Starting phenix.real_space_refine on Fri Oct 23 05:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wvx_66293/10_2026/9wvx_66293.map" } resolution = 2.8 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5475 2.51 5 N 1435 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8543 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1736 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2566 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2009 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 248} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "S" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1753 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.58, per 1000 atoms: 0.18 Number of scatterers: 8543 At special positions: 0 Unit cell: (85.56, 118.11, 118.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1570 8.00 N 1435 7.00 C 5475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.53 Conformation dependent library (CDL) restraints added in 428.1 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.480A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.914A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.658A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.615A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.796A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.707A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 30 through 58 removed outlier: 3.806A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.876A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP R 75 " --> pdb=" O LEU R 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.603A pdb=" N MET R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL R 131 " --> pdb=" O ARG R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 142 through 144 No H-bonds generated for 'chain 'R' and resid 142 through 144' Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.764A pdb=" N VAL R 151 " --> pdb=" O ALA R 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP R 154 " --> pdb=" O CYS R 150 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 158 " --> pdb=" O TRP R 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 206 removed outlier: 3.631A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA R 204 " --> pdb=" O GLY R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 229 removed outlier: 3.921A pdb=" N ILE R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 244 Processing helix chain 'R' and resid 245 through 249 Processing helix chain 'R' and resid 260 through 267 removed outlier: 3.536A pdb=" N VAL R 266 " --> pdb=" O PRO R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 275 Processing helix chain 'R' and resid 276 through 278 No H-bonds generated for 'chain 'R' and resid 276 through 278' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.545A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.521A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (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: 6.856A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.715A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.532A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.574A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.845A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 5.820A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.065A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.395A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.880A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 143 through 148 428 hydrogen bonds defined for protein. 1188 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: 1.29 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2728 1.35 - 1.48: 2322 1.48 - 1.61: 3594 1.61 - 1.74: 0 1.74 - 1.87: 87 Bond restraints: 8731 Sorted by residual: bond pdb=" C ARG R 140 " pdb=" N ARG R 141 " ideal model delta sigma weight residual 1.329 1.290 0.038 1.60e-02 3.91e+03 5.72e+00 bond pdb=" CG LEU R 79 " pdb=" CD2 LEU R 79 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.13e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" CA LYS B 127 " pdb=" CB LYS B 127 " ideal model delta sigma weight residual 1.528 1.486 0.042 2.61e-02 1.47e+03 2.57e+00 ... (remaining 8726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 11649 2.44 - 4.88: 180 4.88 - 7.32: 19 7.32 - 9.77: 3 9.77 - 12.21: 2 Bond angle restraints: 11853 Sorted by residual: angle pdb=" N VAL R 207 " pdb=" CA VAL R 207 " pdb=" C VAL R 207 " ideal model delta sigma weight residual 112.90 106.72 6.18 9.60e-01 1.09e+00 4.15e+01 angle pdb=" N VAL R 231 " pdb=" CA VAL R 231 " pdb=" C VAL R 231 " ideal model delta sigma weight residual 112.83 106.65 6.18 9.90e-01 1.02e+00 3.90e+01 angle pdb=" N ILE R 277 " pdb=" CA ILE R 277 " pdb=" C ILE R 277 " ideal model delta sigma weight residual 112.43 108.00 4.43 9.20e-01 1.18e+00 2.32e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 124.00 -9.60 2.30e+00 1.89e-01 1.74e+01 angle pdb=" N PHE R 232 " pdb=" CA PHE R 232 " pdb=" C PHE R 232 " ideal model delta sigma weight residual 113.41 108.53 4.88 1.22e+00 6.72e-01 1.60e+01 ... (remaining 11848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 4693 16.59 - 33.18: 351 33.18 - 49.77: 53 49.77 - 66.35: 8 66.35 - 82.94: 7 Dihedral angle restraints: 5112 sinusoidal: 1902 harmonic: 3210 Sorted by residual: dihedral pdb=" CB CYS R 168 " pdb=" SG CYS R 168 " pdb=" SG CYS R 180 " pdb=" CB CYS R 180 " ideal model delta sinusoidal sigma weight residual -86.00 -168.94 82.94 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 844 0.041 - 0.082: 392 0.082 - 0.123: 103 0.123 - 0.164: 18 0.164 - 0.205: 5 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA ALA B 299 " pdb=" N ALA B 299 " pdb=" C ALA B 299 " pdb=" CB ALA B 299 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE S 51 " pdb=" CA ILE S 51 " pdb=" CG1 ILE S 51 " pdb=" CG2 ILE S 51 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1359 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 248 " 0.012 2.00e-02 2.50e+03 1.72e-02 7.40e+00 pdb=" CG TRP R 248 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP R 248 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP R 248 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 248 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 248 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 248 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 248 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 248 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 248 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO S 75 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 101 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO R 102 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 102 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 102 " -0.020 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 111 2.63 - 3.20: 7638 3.20 - 3.76: 12870 3.76 - 4.33: 18532 4.33 - 4.90: 31408 Nonbonded interactions: 70559 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.061 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.135 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.190 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.213 3.120 ... (remaining 70554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.008 0.064 8734 Z= 0.340 Angle : 0.807 12.207 11859 Z= 0.472 Chirality : 0.049 0.205 1362 Planarity : 0.004 0.043 1489 Dihedral : 12.140 81.469 3033 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1097 helix: -0.22 (0.29), residues: 371 sheet: -0.21 (0.29), residues: 278 loop : -0.93 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 98 TYR 0.021 0.002 TYR B 105 PHE 0.018 0.002 PHE A 189 TRP 0.045 0.002 TRP R 248 HIS 0.007 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.34 ( 8731) covalent geometry : angle 0.80350 / 0.47 (11853) SS BOND : bond 0.01943 / 1.21 ( 3) SS BOND : angle 3.29266 / 1.27 ( 6) hydrogen bonds : bond 0.17999 / 12.11 ( 419) hydrogen bonds : angle 7.67687 / 5.46 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8984 (t80) cc_final: 0.8763 (t80) REVERT: B 20 ASP cc_start: 0.8850 (m-30) cc_final: 0.8334 (m-30) REVERT: B 153 ASP cc_start: 0.8245 (m-30) cc_final: 0.7999 (m-30) REVERT: B 227 SER cc_start: 0.8958 (m) cc_final: 0.8757 (m) REVERT: B 312 ASP cc_start: 0.8408 (t0) cc_final: 0.8208 (t0) REVERT: C 58 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8530 (mt-10) REVERT: R 166 LYS cc_start: 0.8740 (tmmt) cc_final: 0.8462 (ttpp) REVERT: S 18 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7165 (tpp-160) REVERT: S 73 ASP cc_start: 0.7707 (t0) cc_final: 0.7006 (t0) REVERT: S 87 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7125 (mtm-85) REVERT: S 89 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8317 (mt-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.5579 time to fit residues: 108.7421 Evaluate side-chains 141 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 17 GLN B 75 GLN B 259 GLN B 340 ASN R 82 GLN S 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080269 restraints weight = 12136.835| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.81 r_work: 0.2806 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8734 Z= 0.141 Angle : 0.599 8.342 11859 Z= 0.310 Chirality : 0.043 0.144 1362 Planarity : 0.004 0.036 1489 Dihedral : 4.618 22.903 1192 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.41 % Allowed : 9.54 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.38 (0.26), residues: 1097 helix: 0.56 (0.28), residues: 374 sheet: -0.20 (0.30), residues: 266 loop : -0.87 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.019 0.001 TYR S 178 PHE 0.020 0.001 PHE R 183 TRP 0.021 0.001 TRP R 248 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8731) covalent geometry : angle 0.59729 / 0.31 (11853) SS BOND : bond 0.01273 / 0.79 ( 3) SS BOND : angle 2.20463 / 0.89 ( 6) hydrogen bonds : bond 0.04160 / 2.84 ( 419) hydrogen bonds : angle 4.87999 / 3.56 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: A 316 THR cc_start: 0.8745 (p) cc_final: 0.8353 (t) REVERT: B 20 ASP cc_start: 0.8875 (m-30) cc_final: 0.8388 (m-30) REVERT: B 153 ASP cc_start: 0.8301 (m-30) cc_final: 0.8085 (m-30) REVERT: B 212 ASP cc_start: 0.8466 (t0) cc_final: 0.8222 (t0) REVERT: B 312 ASP cc_start: 0.8685 (t0) cc_final: 0.8369 (t0) REVERT: C 18 GLN cc_start: 0.7972 (tp40) cc_final: 0.7699 (tp40) REVERT: C 58 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8693 (mt-10) REVERT: S 73 ASP cc_start: 0.7810 (t0) cc_final: 0.7061 (t0) outliers start: 22 outliers final: 5 residues processed: 178 average time/residue: 0.4994 time to fit residues: 95.2591 Evaluate side-chains 146 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [52, 67, 10, 47, 75, 11, 40, 82, 101, 49, 15] chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 17 GLN B 259 GLN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.079234 restraints weight = 12072.696| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.80 r_work: 0.2789 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8734 Z= 0.178 Angle : 0.597 10.046 11859 Z= 0.305 Chirality : 0.044 0.160 1362 Planarity : 0.004 0.035 1489 Dihedral : 4.445 22.092 1192 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.40 % Allowed : 13.05 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.09 (0.26), residues: 1097 helix: 1.00 (0.28), residues: 379 sheet: -0.11 (0.30), residues: 265 loop : -0.87 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 148 TYR 0.015 0.001 TYR S 178 PHE 0.018 0.001 PHE R 183 TRP 0.016 0.001 TRP R 248 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 8731) covalent geometry : angle 0.59482 / 0.30 (11853) SS BOND : bond 0.01320 / 0.82 ( 3) SS BOND : angle 2.23527 / 0.89 ( 6) hydrogen bonds : bond 0.03851 / 2.63 ( 419) hydrogen bonds : angle 4.59301 / 3.36 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: A 316 THR cc_start: 0.8771 (p) cc_final: 0.8370 (t) REVERT: B 20 ASP cc_start: 0.8906 (m-30) cc_final: 0.8423 (m-30) REVERT: B 212 ASP cc_start: 0.8449 (t0) cc_final: 0.8228 (t0) REVERT: B 312 ASP cc_start: 0.8678 (t0) cc_final: 0.8348 (t0) REVERT: C 58 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8707 (mt-10) REVERT: R 79 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8016 (mt) REVERT: R 90 LEU cc_start: 0.9351 (mm) cc_final: 0.9055 (mm) REVERT: R 126 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8047 (mm-30) REVERT: S 73 ASP cc_start: 0.7868 (t0) cc_final: 0.7140 (t0) outliers start: 31 outliers final: 14 residues processed: 169 average time/residue: 0.5054 time to fit residues: 91.4768 Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [52, 12, 79, 21, 70, 63, 34, 26, 83, 47, 78] chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 17 GLN B 32 GLN B 75 GLN B 259 GLN S 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.082344 restraints weight = 12255.661| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.85 r_work: 0.2843 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8734 Z= 0.110 Angle : 0.533 7.472 11859 Z= 0.274 Chirality : 0.041 0.159 1362 Planarity : 0.004 0.033 1489 Dihedral : 4.172 22.198 1192 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.74 % Allowed : 14.69 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.17 (0.26), residues: 1097 helix: 1.35 (0.28), residues: 379 sheet: 0.02 (0.30), residues: 270 loop : -0.84 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 32 TYR 0.017 0.001 TYR A 302 PHE 0.016 0.001 PHE R 183 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8731) covalent geometry : angle 0.53101 / 0.27 (11853) SS BOND : bond 0.00890 / 0.55 ( 3) SS BOND : angle 1.93351 / 0.78 ( 6) hydrogen bonds : bond 0.03257 / 2.22 ( 419) hydrogen bonds : angle 4.35048 / 3.18 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: A 306 GLN cc_start: 0.8791 (mm110) cc_final: 0.8514 (mm-40) REVERT: A 316 THR cc_start: 0.8675 (p) cc_final: 0.8288 (t) REVERT: B 20 ASP cc_start: 0.8891 (m-30) cc_final: 0.8417 (m-30) REVERT: B 197 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7921 (tpm-80) REVERT: B 312 ASP cc_start: 0.8713 (t0) cc_final: 0.8401 (t0) REVERT: C 58 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8727 (mt-10) REVERT: R 79 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8014 (mt) REVERT: R 90 LEU cc_start: 0.9361 (mm) cc_final: 0.9136 (mm) REVERT: R 166 LYS cc_start: 0.8444 (tttm) cc_final: 0.8231 (tttm) REVERT: R 171 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8148 (mm) REVERT: S 73 ASP cc_start: 0.7846 (t0) cc_final: 0.7110 (t0) REVERT: S 128 MET cc_start: 0.9179 (mmm) cc_final: 0.8545 (mmm) REVERT: S 174 GLN cc_start: 0.7879 (tt0) cc_final: 0.7563 (pt0) outliers start: 25 outliers final: 7 residues processed: 169 average time/residue: 0.5128 time to fit residues: 92.8154 Evaluate side-chains 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 252 ASP Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [42, 87, 91, 51, 29, 35, 85, 5, 80, 30, 71] chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 259 GLN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.081458 restraints weight = 12755.899| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.76 r_work: 0.2864 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8734 Z= 0.109 Angle : 0.543 8.050 11859 Z= 0.276 Chirality : 0.041 0.157 1362 Planarity : 0.004 0.033 1489 Dihedral : 4.026 26.018 1192 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.63 % Allowed : 16.34 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.45 (0.26), residues: 1097 helix: 1.64 (0.28), residues: 378 sheet: 0.13 (0.30), residues: 276 loop : -0.72 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.013 0.001 TYR S 178 PHE 0.015 0.001 PHE R 183 TRP 0.011 0.001 TRP R 53 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8731) covalent geometry : angle 0.54194 / 0.28 (11853) SS BOND : bond 0.01027 / 0.64 ( 3) SS BOND : angle 1.89372 / 0.73 ( 6) hydrogen bonds : bond 0.03163 / 2.15 ( 419) hydrogen bonds : angle 4.22535 / 3.10 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: A 306 GLN cc_start: 0.8611 (mm110) cc_final: 0.8276 (mt0) REVERT: A 316 THR cc_start: 0.8640 (p) cc_final: 0.8261 (t) REVERT: B 20 ASP cc_start: 0.8873 (m-30) cc_final: 0.8578 (m-30) REVERT: B 312 ASP cc_start: 0.8641 (t0) cc_final: 0.8321 (t0) REVERT: C 48 ASP cc_start: 0.8513 (t0) cc_final: 0.8143 (t0) REVERT: C 58 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8702 (mt-10) REVERT: R 79 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7775 (mt) REVERT: R 90 LEU cc_start: 0.9339 (mm) cc_final: 0.9111 (mm) REVERT: R 171 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7961 (mm) REVERT: S 73 ASP cc_start: 0.7551 (t0) cc_final: 0.6786 (t0) REVERT: S 87 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7367 (mtm-85) REVERT: S 174 GLN cc_start: 0.7618 (tt0) cc_final: 0.7329 (pt0) outliers start: 24 outliers final: 9 residues processed: 165 average time/residue: 0.5097 time to fit residues: 89.9557 Evaluate side-chains 148 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain R residue 252 ASP Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [42, 54, 74, 26, 25, 88, 108, 24, 43, 34, 66] chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 17 GLN B 75 GLN B 259 GLN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080727 restraints weight = 12605.833| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.73 r_work: 0.2853 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8734 Z= 0.123 Angle : 0.539 7.482 11859 Z= 0.276 Chirality : 0.042 0.166 1362 Planarity : 0.003 0.035 1489 Dihedral : 4.001 31.043 1192 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.19 % Allowed : 17.65 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.55 (0.26), residues: 1097 helix: 1.78 (0.28), residues: 379 sheet: 0.14 (0.30), residues: 276 loop : -0.70 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 61 TYR 0.013 0.001 TYR S 178 PHE 0.013 0.001 PHE R 183 TRP 0.022 0.001 TRP R 53 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 8731) covalent geometry : angle 0.53768 / 0.28 (11853) SS BOND : bond 0.01018 / 0.63 ( 3) SS BOND : angle 1.83864 / 0.72 ( 6) hydrogen bonds : bond 0.03197 / 2.17 ( 419) hydrogen bonds : angle 4.20555 / 3.08 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: A 302 TYR cc_start: 0.8693 (t80) cc_final: 0.8462 (t80) REVERT: A 316 THR cc_start: 0.8642 (p) cc_final: 0.8284 (t) REVERT: B 20 ASP cc_start: 0.8872 (m-30) cc_final: 0.8582 (m-30) REVERT: B 229 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 291 ASP cc_start: 0.7926 (m-30) cc_final: 0.7694 (m-30) REVERT: B 312 ASP cc_start: 0.8648 (t0) cc_final: 0.8320 (t0) REVERT: C 58 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8712 (mt-10) REVERT: R 79 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7814 (mt) REVERT: R 90 LEU cc_start: 0.9354 (mm) cc_final: 0.9133 (mm) REVERT: S 73 ASP cc_start: 0.7562 (t0) cc_final: 0.6784 (t0) REVERT: S 174 GLN cc_start: 0.7656 (tt0) cc_final: 0.7296 (pt0) outliers start: 20 outliers final: 7 residues processed: 152 average time/residue: 0.5160 time to fit residues: 83.7668 Evaluate side-chains 147 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [81, 101, 15, 20, 12, 6, 60, 82, 76, 56, 89] chunk 81 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 306 GLN B 259 GLN B 340 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.081331 restraints weight = 12757.635| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.74 r_work: 0.2861 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8734 Z= 0.116 Angle : 0.543 8.655 11859 Z= 0.276 Chirality : 0.041 0.172 1362 Planarity : 0.003 0.034 1489 Dihedral : 3.960 32.729 1192 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.41 % Allowed : 18.64 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.64 (0.26), residues: 1097 helix: 1.86 (0.28), residues: 381 sheet: 0.10 (0.29), residues: 288 loop : -0.61 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 148 TYR 0.013 0.001 TYR S 178 PHE 0.014 0.001 PHE A 189 TRP 0.027 0.001 TRP R 53 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8731) covalent geometry : angle 0.54173 / 0.28 (11853) SS BOND : bond 0.00971 / 0.60 ( 3) SS BOND : angle 1.71854 / 0.67 ( 6) hydrogen bonds : bond 0.03100 / 2.11 ( 419) hydrogen bonds : angle 4.14602 / 3.03 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: A 316 THR cc_start: 0.8668 (p) cc_final: 0.8331 (t) REVERT: B 20 ASP cc_start: 0.8850 (m-30) cc_final: 0.8557 (m-30) REVERT: B 229 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7891 (mt) REVERT: B 291 ASP cc_start: 0.7942 (m-30) cc_final: 0.7737 (m-30) REVERT: B 312 ASP cc_start: 0.8683 (t0) cc_final: 0.8322 (t0) REVERT: C 58 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8657 (mt-10) REVERT: R 79 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7804 (mt) REVERT: R 90 LEU cc_start: 0.9350 (mm) cc_final: 0.9129 (mm) REVERT: R 166 LYS cc_start: 0.8266 (tttm) cc_final: 0.7876 (pptt) REVERT: R 179 TRP cc_start: 0.8050 (m100) cc_final: 0.7709 (m-90) REVERT: S 73 ASP cc_start: 0.7546 (t0) cc_final: 0.6798 (t0) REVERT: S 174 GLN cc_start: 0.7672 (tt0) cc_final: 0.7327 (pt0) outliers start: 22 outliers final: 8 residues processed: 161 average time/residue: 0.4903 time to fit residues: 84.6605 Evaluate side-chains 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [86, 0, 103, 49, 80, 27, 6, 69, 39, 7, 97] chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN A 306 GLN B 259 GLN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080867 restraints weight = 12667.028| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.73 r_work: 0.2856 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8734 Z= 0.128 Angle : 0.550 8.275 11859 Z= 0.281 Chirality : 0.042 0.172 1362 Planarity : 0.003 0.035 1489 Dihedral : 3.924 26.717 1192 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.08 % Allowed : 19.63 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.69 (0.26), residues: 1097 helix: 1.93 (0.28), residues: 381 sheet: 0.12 (0.29), residues: 287 loop : -0.60 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 148 TYR 0.026 0.001 TYR A 302 PHE 0.015 0.001 PHE R 183 TRP 0.028 0.001 TRP R 53 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8731) covalent geometry : angle 0.54837 / 0.28 (11853) SS BOND : bond 0.01033 / 0.64 ( 3) SS BOND : angle 1.72559 / 0.68 ( 6) hydrogen bonds : bond 0.03171 / 2.15 ( 419) hydrogen bonds : angle 4.15479 / 3.03 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: A 306 GLN cc_start: 0.8625 (mm110) cc_final: 0.8291 (mt0) REVERT: A 316 THR cc_start: 0.8668 (p) cc_final: 0.8346 (t) REVERT: B 20 ASP cc_start: 0.8841 (m-30) cc_final: 0.8541 (m-30) REVERT: B 44 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: B 291 ASP cc_start: 0.7892 (m-30) cc_final: 0.7655 (m-30) REVERT: B 312 ASP cc_start: 0.8697 (t0) cc_final: 0.8307 (t0) REVERT: C 58 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8687 (mt-10) REVERT: R 31 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7567 (tm) REVERT: R 35 PHE cc_start: 0.8066 (m-80) cc_final: 0.7692 (m-80) REVERT: R 79 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7805 (mt) REVERT: R 166 LYS cc_start: 0.8271 (tttm) cc_final: 0.8044 (ttpt) REVERT: R 179 TRP cc_start: 0.8044 (m100) cc_final: 0.7685 (m-90) REVERT: S 73 ASP cc_start: 0.7566 (t0) cc_final: 0.6807 (t0) REVERT: S 174 GLN cc_start: 0.7686 (tt0) cc_final: 0.7343 (pt0) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 0.5086 time to fit residues: 84.8788 Evaluate side-chains 150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [73, 14, 75, 55, 57, 84, 1, 70, 22, 63, 94] chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 259 GLN S 3 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.081141 restraints weight = 12629.410| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.73 r_work: 0.2872 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8734 Z= 0.120 Angle : 0.567 9.761 11859 Z= 0.287 Chirality : 0.043 0.268 1362 Planarity : 0.004 0.045 1489 Dihedral : 3.900 25.857 1192 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.30 % Allowed : 19.85 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.26), residues: 1097 helix: 2.03 (0.27), residues: 381 sheet: 0.12 (0.29), residues: 288 loop : -0.54 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 19 TYR 0.013 0.001 TYR B 124 PHE 0.013 0.001 PHE A 189 TRP 0.033 0.001 TRP R 53 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8731) covalent geometry : angle 0.56592 / 0.29 (11853) SS BOND : bond 0.01000 / 0.62 ( 3) SS BOND : angle 1.62739 / 0.64 ( 6) hydrogen bonds : bond 0.03104 / 2.10 ( 419) hydrogen bonds : angle 4.17565 / 3.05 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: A 302 TYR cc_start: 0.8780 (t80) cc_final: 0.8496 (t80) REVERT: A 306 GLN cc_start: 0.8606 (mm110) cc_final: 0.8218 (mt0) REVERT: A 316 THR cc_start: 0.8668 (p) cc_final: 0.8366 (t) REVERT: B 20 ASP cc_start: 0.8817 (m-30) cc_final: 0.8563 (m-30) REVERT: B 44 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: B 270 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9124 (pp) REVERT: B 291 ASP cc_start: 0.7948 (m-30) cc_final: 0.7715 (m-30) REVERT: B 312 ASP cc_start: 0.8701 (t0) cc_final: 0.8330 (t0) REVERT: C 58 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8696 (mt-10) REVERT: R 31 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7572 (tm) REVERT: R 35 PHE cc_start: 0.8144 (m-80) cc_final: 0.7775 (m-80) REVERT: R 79 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7801 (mt) REVERT: R 179 TRP cc_start: 0.8023 (m100) cc_final: 0.7685 (m-90) REVERT: S 73 ASP cc_start: 0.7566 (t0) cc_final: 0.6810 (t0) REVERT: S 174 GLN cc_start: 0.7667 (tt0) cc_final: 0.7326 (pt0) outliers start: 21 outliers final: 13 residues processed: 159 average time/residue: 0.5165 time to fit residues: 87.8517 Evaluate side-chains 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [96, 21, 58, 3, 65, 40, 16, 54, 17, 43, 6] chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 259 GLN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.082470 restraints weight = 12612.519| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.74 r_work: 0.2891 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8734 Z= 0.112 Angle : 0.576 11.357 11859 Z= 0.292 Chirality : 0.042 0.241 1362 Planarity : 0.004 0.050 1489 Dihedral : 3.882 26.869 1192 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.19 % Allowed : 20.50 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.89 (0.26), residues: 1097 helix: 2.16 (0.27), residues: 381 sheet: 0.15 (0.30), residues: 289 loop : -0.49 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 148 TYR 0.013 0.001 TYR B 124 PHE 0.021 0.001 PHE R 183 TRP 0.038 0.001 TRP R 53 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 8731) covalent geometry : angle 0.57547 / 0.29 (11853) SS BOND : bond 0.00873 / 0.54 ( 3) SS BOND : angle 1.48335 / 0.59 ( 6) hydrogen bonds : bond 0.03074 / 2.06 ( 419) hydrogen bonds : angle 4.16338 / 3.03 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8757 (t80) cc_final: 0.8409 (t80) REVERT: A 306 GLN cc_start: 0.8585 (mm110) cc_final: 0.8196 (mt0) REVERT: A 316 THR cc_start: 0.8630 (p) cc_final: 0.8358 (t) REVERT: B 20 ASP cc_start: 0.8825 (m-30) cc_final: 0.8549 (m-30) REVERT: B 44 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: B 291 ASP cc_start: 0.7920 (m-30) cc_final: 0.7691 (m-30) REVERT: B 312 ASP cc_start: 0.8725 (t0) cc_final: 0.8359 (t0) REVERT: R 31 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7504 (tm) REVERT: R 35 PHE cc_start: 0.8144 (m-80) cc_final: 0.7836 (m-80) REVERT: R 79 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7823 (mt) REVERT: R 179 TRP cc_start: 0.8065 (m100) cc_final: 0.7800 (m100) REVERT: S 73 ASP cc_start: 0.7545 (t0) cc_final: 0.6795 (t0) REVERT: S 87 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: S 174 GLN cc_start: 0.7652 (tt0) cc_final: 0.7319 (pt0) outliers start: 20 outliers final: 9 residues processed: 160 average time/residue: 0.4914 time to fit residues: 84.1133 Evaluate side-chains 150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 234 LEU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: [11, 30, 61, 37, 43, 71, 88, 47, 70, 32, 80] chunk 11 optimal weight: 0.0010 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 259 GLN S 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.082751 restraints weight = 12635.298| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.74 r_work: 0.2896 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8734 Z= 0.112 Angle : 0.595 10.967 11859 Z= 0.296 Chirality : 0.042 0.219 1362 Planarity : 0.004 0.056 1489 Dihedral : 3.851 26.795 1192 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.54 % Allowed : 21.38 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.95 (0.26), residues: 1097 helix: 2.24 (0.27), residues: 381 sheet: 0.18 (0.30), residues: 289 loop : -0.48 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 148 TYR 0.013 0.001 TYR B 124 PHE 0.022 0.001 PHE R 183 TRP 0.040 0.001 TRP R 53 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 8731) covalent geometry : angle 0.59421 / 0.30 (11853) SS BOND : bond 0.00861 / 0.53 ( 3) SS BOND : angle 1.46857 / 0.59 ( 6) hydrogen bonds : bond 0.03060 / 2.06 ( 419) hydrogen bonds : angle 4.14996 / 3.03 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.18 seconds wall clock time: 49 minutes 29.37 seconds (2969.37 seconds total)