Starting phenix.real_space_refine on Wed Feb 4 03:54:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9s_47802/02_2026/9e9s_47802.cif" } resolution = 2.68 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= -0.011 sd= 0.608 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 58 5.16 5 C 5364 2.51 5 N 1468 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8551 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1962 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "D" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2392 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'NAG': 1, 'PG2': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 2.14, per 1000 atoms: 0.25 Number of scatterers: 8551 At special positions: 0 Unit cell: (78.12, 99.12, 136.92, 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 58 16.00 O 1661 8.00 N 1468 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG D 402 " - " ASN D 10 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 314.0 milliseconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.0% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.590A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.768A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.587A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.587A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.803A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.585A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.575A 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 Processing helix chain 'D' and resid 20 through 46 removed outlier: 3.603A pdb=" N LEU D 26 " --> pdb=" O MET D 22 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE D 27 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 90 Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 102 through 136 Processing helix chain 'D' and resid 136 through 144 removed outlier: 3.519A pdb=" N ARG D 142 " --> pdb=" O PHE D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 193 through 235 removed outlier: 3.989A pdb=" N TYR D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 234 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 291 removed outlier: 3.519A pdb=" N LEU D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) Proline residue: D 280 - end of helix removed outlier: 3.659A pdb=" N ALA D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 297 through 313 removed outlier: 3.836A pdb=" N ALA D 303 " --> pdb=" O THR D 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.708A pdb=" N ILE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 328 through 336 removed outlier: 4.782A pdb=" N PHE D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE D 335 " --> pdb=" O PHE D 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.713A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.618A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.452A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.531A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.679A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.977A 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: 6.846A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.337A 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: 3.764A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.064A 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: 6.575A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.646A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.723A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 177 removed outlier: 4.531A pdb=" N TRP D 182 " --> pdb=" O TYR D 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.927A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1227 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: 1.41 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1797 1.33 - 1.45: 1980 1.45 - 1.57: 4770 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8630 Sorted by residual: bond pdb=" CAI Y01 D 403 " pdb=" CAZ Y01 D 403 " ideal model delta sigma weight residual 1.332 1.297 0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" CAL Y01 D 403 " pdb=" CAX Y01 D 403 " ideal model delta sigma weight residual 1.540 1.507 0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" CBF Y01 D 403 " pdb=" CBH Y01 D 403 " ideal model delta sigma weight residual 1.550 1.521 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CBG Y01 D 403 " pdb=" CBI Y01 D 403 " ideal model delta sigma weight residual 1.537 1.558 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C LEU D 279 " pdb=" N PRO D 280 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 1.07e+00 ... (remaining 8625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 11522 1.82 - 3.64: 122 3.64 - 5.46: 23 5.46 - 7.28: 8 7.28 - 9.10: 1 Bond angle restraints: 11676 Sorted by residual: angle pdb=" CAM Y01 D 403 " pdb=" CAY Y01 D 403 " pdb=" OAW Y01 D 403 " ideal model delta sigma weight residual 111.19 120.29 -9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" C LEU D 100 " pdb=" N ASP D 101 " pdb=" CA ASP D 101 " ideal model delta sigma weight residual 122.89 127.50 -4.61 1.72e+00 3.38e-01 7.19e+00 angle pdb=" C14 PG2 D 401 " pdb=" C15 PG2 D 401 " pdb=" O5 PG2 D 401 " ideal model delta sigma weight residual 113.07 106.66 6.41 3.00e+00 1.11e-01 4.56e+00 angle pdb=" OAF Y01 D 403 " pdb=" CAX Y01 D 403 " pdb=" OAH Y01 D 403 " ideal model delta sigma weight residual 126.47 120.21 6.26 3.00e+00 1.11e-01 4.36e+00 angle pdb=" C1 PG2 D 401 " pdb=" C2 PG2 D 401 " pdb=" C3 PG2 D 401 " ideal model delta sigma weight residual 116.23 110.06 6.17 3.00e+00 1.11e-01 4.24e+00 ... (remaining 11671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.88: 5020 22.88 - 45.76: 208 45.76 - 68.64: 11 68.64 - 91.52: 2 91.52 - 114.40: 1 Dihedral angle restraints: 5242 sinusoidal: 2141 harmonic: 3101 Sorted by residual: dihedral pdb=" CB CYS D 105 " pdb=" SG CYS D 105 " pdb=" SG CYS D 183 " pdb=" CB CYS D 183 " ideal model delta sinusoidal sigma weight residual -86.00 -124.13 38.13 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" C17 PG2 D 401 " pdb=" C15 PG2 D 401 " pdb=" C16 PG2 D 401 " pdb=" O5 PG2 D 401 " ideal model delta sinusoidal sigma weight residual 57.42 -56.98 114.40 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CA ASP D 262 " pdb=" C ASP D 262 " pdb=" N HIS D 263 " pdb=" CA HIS D 263 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1217 0.082 - 0.164: 96 0.164 - 0.246: 2 0.246 - 0.327: 1 0.327 - 0.409: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CBG Y01 D 403 " pdb=" CAQ Y01 D 403 " pdb=" CBD Y01 D 403 " pdb=" CBI Y01 D 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CBH Y01 D 403 " pdb=" CAT Y01 D 403 " pdb=" CAZ Y01 D 403 " pdb=" CBF Y01 D 403 " both_signs ideal model delta sigma weight residual False -2.85 -2.56 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CBE Y01 D 403 " pdb=" CAP Y01 D 403 " pdb=" CBB Y01 D 403 " pdb=" CBI Y01 D 403 " both_signs ideal model delta sigma weight residual False 2.57 2.79 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1314 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.013 2.00e-02 2.50e+03 1.10e-02 2.43e+00 pdb=" CG TYR B 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 166 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO D 167 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.021 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2122 2.79 - 3.32: 7391 3.32 - 3.85: 13904 3.85 - 4.37: 17627 4.37 - 4.90: 29852 Nonbonded interactions: 70896 Sorted by model distance: nonbonded pdb=" O ALA D 308 " pdb=" O HOH D 501 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.272 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.318 3.120 nonbonded pdb=" O GLU A 230 " pdb=" O HOH A 401 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.320 3.040 ... (remaining 70891 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: 3.450 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.003 0.041 8635 Z= 0.125 Angle : 0.524 9.102 11687 Z= 0.261 Chirality : 0.045 0.409 1317 Planarity : 0.004 0.048 1490 Dihedral : 11.644 114.399 3226 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.23), residues: 1053 helix: -1.62 (0.20), residues: 397 sheet: 0.56 (0.34), residues: 224 loop : -0.33 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 7 TYR 0.027 0.001 TYR B 59 PHE 0.011 0.001 PHE B 234 TRP 0.011 0.001 TRP A 234 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8630) covalent geometry : angle 0.52398 (11676) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.60627 ( 8) hydrogen bonds : bond 0.25627 ( 428) hydrogen bonds : angle 7.94319 ( 1227) link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 0.78919 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7543 (mtp-110) REVERT: A 21 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7393 (tp30) REVERT: A 31 GLN cc_start: 0.8027 (mt0) cc_final: 0.7364 (pt0) REVERT: A 216 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8269 (mtmt) REVERT: A 356 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.6959 (ptt-90) REVERT: A 358 TYR cc_start: 0.8684 (m-80) cc_final: 0.8246 (m-80) REVERT: B 42 ARG cc_start: 0.8213 (tpt-90) cc_final: 0.7542 (tpt170) REVERT: B 215 GLU cc_start: 0.8475 (mp0) cc_final: 0.8088 (mp0) REVERT: B 217 MET cc_start: 0.8730 (ptp) cc_final: 0.8415 (ptt) REVERT: D 16 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8306 (mttm) REVERT: D 78 LEU cc_start: 0.8700 (tp) cc_final: 0.8440 (tt) REVERT: D 145 THR cc_start: 0.8403 (m) cc_final: 0.7999 (p) REVERT: D 147 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7793 (ttp-170) REVERT: D 190 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7910 (mp0) REVERT: D 262 ASP cc_start: 0.8338 (p0) cc_final: 0.8000 (m-30) REVERT: D 276 MET cc_start: 0.8506 (ttp) cc_final: 0.8221 (ttm) REVERT: N 110 VAL cc_start: 0.8435 (t) cc_final: 0.8134 (m) REVERT: N 127 SER cc_start: 0.8679 (p) cc_final: 0.8295 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.7546 time to fit residues: 125.7492 Evaluate side-chains 132 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 35 ASN D 233 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110330 restraints weight = 10350.886| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8635 Z= 0.133 Angle : 0.506 7.763 11687 Z= 0.275 Chirality : 0.042 0.150 1317 Planarity : 0.004 0.043 1490 Dihedral : 5.618 100.134 1290 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.66 % Allowed : 7.73 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1053 helix: 1.37 (0.24), residues: 399 sheet: 0.83 (0.35), residues: 216 loop : -0.35 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.012 0.001 TYR D 199 PHE 0.015 0.001 PHE A 212 TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8630) covalent geometry : angle 0.50567 (11676) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.63689 ( 8) hydrogen bonds : bond 0.05182 ( 428) hydrogen bonds : angle 4.71604 ( 1227) link_NAG-ASN : bond 0.00175 ( 1) link_NAG-ASN : angle 0.70210 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6663 (mm-30) REVERT: A 31 GLN cc_start: 0.7492 (mt0) cc_final: 0.6837 (pt0) REVERT: A 216 LYS cc_start: 0.8317 (mtmt) cc_final: 0.8039 (mtmt) REVERT: A 293 LYS cc_start: 0.6512 (mttp) cc_final: 0.6117 (mtpt) REVERT: A 347 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7433 (ttp-110) REVERT: A 356 ARG cc_start: 0.7139 (mtm-85) cc_final: 0.6927 (ptt-90) REVERT: A 358 TYR cc_start: 0.8373 (m-80) cc_final: 0.7859 (m-80) REVERT: B 13 GLN cc_start: 0.7574 (tm-30) cc_final: 0.7279 (tp40) REVERT: B 42 ARG cc_start: 0.8129 (tpt-90) cc_final: 0.7283 (tpt170) REVERT: B 44 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7586 (mt0) REVERT: B 215 GLU cc_start: 0.8101 (mp0) cc_final: 0.7607 (mp0) REVERT: B 217 MET cc_start: 0.8289 (ptp) cc_final: 0.7786 (ptt) REVERT: C 13 ARG cc_start: 0.7185 (ttp-170) cc_final: 0.6932 (ttp-110) REVERT: C 21 MET cc_start: 0.7629 (mmm) cc_final: 0.7286 (tpp) REVERT: C 42 GLU cc_start: 0.7594 (tt0) cc_final: 0.7093 (mt-10) REVERT: D 16 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8259 (mttm) REVERT: D 43 ARG cc_start: 0.7221 (ttt90) cc_final: 0.6994 (ttm-80) REVERT: D 147 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7509 (ttt-90) REVERT: D 190 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7990 (mp0) REVERT: D 262 ASP cc_start: 0.8446 (p0) cc_final: 0.8104 (m-30) REVERT: D 276 MET cc_start: 0.8621 (ttp) cc_final: 0.8353 (ttm) REVERT: N 53 GLN cc_start: 0.7131 (mp10) cc_final: 0.6868 (mp10) REVERT: N 76 LYS cc_start: 0.7467 (mtmt) cc_final: 0.7244 (mtmm) REVERT: N 110 VAL cc_start: 0.8236 (t) cc_final: 0.7934 (m) REVERT: N 127 SER cc_start: 0.8491 (p) cc_final: 0.8106 (t) outliers start: 6 outliers final: 2 residues processed: 145 average time/residue: 0.7807 time to fit residues: 118.8371 Evaluate side-chains 136 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 138 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 17 GLN B 35 ASN D 102 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110114 restraints weight = 10272.893| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.05 r_work: 0.3225 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8635 Z= 0.118 Angle : 0.475 7.590 11687 Z= 0.254 Chirality : 0.041 0.147 1317 Planarity : 0.003 0.040 1490 Dihedral : 5.427 99.581 1290 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 9.94 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1053 helix: 2.42 (0.25), residues: 401 sheet: 0.69 (0.35), residues: 222 loop : -0.26 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.012 0.001 TYR D 199 PHE 0.012 0.001 PHE A 212 TRP 0.022 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8630) covalent geometry : angle 0.47434 (11676) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.58224 ( 8) hydrogen bonds : bond 0.04549 ( 428) hydrogen bonds : angle 4.33546 ( 1227) link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 0.73265 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6579 (mm-30) REVERT: A 27 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7309 (mt-10) REVERT: A 31 GLN cc_start: 0.7324 (mt0) cc_final: 0.6738 (pt0) REVERT: A 216 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8039 (mtmt) REVERT: A 293 LYS cc_start: 0.6339 (mttp) cc_final: 0.5971 (mtpt) REVERT: A 322 GLU cc_start: 0.7798 (tp30) cc_final: 0.7594 (mm-30) REVERT: A 347 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7395 (ttp-110) REVERT: A 356 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6856 (ptt-90) REVERT: A 358 TYR cc_start: 0.8376 (m-80) cc_final: 0.7894 (m-80) REVERT: B 13 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7160 (tp40) REVERT: B 42 ARG cc_start: 0.8103 (tpt-90) cc_final: 0.7185 (tpt170) REVERT: B 44 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: B 214 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7350 (mmp80) REVERT: B 215 GLU cc_start: 0.8061 (mp0) cc_final: 0.7535 (mp0) REVERT: B 217 MET cc_start: 0.8218 (ptp) cc_final: 0.7683 (ptt) REVERT: C 21 MET cc_start: 0.7530 (mmm) cc_final: 0.7190 (tpp) REVERT: C 42 GLU cc_start: 0.7553 (tt0) cc_final: 0.7041 (mt-10) REVERT: D 16 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8258 (mttm) REVERT: D 144 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8514 (mt) REVERT: D 151 LEU cc_start: 0.7563 (pp) cc_final: 0.7028 (mt) REVERT: D 190 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7986 (mp0) REVERT: D 276 MET cc_start: 0.8616 (ttp) cc_final: 0.8347 (ttm) REVERT: N 53 GLN cc_start: 0.7064 (mp10) cc_final: 0.6765 (mp10) REVERT: N 110 VAL cc_start: 0.8315 (t) cc_final: 0.7920 (m) REVERT: N 127 SER cc_start: 0.8485 (p) cc_final: 0.8096 (t) outliers start: 14 outliers final: 3 residues processed: 140 average time/residue: 0.7629 time to fit residues: 112.2221 Evaluate side-chains 134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 144 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 35 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109778 restraints weight = 10479.455| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.09 r_work: 0.3182 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8635 Z= 0.112 Angle : 0.465 7.443 11687 Z= 0.248 Chirality : 0.041 0.143 1317 Planarity : 0.004 0.052 1490 Dihedral : 5.351 99.021 1290 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.33 % Allowed : 11.05 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1053 helix: 2.78 (0.26), residues: 401 sheet: 0.66 (0.35), residues: 222 loop : -0.23 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.013 0.001 TYR D 287 PHE 0.012 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8630) covalent geometry : angle 0.46517 (11676) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.54835 ( 8) hydrogen bonds : bond 0.04139 ( 428) hydrogen bonds : angle 4.18222 ( 1227) link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 0.74293 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6551 (mm-30) REVERT: A 27 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7295 (mt-10) REVERT: A 31 GLN cc_start: 0.7319 (mt0) cc_final: 0.6728 (pt0) REVERT: A 216 LYS cc_start: 0.8296 (mtmt) cc_final: 0.8012 (mtmt) REVERT: A 293 LYS cc_start: 0.6305 (mttp) cc_final: 0.5938 (mtpt) REVERT: A 322 GLU cc_start: 0.7806 (tp30) cc_final: 0.7602 (mm-30) REVERT: A 347 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7361 (ttp-110) REVERT: A 358 TYR cc_start: 0.8316 (m-80) cc_final: 0.7796 (m-80) REVERT: B 13 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7128 (tp40) REVERT: B 44 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: B 134 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6770 (ptp-110) REVERT: B 214 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.7303 (mmp80) REVERT: B 215 GLU cc_start: 0.7912 (mp0) cc_final: 0.7348 (mp0) REVERT: B 217 MET cc_start: 0.8113 (ptp) cc_final: 0.7563 (ptt) REVERT: C 21 MET cc_start: 0.7516 (mmm) cc_final: 0.7164 (tpp) REVERT: C 42 GLU cc_start: 0.7518 (tt0) cc_final: 0.7007 (mt-10) REVERT: D 151 LEU cc_start: 0.7450 (pp) cc_final: 0.7047 (mt) REVERT: D 190 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8003 (mp0) REVERT: D 276 MET cc_start: 0.8596 (ttp) cc_final: 0.8315 (ttm) REVERT: N 53 GLN cc_start: 0.7035 (mp10) cc_final: 0.6729 (mp10) REVERT: N 110 VAL cc_start: 0.8239 (t) cc_final: 0.7846 (m) REVERT: N 127 SER cc_start: 0.8380 (p) cc_final: 0.7990 (t) outliers start: 12 outliers final: 4 residues processed: 136 average time/residue: 0.7653 time to fit residues: 109.1314 Evaluate side-chains 128 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.0170 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 35 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110291 restraints weight = 10461.918| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.08 r_work: 0.3190 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8635 Z= 0.105 Angle : 0.454 7.269 11687 Z= 0.242 Chirality : 0.041 0.140 1317 Planarity : 0.003 0.039 1490 Dihedral : 5.268 98.624 1290 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 11.49 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1053 helix: 2.97 (0.26), residues: 401 sheet: 0.65 (0.35), residues: 227 loop : -0.24 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.012 0.001 TYR D 199 PHE 0.012 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8630) covalent geometry : angle 0.45420 (11676) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.52287 ( 8) hydrogen bonds : bond 0.03949 ( 428) hydrogen bonds : angle 4.09105 ( 1227) link_NAG-ASN : bond 0.00166 ( 1) link_NAG-ASN : angle 0.73792 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7288 (mt0) cc_final: 0.6720 (pt0) REVERT: A 216 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8065 (mtmt) REVERT: A 293 LYS cc_start: 0.6306 (mttp) cc_final: 0.5943 (mtpt) REVERT: A 358 TYR cc_start: 0.8337 (m-80) cc_final: 0.7811 (m-80) REVERT: B 13 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7168 (tp40) REVERT: B 44 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: B 134 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6895 (ptp-110) REVERT: B 214 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.7315 (mmp80) REVERT: B 215 GLU cc_start: 0.7920 (mp0) cc_final: 0.7347 (mp0) REVERT: B 217 MET cc_start: 0.8115 (ptp) cc_final: 0.7562 (ptt) REVERT: C 21 MET cc_start: 0.7528 (mmm) cc_final: 0.7165 (tpp) REVERT: D 151 LEU cc_start: 0.7365 (pp) cc_final: 0.7067 (mt) REVERT: D 190 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8001 (mp0) REVERT: D 276 MET cc_start: 0.8599 (ttp) cc_final: 0.8286 (ttm) REVERT: N 53 GLN cc_start: 0.7014 (mp10) cc_final: 0.6709 (mp10) REVERT: N 110 VAL cc_start: 0.8229 (t) cc_final: 0.7864 (m) REVERT: N 127 SER cc_start: 0.8382 (p) cc_final: 0.7991 (t) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 0.7167 time to fit residues: 101.6106 Evaluate side-chains 125 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 35 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109359 restraints weight = 10343.816| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.08 r_work: 0.3174 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8635 Z= 0.119 Angle : 0.469 7.618 11687 Z= 0.249 Chirality : 0.041 0.142 1317 Planarity : 0.003 0.039 1490 Dihedral : 5.319 98.883 1290 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.55 % Allowed : 11.93 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.26), residues: 1053 helix: 2.99 (0.26), residues: 401 sheet: 0.56 (0.34), residues: 229 loop : -0.26 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.013 0.001 TYR D 199 PHE 0.011 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8630) covalent geometry : angle 0.46919 (11676) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.52404 ( 8) hydrogen bonds : bond 0.04097 ( 428) hydrogen bonds : angle 4.11035 ( 1227) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 0.69114 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7298 (mt0) cc_final: 0.6761 (pt0) REVERT: A 209 GLU cc_start: 0.7880 (tt0) cc_final: 0.7315 (tt0) REVERT: A 293 LYS cc_start: 0.6361 (mttp) cc_final: 0.6005 (mtpt) REVERT: A 347 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7192 (ttp-110) REVERT: A 358 TYR cc_start: 0.8286 (m-80) cc_final: 0.7784 (m-80) REVERT: B 13 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7173 (tp40) REVERT: B 214 ARG cc_start: 0.7592 (mmt-90) cc_final: 0.7314 (mmp80) REVERT: B 215 GLU cc_start: 0.7911 (mp0) cc_final: 0.7358 (mp0) REVERT: B 217 MET cc_start: 0.8116 (ptp) cc_final: 0.7618 (ptt) REVERT: C 21 MET cc_start: 0.7478 (mmm) cc_final: 0.7123 (tpp) REVERT: D 151 LEU cc_start: 0.7385 (pp) cc_final: 0.7095 (mt) REVERT: D 190 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8015 (mp0) REVERT: D 259 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: D 276 MET cc_start: 0.8587 (ttp) cc_final: 0.8320 (ttm) REVERT: N 53 GLN cc_start: 0.7054 (mp10) cc_final: 0.6742 (mp10) REVERT: N 110 VAL cc_start: 0.8292 (t) cc_final: 0.7884 (m) REVERT: N 127 SER cc_start: 0.8384 (p) cc_final: 0.7985 (t) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 0.6882 time to fit residues: 92.5507 Evaluate side-chains 128 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 259 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 102 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108737 restraints weight = 10457.968| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.09 r_work: 0.3164 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8635 Z= 0.122 Angle : 0.479 7.592 11687 Z= 0.254 Chirality : 0.041 0.142 1317 Planarity : 0.004 0.056 1490 Dihedral : 5.340 99.170 1290 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.77 % Allowed : 11.60 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1053 helix: 2.99 (0.25), residues: 401 sheet: 0.42 (0.34), residues: 240 loop : -0.22 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 134 TYR 0.013 0.001 TYR D 199 PHE 0.011 0.001 PHE A 212 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8630) covalent geometry : angle 0.47905 (11676) SS BOND : bond 0.00329 ( 4) SS BOND : angle 0.54987 ( 8) hydrogen bonds : bond 0.04117 ( 428) hydrogen bonds : angle 4.12358 ( 1227) link_NAG-ASN : bond 0.00178 ( 1) link_NAG-ASN : angle 0.69655 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7398 (mt0) cc_final: 0.6869 (pt0) REVERT: A 293 LYS cc_start: 0.6448 (mttp) cc_final: 0.6078 (mtpt) REVERT: A 358 TYR cc_start: 0.8354 (m-80) cc_final: 0.7868 (m-80) REVERT: B 13 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7209 (tp40) REVERT: B 214 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7359 (mmp80) REVERT: B 215 GLU cc_start: 0.7982 (mp0) cc_final: 0.7435 (mp0) REVERT: B 217 MET cc_start: 0.8209 (ptp) cc_final: 0.7726 (ptt) REVERT: C 21 MET cc_start: 0.7592 (mmm) cc_final: 0.7236 (tpp) REVERT: D 151 LEU cc_start: 0.7519 (pp) cc_final: 0.7154 (mt) REVERT: D 190 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8037 (mp0) REVERT: D 259 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: D 276 MET cc_start: 0.8629 (ttp) cc_final: 0.8347 (ttm) REVERT: N 53 GLN cc_start: 0.7129 (mp10) cc_final: 0.6822 (mp10) REVERT: N 110 VAL cc_start: 0.8359 (t) cc_final: 0.7956 (m) REVERT: N 127 SER cc_start: 0.8427 (p) cc_final: 0.8020 (t) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.7026 time to fit residues: 95.4652 Evaluate side-chains 127 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 259 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.144570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108688 restraints weight = 10384.319| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.08 r_work: 0.3160 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8635 Z= 0.127 Angle : 0.482 7.653 11687 Z= 0.255 Chirality : 0.042 0.141 1317 Planarity : 0.003 0.039 1490 Dihedral : 5.375 99.313 1290 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.55 % Allowed : 12.60 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1053 helix: 2.98 (0.25), residues: 401 sheet: 0.42 (0.34), residues: 240 loop : -0.24 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.013 0.001 TYR D 199 PHE 0.011 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8630) covalent geometry : angle 0.48160 (11676) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.55806 ( 8) hydrogen bonds : bond 0.04182 ( 428) hydrogen bonds : angle 4.13825 ( 1227) link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 0.69009 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7333 (mt0) cc_final: 0.6798 (pt0) REVERT: A 293 LYS cc_start: 0.6402 (mttp) cc_final: 0.6034 (mtpt) REVERT: A 358 TYR cc_start: 0.8303 (m-80) cc_final: 0.7819 (m-80) REVERT: B 13 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7165 (tp40) REVERT: B 214 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.7329 (mmp80) REVERT: B 215 GLU cc_start: 0.7927 (mp0) cc_final: 0.7523 (mp0) REVERT: B 217 MET cc_start: 0.8138 (ptp) cc_final: 0.7691 (ptt) REVERT: C 21 MET cc_start: 0.7489 (mmm) cc_final: 0.7131 (tpp) REVERT: D 151 LEU cc_start: 0.7402 (pp) cc_final: 0.7147 (mt) REVERT: D 190 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8118 (mp0) REVERT: D 259 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: D 276 MET cc_start: 0.8595 (ttp) cc_final: 0.8316 (ttm) REVERT: N 53 GLN cc_start: 0.7084 (mp10) cc_final: 0.6768 (mp10) REVERT: N 110 VAL cc_start: 0.8312 (t) cc_final: 0.7907 (m) REVERT: N 127 SER cc_start: 0.8395 (p) cc_final: 0.7990 (t) outliers start: 14 outliers final: 10 residues processed: 126 average time/residue: 0.6218 time to fit residues: 82.4862 Evaluate side-chains 129 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 291 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 40 optimal weight: 0.0170 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 102 ASN N 31 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110736 restraints weight = 10353.898| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.09 r_work: 0.3194 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8635 Z= 0.098 Angle : 0.455 7.191 11687 Z= 0.241 Chirality : 0.040 0.138 1317 Planarity : 0.004 0.061 1490 Dihedral : 5.181 98.501 1290 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.44 % Allowed : 12.93 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1053 helix: 3.13 (0.26), residues: 402 sheet: 0.54 (0.35), residues: 223 loop : -0.30 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 134 TYR 0.010 0.001 TYR D 199 PHE 0.010 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8630) covalent geometry : angle 0.45518 (11676) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.52725 ( 8) hydrogen bonds : bond 0.03684 ( 428) hydrogen bonds : angle 3.99327 ( 1227) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 0.76616 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7333 (mt0) cc_final: 0.6800 (pt0) REVERT: A 293 LYS cc_start: 0.6325 (mttp) cc_final: 0.5954 (mtpt) REVERT: A 358 TYR cc_start: 0.8349 (m-80) cc_final: 0.7862 (m-80) REVERT: B 13 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7149 (tp40) REVERT: B 214 ARG cc_start: 0.7593 (mmt-90) cc_final: 0.7317 (mmp80) REVERT: B 215 GLU cc_start: 0.7941 (mp0) cc_final: 0.7384 (mp0) REVERT: B 217 MET cc_start: 0.8127 (ptp) cc_final: 0.7634 (ptt) REVERT: C 21 MET cc_start: 0.7540 (mmm) cc_final: 0.7122 (tpp) REVERT: D 151 LEU cc_start: 0.7361 (pp) cc_final: 0.7137 (mt) REVERT: D 190 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8011 (mp0) REVERT: D 276 MET cc_start: 0.8581 (ttp) cc_final: 0.8220 (ttm) REVERT: D 298 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6751 (mmm-85) REVERT: D 300 SER cc_start: 0.8480 (m) cc_final: 0.8264 (p) REVERT: N 39 GLN cc_start: 0.8638 (tt0) cc_final: 0.8284 (tp40) REVERT: N 53 GLN cc_start: 0.7040 (mp10) cc_final: 0.6728 (mp10) REVERT: N 105 ARG cc_start: 0.7207 (mtp180) cc_final: 0.6937 (mpp80) REVERT: N 110 VAL cc_start: 0.8123 (t) cc_final: 0.7805 (m) REVERT: N 127 SER cc_start: 0.8391 (p) cc_final: 0.7977 (t) outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.7342 time to fit residues: 104.9231 Evaluate side-chains 132 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108482 restraints weight = 10407.479| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.10 r_work: 0.3162 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8635 Z= 0.131 Angle : 0.487 7.616 11687 Z= 0.257 Chirality : 0.042 0.142 1317 Planarity : 0.003 0.039 1490 Dihedral : 5.343 98.879 1290 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.22 % Allowed : 13.81 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1053 helix: 3.02 (0.25), residues: 402 sheet: 0.30 (0.33), residues: 243 loop : -0.21 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.014 0.001 TYR D 199 PHE 0.012 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8630) covalent geometry : angle 0.48673 (11676) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.57784 ( 8) hydrogen bonds : bond 0.04183 ( 428) hydrogen bonds : angle 4.10630 ( 1227) link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 0.62478 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7310 (mt0) cc_final: 0.6733 (pt0) REVERT: A 293 LYS cc_start: 0.6373 (mttp) cc_final: 0.6013 (mtpt) REVERT: A 358 TYR cc_start: 0.8293 (m-80) cc_final: 0.7806 (m-80) REVERT: B 13 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7176 (tp40) REVERT: B 214 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7332 (mmp80) REVERT: B 215 GLU cc_start: 0.7937 (mp0) cc_final: 0.7525 (mp0) REVERT: C 21 MET cc_start: 0.7471 (mmm) cc_final: 0.7076 (tpp) REVERT: D 190 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8022 (mp0) REVERT: D 276 MET cc_start: 0.8595 (ttp) cc_final: 0.8308 (ttm) REVERT: D 300 SER cc_start: 0.8520 (m) cc_final: 0.8280 (p) REVERT: N 53 GLN cc_start: 0.7083 (mp10) cc_final: 0.6770 (mp10) REVERT: N 110 VAL cc_start: 0.8311 (t) cc_final: 0.7914 (m) REVERT: N 127 SER cc_start: 0.8399 (p) cc_final: 0.7988 (t) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.7313 time to fit residues: 97.6031 Evaluate side-chains 128 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.0070 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 69 optimal weight: 0.0030 chunk 53 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 102 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111140 restraints weight = 10339.716| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8635 Z= 0.097 Angle : 0.457 7.138 11687 Z= 0.242 Chirality : 0.040 0.138 1317 Planarity : 0.004 0.068 1490 Dihedral : 5.171 98.381 1290 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.22 % Allowed : 13.92 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.26), residues: 1053 helix: 3.15 (0.25), residues: 402 sheet: 0.42 (0.33), residues: 240 loop : -0.16 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 134 TYR 0.010 0.001 TYR D 199 PHE 0.011 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8630) covalent geometry : angle 0.45658 (11676) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.52871 ( 8) hydrogen bonds : bond 0.03643 ( 428) hydrogen bonds : angle 3.97348 ( 1227) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 0.81145 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.68 seconds wall clock time: 64 minutes 18.11 seconds (3858.11 seconds total)