Starting phenix.real_space_refine on Thu Jul 2 16:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zi_67431/07_2026/20zi_67431.map" } resolution = 2.7 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= 0.002 sd= 0.013 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 62 5.16 5 C 5680 2.51 5 N 1522 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1754 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1758 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'TRP:plan': 2, 'PHE:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.23 Number of scatterers: 8934 At special positions: 0 Unit cell: (91.3, 120.35, 126.99, 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 62 16.00 O 1670 8.00 N 1522 7.00 C 5680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.36 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: 0.70 Conformation dependent library (CDL) restraints added in 458.6 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 41.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 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 212 removed outlier: 4.103A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.616A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.666A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.087A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.051A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.605A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.616A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.796A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 98 through 128 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 140 through 171 removed outlier: 3.615A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 180 removed outlier: 3.632A pdb=" N MET R 180 " --> pdb=" O ALA R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 206 Proline residue: R 202 - end of helix Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix removed outlier: 3.548A pdb=" N GLN R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 329 Proline residue: R 318 - end of helix removed outlier: 4.095A pdb=" N MET R 325 " --> pdb=" O VAL R 321 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 334 Processing helix chain 'R' and resid 335 through 368 Proline residue: R 361 - end of helix removed outlier: 4.227A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 removed outlier: 3.739A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.186A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.650A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.717A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.152A 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: 6.093A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.788A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.850A 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: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.200A 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: 6.633A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.221A 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: 3.522A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.707A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.067A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.802A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 207 through 208 492 hydrogen bonds defined for protein. 1389 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: 1.63 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1473 1.31 - 1.44: 2492 1.44 - 1.57: 5057 1.57 - 1.69: 4 1.69 - 1.82: 90 Bond restraints: 9116 Sorted by residual: bond pdb=" CA SER R 330 " pdb=" CB SER R 330 " ideal model delta sigma weight residual 1.528 1.405 0.123 1.66e-02 3.63e+03 5.53e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.534 1.428 0.107 1.77e-02 3.19e+03 3.62e+01 bond pdb=" CE1 HIS B 142 " pdb=" NE2 HIS B 142 " ideal model delta sigma weight residual 1.321 1.261 0.060 1.00e-02 1.00e+04 3.56e+01 bond pdb=" CB ILE D 51 " pdb=" CG1 ILE D 51 " ideal model delta sigma weight residual 1.530 1.414 0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" CA SER D 53 " pdb=" CB SER D 53 " ideal model delta sigma weight residual 1.530 1.442 0.088 1.62e-02 3.81e+03 2.98e+01 ... (remaining 9111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 10541 3.12 - 6.25: 1573 6.25 - 9.37: 202 9.37 - 12.50: 35 12.50 - 15.62: 10 Bond angle restraints: 12361 Sorted by residual: angle pdb=" NE ARG B 129 " pdb=" CZ ARG B 129 " pdb=" NH2 ARG B 129 " ideal model delta sigma weight residual 119.20 107.06 12.14 9.00e-01 1.23e+00 1.82e+02 angle pdb=" NE ARG A 21 " pdb=" CZ ARG A 21 " pdb=" NH2 ARG A 21 " ideal model delta sigma weight residual 119.20 107.75 11.45 9.00e-01 1.23e+00 1.62e+02 angle pdb=" NE ARG R 306 " pdb=" CZ ARG R 306 " pdb=" NH2 ARG R 306 " ideal model delta sigma weight residual 119.20 110.15 9.05 9.00e-01 1.23e+00 1.01e+02 angle pdb=" C HIS R 172 " pdb=" CA HIS R 172 " pdb=" CB HIS R 172 " ideal model delta sigma weight residual 113.04 98.59 14.45 1.63e+00 3.76e-01 7.86e+01 angle pdb=" CA ASP B 333 " pdb=" CB ASP B 333 " pdb=" CG ASP B 333 " ideal model delta sigma weight residual 112.60 121.37 -8.77 1.00e+00 1.00e+00 7.70e+01 ... (remaining 12356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4796 17.85 - 35.70: 431 35.70 - 53.56: 136 53.56 - 71.41: 32 71.41 - 89.26: 10 Dihedral angle restraints: 5405 sinusoidal: 2054 harmonic: 3351 Sorted by residual: dihedral pdb=" CD ARG R 182 " pdb=" NE ARG R 182 " pdb=" CZ ARG R 182 " pdb=" NH1 ARG R 182 " ideal model delta sinusoidal sigma weight residual 0.00 -88.12 88.12 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" C ARG B 52 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " pdb=" CB ARG B 52 " ideal model delta harmonic sigma weight residual -122.60 -104.49 -18.11 0 2.50e+00 1.60e-01 5.25e+01 dihedral pdb=" C ARG A 21 " pdb=" N ARG A 21 " pdb=" CA ARG A 21 " pdb=" CB ARG A 21 " ideal model delta harmonic sigma weight residual -122.60 -104.89 -17.71 0 2.50e+00 1.60e-01 5.02e+01 ... (remaining 5402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 975 0.117 - 0.233: 352 0.233 - 0.349: 75 0.349 - 0.466: 16 0.466 - 0.582: 6 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CA GLU R 332 " pdb=" N GLU R 332 " pdb=" C GLU R 332 " pdb=" CB GLU R 332 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CB THR R 335 " pdb=" CA THR R 335 " pdb=" OG1 THR R 335 " pdb=" CG2 THR R 335 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 1421 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 322 " 0.949 9.50e-02 1.11e+02 4.33e-01 1.87e+02 pdb=" NE ARG R 322 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG R 322 " -0.162 2.00e-02 2.50e+03 pdb=" NH1 ARG R 322 " 0.057 2.00e-02 2.50e+03 pdb=" NH2 ARG R 322 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG R 182 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 21 " 0.854 9.50e-02 1.11e+02 3.84e-01 1.03e+02 pdb=" NE ARG A 21 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG A 21 " 0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG A 21 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 21 " 0.006 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1536 2.80 - 3.33: 9106 3.33 - 3.85: 14665 3.85 - 4.38: 18294 4.38 - 4.90: 29505 Nonbonded interactions: 73106 Sorted by model distance: nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.280 3.040 nonbonded pdb=" O GLN R 98 " pdb=" N VAL R 101 " model vdw 2.312 3.120 nonbonded pdb=" O SER B 227 " pdb=" OG SER B 245 " model vdw 2.328 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.338 3.040 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.355 3.040 ... (remaining 73101 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: 2.540 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 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 : 0.013 0.329 9117 Z= 0.844 Angle : 2.337 15.621 12363 Z= 1.598 Chirality : 0.130 0.582 1424 Planarity : 0.030 0.496 1559 Dihedral : 16.409 89.260 3238 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 9.00 % Allowed : 11.07 % Favored : 79.94 % Cbeta Deviations : 3.23 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.53 (0.23), residues: 1130 helix: 0.91 (0.23), residues: 409 sheet: -0.34 (0.30), residues: 255 loop : -1.46 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.151 0.012 ARG R 322 TYR 0.051 0.009 TYR L 11 PHE 0.032 0.008 PHE B 241 TRP 0.040 0.010 TRP B 297 HIS 0.024 0.007 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.01268 / 0.83 ( 9116) covalent geometry : angle 2.33674 / 1.60 (12361) SS BOND : bond 0.32948 / 17.34 ( 1) SS BOND : angle 1.73658 / 0.97 ( 2) hydrogen bonds : bond 0.21989 / 14.82 ( 485) hydrogen bonds : angle 8.56078 / 6.14 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 307 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9250 (m-30) cc_final: 0.8901 (p0) REVERT: A 283 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (tt) REVERT: A 298 GLU cc_start: 0.9192 (tp30) cc_final: 0.8914 (tp30) REVERT: A 305 CYS cc_start: 0.9031 (m) cc_final: 0.8422 (t) REVERT: B 8 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8876 (tmm160) REVERT: B 13 GLN cc_start: 0.9155 (tm130) cc_final: 0.8900 (tm-30) REVERT: B 44 GLN cc_start: 0.8931 (mt0) cc_final: 0.8562 (mt0) REVERT: B 46 ARG cc_start: 0.9147 (mtp-110) cc_final: 0.8930 (ttp-110) REVERT: B 228 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8695 (m-30) REVERT: B 229 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8925 (mt) REVERT: D 51 ILE cc_start: 0.8394 (mt) cc_final: 0.8035 (tt) REVERT: D 192 SER cc_start: 0.8898 (t) cc_final: 0.8403 (p) REVERT: R 63 LYS cc_start: 0.8157 (mttp) cc_final: 0.7715 (tttp) REVERT: R 120 MET cc_start: 0.8648 (tpt) cc_final: 0.8244 (tpp) REVERT: R 141 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.6843 (t) REVERT: R 146 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7763 (t80) REVERT: R 179 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8782 (mt) REVERT: R 194 LEU cc_start: 0.8389 (tp) cc_final: 0.8050 (mt) REVERT: R 210 GLN cc_start: 0.7535 (mt0) cc_final: 0.6965 (mp10) REVERT: R 234 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8125 (ttmt) REVERT: R 266 MET cc_start: 0.8881 (mtp) cc_final: 0.8663 (mtt) REVERT: R 338 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7734 (pt) REVERT: R 359 ILE cc_start: 0.8723 (mt) cc_final: 0.8443 (mm) REVERT: R 371 PHE cc_start: 0.8209 (t80) cc_final: 0.7932 (t80) REVERT: R 376 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8655 (tt) outliers start: 87 outliers final: 14 residues processed: 365 average time/residue: 0.5824 time to fit residues: 225.3776 Evaluate side-chains 215 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 146 PHE Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 364 TYR Chi-restraints excluded: chain R residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 333 GLN B 32 GLN B 44 GLN B 175 GLN B 176 GLN B 259 GLN D 13 GLN D 159 ASN D 174 GLN D 182 ASN R 95 GLN R 261 ASN R 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.090024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069131 restraints weight = 19619.517| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.46 r_work: 0.2899 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 9117 Z= 0.194 Angle : 0.766 11.722 12363 Z= 0.402 Chirality : 0.048 0.278 1424 Planarity : 0.006 0.062 1559 Dihedral : 8.580 89.916 1290 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 6.20 % Allowed : 21.61 % Favored : 72.18 % 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: 0.59 (0.24), residues: 1130 helix: 2.18 (0.25), residues: 405 sheet: 0.00 (0.28), residues: 292 loop : -1.06 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.026 0.003 TYR L 11 PHE 0.027 0.002 PHE R 375 TRP 0.018 0.002 TRP B 82 HIS 0.009 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 9116) covalent geometry : angle 0.76574 / 0.40 (12361) SS BOND : bond 0.00241 / 0.13 ( 1) SS BOND : angle 1.50271 / 0.74 ( 2) hydrogen bonds : bond 0.05973 / 3.94 ( 485) hydrogen bonds : angle 5.46725 / 3.82 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.377 Fit side-chains REVERT: A 192 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9100 (mttm) REVERT: B 42 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7467 (tmm-80) REVERT: B 44 GLN cc_start: 0.8727 (mt0) cc_final: 0.8173 (mt0) REVERT: B 46 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.8350 (ttm-80) REVERT: B 254 ASP cc_start: 0.8869 (t0) cc_final: 0.8642 (t70) REVERT: C 58 GLU cc_start: 0.9150 (mp0) cc_final: 0.8812 (mp0) REVERT: D 135 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8023 (m) REVERT: D 192 SER cc_start: 0.9087 (t) cc_final: 0.8620 (p) REVERT: D 211 ASP cc_start: 0.8898 (t0) cc_final: 0.8689 (t0) REVERT: R 63 LYS cc_start: 0.8379 (mttp) cc_final: 0.7758 (tptt) REVERT: R 141 CYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6852 (t) REVERT: R 194 LEU cc_start: 0.8237 (tp) cc_final: 0.7976 (mt) REVERT: R 210 GLN cc_start: 0.7497 (mt0) cc_final: 0.6874 (pt0) REVERT: R 234 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7846 (tttm) REVERT: R 238 GLN cc_start: 0.8749 (mt0) cc_final: 0.7940 (mp10) REVERT: R 376 LEU cc_start: 0.8411 (mp) cc_final: 0.7981 (tt) outliers start: 60 outliers final: 16 residues processed: 247 average time/residue: 0.5474 time to fit residues: 144.3519 Evaluate side-chains 180 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 141 CYS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 259 GLN D 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.067268 restraints weight = 19645.825| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.45 r_work: 0.2860 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9117 Z= 0.170 Angle : 0.688 10.162 12363 Z= 0.361 Chirality : 0.045 0.271 1424 Planarity : 0.005 0.041 1559 Dihedral : 6.333 60.891 1257 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 6.00 % Allowed : 22.85 % Favored : 71.15 % 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: 0.65 (0.25), residues: 1130 helix: 2.13 (0.25), residues: 409 sheet: 0.19 (0.30), residues: 279 loop : -1.04 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 8 TYR 0.029 0.002 TYR A 290 PHE 0.025 0.002 PHE R 174 TRP 0.021 0.002 TRP B 82 HIS 0.011 0.001 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 9116) covalent geometry : angle 0.68784 / 0.36 (12361) SS BOND : bond 0.00776 / 0.41 ( 1) SS BOND : angle 1.69221 / 0.85 ( 2) hydrogen bonds : bond 0.05305 / 3.51 ( 485) hydrogen bonds : angle 5.05142 / 3.53 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.447 Fit side-chains REVERT: A 234 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7365 (tm) REVERT: A 302 TYR cc_start: 0.9225 (t80) cc_final: 0.8922 (t80) REVERT: B 13 GLN cc_start: 0.8403 (pp30) cc_final: 0.8182 (pp30) REVERT: B 42 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7358 (tmm-80) REVERT: B 44 GLN cc_start: 0.8816 (mt0) cc_final: 0.8235 (mt0) REVERT: B 46 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8415 (ttm-80) REVERT: B 142 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8236 (t70) REVERT: B 215 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 229 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8594 (mt) REVERT: C 18 GLN cc_start: 0.8756 (tp40) cc_final: 0.8452 (tp40) REVERT: C 52 THR cc_start: 0.8609 (m) cc_final: 0.8246 (p) REVERT: D 192 SER cc_start: 0.9081 (t) cc_final: 0.8583 (p) REVERT: D 211 ASP cc_start: 0.8947 (t0) cc_final: 0.8703 (t0) REVERT: R 63 LYS cc_start: 0.8580 (mttp) cc_final: 0.8053 (tttp) REVERT: R 170 ILE cc_start: 0.6429 (OUTLIER) cc_final: 0.6118 (mp) REVERT: R 180 MET cc_start: 0.8638 (mpp) cc_final: 0.8386 (mpp) REVERT: R 210 GLN cc_start: 0.7583 (mt0) cc_final: 0.7004 (pt0) REVERT: R 234 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7972 (tttm) REVERT: R 238 GLN cc_start: 0.8628 (mt0) cc_final: 0.7843 (mp10) REVERT: R 376 LEU cc_start: 0.8451 (mp) cc_final: 0.8080 (tt) outliers start: 58 outliers final: 18 residues processed: 215 average time/residue: 0.6169 time to fit residues: 140.8870 Evaluate side-chains 186 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 347 ASN B 13 GLN B 119 ASN B 175 GLN B 259 GLN D 13 GLN D 159 ASN R 273 GLN R 320 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064412 restraints weight = 20004.321| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.45 r_work: 0.2788 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9117 Z= 0.226 Angle : 0.672 9.447 12363 Z= 0.357 Chirality : 0.046 0.204 1424 Planarity : 0.005 0.041 1559 Dihedral : 6.183 58.500 1256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 6.31 % Allowed : 22.34 % Favored : 71.35 % 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: 1130 helix: 2.19 (0.25), residues: 410 sheet: 0.30 (0.30), residues: 279 loop : -0.93 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.020 0.002 TYR L 11 PHE 0.023 0.002 PHE R 375 TRP 0.019 0.002 TRP B 82 HIS 0.008 0.002 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 ( 9116) covalent geometry : angle 0.67190 / 0.36 (12361) SS BOND : bond 0.00675 / 0.36 ( 1) SS BOND : angle 1.60178 / 0.79 ( 2) hydrogen bonds : bond 0.05201 / 3.47 ( 485) hydrogen bonds : angle 5.01314 / 3.53 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 234 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7548 (tm) REVERT: B 46 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8409 (mtm-85) REVERT: B 142 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8032 (t70) REVERT: B 215 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: B 229 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 275 SER cc_start: 0.8944 (m) cc_final: 0.8676 (m) REVERT: B 314 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.7962 (mtm180) REVERT: C 52 THR cc_start: 0.8594 (m) cc_final: 0.8214 (p) REVERT: C 58 GLU cc_start: 0.9093 (mp0) cc_final: 0.8749 (pm20) REVERT: D 206 ARG cc_start: 0.8396 (ptp-110) cc_final: 0.8081 (ttp-110) REVERT: D 211 ASP cc_start: 0.9031 (t0) cc_final: 0.8782 (t0) REVERT: R 63 LYS cc_start: 0.8696 (mttp) cc_final: 0.8122 (tttp) REVERT: R 165 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8365 (tm-30) REVERT: R 170 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.6153 (mp) REVERT: R 174 PHE cc_start: 0.7946 (t80) cc_final: 0.7653 (t80) REVERT: R 180 MET cc_start: 0.8661 (mpp) cc_final: 0.8257 (mpp) REVERT: R 194 LEU cc_start: 0.7245 (mt) cc_final: 0.6928 (mp) REVERT: R 204 LEU cc_start: 0.8949 (tp) cc_final: 0.8502 (tp) REVERT: R 210 GLN cc_start: 0.7498 (mt0) cc_final: 0.7046 (pt0) REVERT: R 238 GLN cc_start: 0.8814 (mt0) cc_final: 0.8062 (mp10) REVERT: R 333 GLN cc_start: 0.7723 (tp-100) cc_final: 0.7486 (tp-100) REVERT: R 376 LEU cc_start: 0.8309 (mp) cc_final: 0.7983 (tt) outliers start: 61 outliers final: 25 residues processed: 216 average time/residue: 0.6167 time to fit residues: 141.6013 Evaluate side-chains 193 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 347 ASN B 13 GLN B 175 GLN B 259 GLN B 266 HIS D 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.065261 restraints weight = 19750.885| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.43 r_work: 0.2814 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9117 Z= 0.154 Angle : 0.641 11.223 12363 Z= 0.335 Chirality : 0.043 0.195 1424 Planarity : 0.004 0.044 1559 Dihedral : 5.684 54.427 1252 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.65 % Allowed : 24.92 % Favored : 70.42 % 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: 0.88 (0.25), residues: 1130 helix: 2.27 (0.25), residues: 410 sheet: 0.38 (0.30), residues: 272 loop : -0.89 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 142 TYR 0.020 0.002 TYR A 296 PHE 0.016 0.001 PHE R 375 TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9116) covalent geometry : angle 0.64121 / 0.33 (12361) SS BOND : bond 0.00556 / 0.29 ( 1) SS BOND : angle 1.10901 / 0.55 ( 2) hydrogen bonds : bond 0.04889 / 3.25 ( 485) hydrogen bonds : angle 4.84955 / 3.42 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.355 Fit side-chains REVERT: A 234 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7559 (tm) REVERT: B 42 ARG cc_start: 0.8075 (tmm-80) cc_final: 0.7833 (tmm-80) REVERT: B 46 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8424 (mtm-85) REVERT: B 142 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.7970 (t70) REVERT: B 229 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 275 SER cc_start: 0.8958 (m) cc_final: 0.8723 (m) REVERT: C 52 THR cc_start: 0.8517 (m) cc_final: 0.8190 (p) REVERT: C 58 GLU cc_start: 0.9065 (mp0) cc_final: 0.8753 (pm20) REVERT: D 206 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.8083 (ttp-110) REVERT: D 211 ASP cc_start: 0.8946 (t0) cc_final: 0.8714 (t0) REVERT: R 63 LYS cc_start: 0.8679 (mttp) cc_final: 0.8114 (tttp) REVERT: R 165 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8388 (tm-30) REVERT: R 170 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5959 (mp) REVERT: R 180 MET cc_start: 0.8649 (mpp) cc_final: 0.8286 (mpp) REVERT: R 210 GLN cc_start: 0.7568 (mt0) cc_final: 0.7107 (pt0) REVERT: R 238 GLN cc_start: 0.8777 (mt0) cc_final: 0.7998 (mp10) REVERT: R 333 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7598 (tp-100) REVERT: R 376 LEU cc_start: 0.8283 (mp) cc_final: 0.7960 (tt) outliers start: 45 outliers final: 22 residues processed: 204 average time/residue: 0.5927 time to fit residues: 128.5771 Evaluate side-chains 188 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN B 13 GLN B 142 HIS B 175 GLN B 259 GLN D 13 GLN R 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.063931 restraints weight = 20018.877| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.43 r_work: 0.2785 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9117 Z= 0.188 Angle : 0.651 13.680 12363 Z= 0.337 Chirality : 0.044 0.181 1424 Planarity : 0.004 0.040 1559 Dihedral : 5.550 54.693 1251 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.65 % Allowed : 25.34 % Favored : 70.01 % 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: 0.84 (0.25), residues: 1130 helix: 2.21 (0.25), residues: 412 sheet: 0.35 (0.30), residues: 278 loop : -0.91 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 8 TYR 0.022 0.002 TYR A 296 PHE 0.017 0.001 PHE R 375 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9116) covalent geometry : angle 0.65055 / 0.34 (12361) SS BOND : bond 0.00642 / 0.34 ( 1) SS BOND : angle 1.31302 / 0.65 ( 2) hydrogen bonds : bond 0.04936 / 3.25 ( 485) hydrogen bonds : angle 4.80891 / 3.38 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.371 Fit side-chains REVERT: A 234 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7700 (tm) REVERT: A 302 TYR cc_start: 0.9328 (t80) cc_final: 0.9082 (t80) REVERT: B 46 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8484 (mtm-85) REVERT: B 142 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.7453 (t-90) REVERT: B 229 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 243 THR cc_start: 0.9257 (m) cc_final: 0.8863 (p) REVERT: C 22 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 52 THR cc_start: 0.8593 (m) cc_final: 0.8317 (p) REVERT: C 58 GLU cc_start: 0.9045 (mp0) cc_final: 0.8752 (pm20) REVERT: D 206 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8138 (ttp-110) REVERT: D 211 ASP cc_start: 0.8946 (t0) cc_final: 0.8716 (t0) REVERT: R 63 LYS cc_start: 0.8747 (mttp) cc_final: 0.8296 (tttp) REVERT: R 165 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8424 (tm-30) REVERT: R 170 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.5963 (mp) REVERT: R 180 MET cc_start: 0.8646 (mpp) cc_final: 0.8246 (mpp) REVERT: R 210 GLN cc_start: 0.7679 (mt0) cc_final: 0.7179 (pt0) REVERT: R 238 GLN cc_start: 0.8790 (mt0) cc_final: 0.8005 (mp10) REVERT: R 316 TRP cc_start: 0.8513 (m100) cc_final: 0.8299 (m100) REVERT: R 333 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7775 (tp-100) REVERT: R 376 LEU cc_start: 0.8297 (mp) cc_final: 0.7924 (tt) outliers start: 45 outliers final: 25 residues processed: 201 average time/residue: 0.5386 time to fit residues: 115.3974 Evaluate side-chains 193 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 0.0020 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.063289 restraints weight = 20144.943| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.43 r_work: 0.2773 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9117 Z= 0.210 Angle : 0.670 12.399 12363 Z= 0.347 Chirality : 0.044 0.180 1424 Planarity : 0.004 0.046 1559 Dihedral : 5.557 57.304 1251 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.76 % Allowed : 25.65 % Favored : 69.60 % 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: 0.83 (0.25), residues: 1130 helix: 2.04 (0.25), residues: 419 sheet: 0.27 (0.29), residues: 288 loop : -0.76 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 8 TYR 0.023 0.002 TYR R 328 PHE 0.021 0.002 PHE R 375 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 9116) covalent geometry : angle 0.67034 / 0.35 (12361) SS BOND : bond 0.00590 / 0.31 ( 1) SS BOND : angle 1.23863 / 0.60 ( 2) hydrogen bonds : bond 0.04991 / 3.30 ( 485) hydrogen bonds : angle 4.84265 / 3.40 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.466 Fit side-chains REVERT: A 232 LEU cc_start: 0.9290 (mt) cc_final: 0.9037 (mp) REVERT: A 234 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7612 (tm) REVERT: B 5 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8103 (p0) REVERT: B 46 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8506 (mtm-85) REVERT: B 229 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 243 THR cc_start: 0.9258 (m) cc_final: 0.8886 (p) REVERT: B 275 SER cc_start: 0.8956 (m) cc_final: 0.8715 (m) REVERT: C 22 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 52 THR cc_start: 0.8617 (m) cc_final: 0.8323 (p) REVERT: C 58 GLU cc_start: 0.9027 (mp0) cc_final: 0.8746 (pm20) REVERT: D 206 ARG cc_start: 0.8401 (ptp-110) cc_final: 0.8170 (ttp-110) REVERT: D 211 ASP cc_start: 0.8925 (t0) cc_final: 0.8683 (t0) REVERT: R 63 LYS cc_start: 0.8787 (mttp) cc_final: 0.8364 (tttp) REVERT: R 165 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8451 (tm-30) REVERT: R 170 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6031 (mp) REVERT: R 179 LEU cc_start: 0.8990 (mp) cc_final: 0.8700 (pp) REVERT: R 180 MET cc_start: 0.8564 (mpp) cc_final: 0.8089 (mmm) REVERT: R 210 GLN cc_start: 0.7783 (mt0) cc_final: 0.7348 (pt0) REVERT: R 238 GLN cc_start: 0.8773 (mt0) cc_final: 0.7962 (mp10) REVERT: R 333 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7896 (tp-100) REVERT: R 376 LEU cc_start: 0.8289 (mp) cc_final: 0.7938 (tt) outliers start: 46 outliers final: 29 residues processed: 205 average time/residue: 0.5091 time to fit residues: 111.3220 Evaluate side-chains 201 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 170 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.065634 restraints weight = 20041.448| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.44 r_work: 0.2830 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9117 Z= 0.134 Angle : 0.642 11.795 12363 Z= 0.328 Chirality : 0.042 0.161 1424 Planarity : 0.004 0.038 1559 Dihedral : 5.334 58.429 1251 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 26.78 % Favored : 69.18 % 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: 0.91 (0.25), residues: 1130 helix: 2.17 (0.25), residues: 419 sheet: 0.39 (0.30), residues: 270 loop : -0.79 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 8 TYR 0.018 0.001 TYR R 70 PHE 0.020 0.001 PHE R 375 TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9116) covalent geometry : angle 0.64209 / 0.33 (12361) SS BOND : bond 0.00504 / 0.27 ( 1) SS BOND : angle 0.88143 / 0.44 ( 2) hydrogen bonds : bond 0.04465 / 2.96 ( 485) hydrogen bonds : angle 4.71914 / 3.31 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8612 (ttm-80) REVERT: A 234 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7729 (tm) REVERT: A 242 ARG cc_start: 0.8908 (mtm-85) cc_final: 0.8675 (ttp-110) REVERT: B 5 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7841 (p0) REVERT: B 46 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8497 (mtm-85) REVERT: B 243 THR cc_start: 0.9224 (m) cc_final: 0.8956 (p) REVERT: B 323 ASP cc_start: 0.8945 (t0) cc_final: 0.8736 (t0) REVERT: C 22 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8485 (mt-10) REVERT: C 52 THR cc_start: 0.8591 (m) cc_final: 0.8378 (p) REVERT: C 58 GLU cc_start: 0.9005 (mp0) cc_final: 0.8717 (pm20) REVERT: D 206 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.8010 (ttp-110) REVERT: D 211 ASP cc_start: 0.8847 (t0) cc_final: 0.8634 (t0) REVERT: R 63 LYS cc_start: 0.8834 (mttp) cc_final: 0.8442 (tmtp) REVERT: R 120 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8454 (mmm) REVERT: R 165 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8444 (tm-30) REVERT: R 210 GLN cc_start: 0.7980 (mt0) cc_final: 0.7522 (pt0) REVERT: R 238 GLN cc_start: 0.8754 (mt0) cc_final: 0.7955 (mp10) REVERT: R 333 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7877 (tp-100) REVERT: R 376 LEU cc_start: 0.8141 (mp) cc_final: 0.7853 (tt) outliers start: 39 outliers final: 19 residues processed: 202 average time/residue: 0.5044 time to fit residues: 108.7796 Evaluate side-chains 186 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064516 restraints weight = 19909.181| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.45 r_work: 0.2803 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9117 Z= 0.162 Angle : 0.692 11.941 12363 Z= 0.346 Chirality : 0.043 0.167 1424 Planarity : 0.004 0.038 1559 Dihedral : 5.098 57.952 1249 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.90 % Allowed : 28.13 % Favored : 68.98 % 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: 0.90 (0.25), residues: 1130 helix: 2.14 (0.25), residues: 419 sheet: 0.32 (0.30), residues: 275 loop : -0.73 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 8 TYR 0.027 0.002 TYR A 290 PHE 0.022 0.001 PHE R 375 TRP 0.024 0.001 TRP R 316 HIS 0.006 0.001 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9116) covalent geometry : angle 0.69160 / 0.35 (12361) SS BOND : bond 0.00514 / 0.27 ( 1) SS BOND : angle 1.07014 / 0.53 ( 2) hydrogen bonds : bond 0.04537 / 3.01 ( 485) hydrogen bonds : angle 4.72787 / 3.31 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8650 (ttm-80) REVERT: A 234 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7687 (tm) REVERT: B 46 ARG cc_start: 0.8857 (mtp-110) cc_final: 0.8529 (mtm-85) REVERT: B 275 SER cc_start: 0.8955 (m) cc_final: 0.8705 (m) REVERT: B 323 ASP cc_start: 0.8969 (t0) cc_final: 0.8769 (t0) REVERT: C 22 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 58 GLU cc_start: 0.9012 (mp0) cc_final: 0.8748 (pm20) REVERT: D 206 ARG cc_start: 0.8357 (ptp-110) cc_final: 0.8081 (ttp-110) REVERT: D 211 ASP cc_start: 0.8865 (t0) cc_final: 0.8625 (t0) REVERT: R 63 LYS cc_start: 0.8835 (mttp) cc_final: 0.8450 (tmtp) REVERT: R 120 MET cc_start: 0.8794 (tpt) cc_final: 0.8501 (mmm) REVERT: R 165 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8459 (tm-30) REVERT: R 210 GLN cc_start: 0.7985 (mt0) cc_final: 0.7745 (pt0) REVERT: R 238 GLN cc_start: 0.8764 (mt0) cc_final: 0.7965 (mp10) REVERT: R 333 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7864 (tp-100) REVERT: R 376 LEU cc_start: 0.8174 (mp) cc_final: 0.7904 (tt) outliers start: 28 outliers final: 18 residues processed: 184 average time/residue: 0.6090 time to fit residues: 118.9699 Evaluate side-chains 178 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.086895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.066004 restraints weight = 19788.873| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.45 r_work: 0.2836 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9117 Z= 0.130 Angle : 0.682 11.936 12363 Z= 0.341 Chirality : 0.043 0.194 1424 Planarity : 0.004 0.042 1559 Dihedral : 4.993 57.736 1249 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.38 % Allowed : 29.16 % Favored : 68.46 % 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: 0.91 (0.25), residues: 1130 helix: 2.13 (0.25), residues: 420 sheet: 0.30 (0.30), residues: 271 loop : -0.68 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.028 0.001 TYR A 290 PHE 0.020 0.001 PHE R 375 TRP 0.031 0.001 TRP R 316 HIS 0.006 0.001 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9116) covalent geometry : angle 0.68191 / 0.34 (12361) SS BOND : bond 0.00486 / 0.26 ( 1) SS BOND : angle 0.95622 / 0.47 ( 2) hydrogen bonds : bond 0.04282 / 2.85 ( 485) hydrogen bonds : angle 4.66145 / 3.26 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8936 (ttm-80) cc_final: 0.8627 (ttm-80) REVERT: A 234 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7825 (tm) REVERT: B 46 ARG cc_start: 0.8795 (mtp-110) cc_final: 0.8458 (mtm-85) REVERT: B 275 SER cc_start: 0.8916 (m) cc_final: 0.8648 (m) REVERT: B 323 ASP cc_start: 0.8944 (t0) cc_final: 0.8728 (t0) REVERT: C 22 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8473 (mt-10) REVERT: C 58 GLU cc_start: 0.8982 (mp0) cc_final: 0.8655 (pm20) REVERT: D 206 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.8035 (ttp-110) REVERT: D 211 ASP cc_start: 0.8823 (t0) cc_final: 0.8591 (t0) REVERT: R 63 LYS cc_start: 0.8860 (mttp) cc_final: 0.8489 (tmtp) REVERT: R 120 MET cc_start: 0.8781 (tpt) cc_final: 0.8338 (mmm) REVERT: R 165 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8467 (tm-30) REVERT: R 210 GLN cc_start: 0.7961 (mt0) cc_final: 0.7716 (pt0) REVERT: R 238 GLN cc_start: 0.8740 (mt0) cc_final: 0.8042 (mp10) REVERT: R 333 GLN cc_start: 0.8305 (tp-100) cc_final: 0.7872 (tp-100) REVERT: R 376 LEU cc_start: 0.8163 (mp) cc_final: 0.7888 (tt) outliers start: 23 outliers final: 19 residues processed: 179 average time/residue: 0.6287 time to fit residues: 119.3178 Evaluate side-chains 182 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 205 PHE Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 267 VAL Chi-restraints excluded: chain R residue 335 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064615 restraints weight = 19802.974| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.43 r_work: 0.2802 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9117 Z= 0.192 Angle : 0.715 11.517 12363 Z= 0.358 Chirality : 0.044 0.223 1424 Planarity : 0.004 0.042 1559 Dihedral : 5.063 57.187 1249 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.28 % Allowed : 28.96 % Favored : 68.77 % 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: 0.91 (0.25), residues: 1130 helix: 2.10 (0.25), residues: 421 sheet: 0.27 (0.30), residues: 288 loop : -0.65 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 8 TYR 0.024 0.002 TYR A 290 PHE 0.022 0.001 PHE R 375 TRP 0.037 0.002 TRP R 316 HIS 0.006 0.001 HIS R 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 9116) covalent geometry : angle 0.71457 / 0.36 (12361) SS BOND : bond 0.00574 / 0.30 ( 1) SS BOND : angle 1.27281 / 0.63 ( 2) hydrogen bonds : bond 0.04491 / 2.99 ( 485) hydrogen bonds : angle 4.71801 / 3.29 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.02 seconds wall clock time: 65 minutes 54.66 seconds (3954.66 seconds total)