASP cc_start: 0.7784 (t0) cc_final: 0.7573 (t0) REVERT: A 245 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 273 LEU cc_start: 0.8491 (tp) cc_final: 0.8264 (tp) REVERT: B 198 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7904 (pp) REVERT: C 41 PHE cc_start: 0.6456 (t80) cc_final: 0.6160 (t80) REVERT: C 52 ILE cc_start: 0.8391 (pt) cc_final: 0.8086 (mt) REVERT: C 144 PHE cc_start: 0.6361 (t80) cc_final: 0.6009 (t80) REVERT: C 244 TYR cc_start: 0.7552 (t80) cc_final: 0.7314 (t80) REVERT: C 274 ARG cc_start: 0.7871 (ttm110) cc_final: 0.6886 (mmt180) REVERT: F 200 MET cc_start: 0.7650 (tpt) cc_final: 0.6854 (tpt) outliers start: 27 outliers final: 21 residues processed: 190 average time/residue: 0.1242 time to fit residues: 32.0394 Evaluate side-chains 187 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.156892 restraints weight = 29046.520| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 5.18 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11428 Z= 0.134 Angle : 0.558 9.652 15493 Z= 0.292 Chirality : 0.042 0.212 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.332 30.295 1537 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.93 % Allowed : 14.67 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1405 helix: 1.47 (0.25), residues: 437 sheet: 0.13 (0.27), residues: 369 loop : -0.41 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 31 TYR 0.016 0.001 TYR B 59 PHE 0.011 0.001 PHE A 189 TRP 0.011 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00307 (11420) covalent geometry : angle 0.55683 (15477) SS BOND : bond 0.00279 ( 8) SS BOND : angle 1.25346 ( 16) hydrogen bonds : bond 0.03550 ( 540) hydrogen bonds : angle 4.55647 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.447 Fit side-chains REVERT: A 245 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6494 (tm-30) REVERT: B 198 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7637 (pp) REVERT: B 234 PHE cc_start: 0.5759 (p90) cc_final: 0.5349 (p90) REVERT: C 41 PHE cc_start: 0.5821 (t80) cc_final: 0.5514 (t80) REVERT: C 52 ILE cc_start: 0.7956 (pt) cc_final: 0.7649 (mt) REVERT: C 274 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6723 (mmt180) REVERT: F 200 MET cc_start: 0.7095 (tpt) cc_final: 0.6626 (tpt) REVERT: F 217 TYR cc_start: 0.6146 (m-80) cc_final: 0.5669 (m-80) outliers start: 24 outliers final: 18 residues processed: 200 average time/residue: 0.1219 time to fit residues: 33.4364 Evaluate side-chains 185 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 19 optimal weight: 0.0020 chunk 108 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.190430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158364 restraints weight = 27366.655| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 5.05 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3934 r_free = 0.3934 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11428 Z= 0.126 Angle : 0.570 9.591 15493 Z= 0.297 Chirality : 0.042 0.188 1747 Planarity : 0.004 0.052 1959 Dihedral : 4.230 28.480 1537 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.77 % Allowed : 15.31 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1405 helix: 1.48 (0.25), residues: 438 sheet: 0.10 (0.26), residues: 369 loop : -0.39 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 44 TYR 0.017 0.001 TYR C 244 PHE 0.012 0.001 PHE A 189 TRP 0.016 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00285 (11420) covalent geometry : angle 0.56959 (15477) SS BOND : bond 0.00294 ( 8) SS BOND : angle 1.09739 ( 16) hydrogen bonds : bond 0.03466 ( 540) hydrogen bonds : angle 4.54288 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.372 Fit side-chains REVERT: A 245 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6531 (tm-30) REVERT: B 46 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6896 (mtm110) REVERT: B 198 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7601 (pp) REVERT: B 234 PHE cc_start: 0.5754 (p90) cc_final: 0.5390 (p90) REVERT: C 41 PHE cc_start: 0.5671 (t80) cc_final: 0.5428 (t80) REVERT: C 52 ILE cc_start: 0.7910 (pt) cc_final: 0.7670 (mt) REVERT: C 274 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6514 (mmt180) REVERT: F 200 MET cc_start: 0.7079 (tpt) cc_final: 0.6655 (tpt) REVERT: F 217 TYR cc_start: 0.6148 (m-80) cc_final: 0.5758 (m-80) outliers start: 22 outliers final: 19 residues processed: 183 average time/residue: 0.1179 time to fit residues: 29.9104 Evaluate side-chains 183 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN G 21 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.189967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157595 restraints weight = 29442.428| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 5.25 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11428 Z= 0.134 Angle : 0.571 10.543 15493 Z= 0.295 Chirality : 0.042 0.197 1747 Planarity : 0.004 0.052 1959 Dihedral : 4.267 28.828 1537 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.93 % Allowed : 16.04 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1405 helix: 1.53 (0.25), residues: 437 sheet: 0.03 (0.26), residues: 379 loop : -0.43 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 31 TYR 0.022 0.001 TYR C 108 PHE 0.013 0.001 PHE A 189 TRP 0.010 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00311 (11420) covalent geometry : angle 0.56998 (15477) SS BOND : bond 0.00298 ( 8) SS BOND : angle 1.07280 ( 16) hydrogen bonds : bond 0.03470 ( 540) hydrogen bonds : angle 4.55782 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.432 Fit side-chains REVERT: A 193 ASP cc_start: 0.7551 (t70) cc_final: 0.7274 (t0) REVERT: B 46 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7031 (mtm180) REVERT: B 198 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7634 (pp) REVERT: B 234 PHE cc_start: 0.5818 (p90) cc_final: 0.5456 (p90) REVERT: C 31 ARG cc_start: 0.6228 (ttp80) cc_final: 0.5967 (tmm160) REVERT: C 52 ILE cc_start: 0.7985 (pt) cc_final: 0.7748 (mt) REVERT: C 274 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6529 (mmt180) REVERT: F 200 MET cc_start: 0.7092 (tpt) cc_final: 0.6608 (tpt) REVERT: F 217 TYR cc_start: 0.6186 (m-80) cc_final: 0.5753 (m-80) outliers start: 24 outliers final: 21 residues processed: 182 average time/residue: 0.1184 time to fit residues: 29.6187 Evaluate side-chains 184 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.190588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158333 restraints weight = 26879.830| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 5.04 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11428 Z= 0.120 Angle : 0.563 11.126 15493 Z= 0.294 Chirality : 0.042 0.204 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.192 27.312 1537 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 16.28 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.23), residues: 1405 helix: 1.53 (0.25), residues: 437 sheet: 0.03 (0.26), residues: 372 loop : -0.40 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 31 TYR 0.020 0.001 TYR C 108 PHE 0.023 0.001 PHE C 41 TRP 0.009 0.001 TRP C 94 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00272 (11420) covalent geometry : angle 0.56245 (15477) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.01470 ( 16) hydrogen bonds : bond 0.03416 ( 540) hydrogen bonds : angle 4.52234 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.303 Fit side-chains REVERT: A 25 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6605 (tt0) REVERT: A 193 ASP cc_start: 0.7473 (t70) cc_final: 0.7192 (t0) REVERT: B 46 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6911 (mtm180) REVERT: B 198 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7590 (pp) REVERT: B 234 PHE cc_start: 0.5820 (p90) cc_final: 0.5457 (p90) REVERT: C 31 ARG cc_start: 0.6142 (ttp80) cc_final: 0.5900 (tmm160) REVERT: C 148 THR cc_start: 0.8177 (t) cc_final: 0.7975 (t) REVERT: C 274 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6470 (mmt180) REVERT: F 200 MET cc_start: 0.7049 (tpt) cc_final: 0.6580 (tpt) REVERT: F 217 TYR cc_start: 0.6150 (m-80) cc_final: 0.5790 (m-80) outliers start: 24 outliers final: 21 residues processed: 179 average time/residue: 0.1179 time to fit residues: 28.9943 Evaluate side-chains 181 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain F residue 204 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.189291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146000 restraints weight = 37343.980| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.32 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11428 Z= 0.145 Angle : 0.582 11.088 15493 Z= 0.304 Chirality : 0.042 0.199 1747 Planarity : 0.004 0.053 1959 Dihedral : 4.239 29.289 1537 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.69 % Allowed : 16.84 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1405 helix: 1.43 (0.25), residues: 437 sheet: 0.05 (0.26), residues: 381 loop : -0.44 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 31 TYR 0.021 0.001 TYR C 108 PHE 0.016 0.001 PHE A 189 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00337 (11420) covalent geometry : angle 0.58128 (15477) SS BOND : bond 0.00304 ( 8) SS BOND : angle 1.08966 ( 16) hydrogen bonds : bond 0.03541 ( 540) hydrogen bonds : angle 4.59483 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.71 seconds wall clock time: 48 minutes 49.46 seconds (2929.46 seconds total)