Starting phenix.real_space_refine on Fri Oct 10 22:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6p_36010/10_2025/8j6p_36010.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 69 5.16 5 C 5878 2.51 5 N 1555 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9189 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'CLR': 2, 'IX8': 1, 'NAG': 1, 'NIO': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.28 Number of scatterers: 9189 At special positions: 0 Unit cell: (106.02, 119.97, 113.46, 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 69 16.00 O 1687 8.00 N 1555 7.00 C 5878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 405 " - " ASN R 17 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 367.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.560A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.436A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.120A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.751A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.679A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.976A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.605A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'R' and resid 23 through 54 removed outlier: 3.824A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.604A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.691A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 165 removed outlier: 3.635A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.986A pdb=" N GLY R 173 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.700A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 removed outlier: 3.902A pdb=" N ARG R 222 " --> pdb=" O GLN R 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 222' Processing helix chain 'R' and resid 223 through 261 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 265 through 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 295 removed outlier: 4.632A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 5.970A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.999A 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: 3.614A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.730A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.730A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.378A 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: 3.769A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.223A 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: 6.107A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.702A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA S 40 " --> pdb=" O GLY S 44 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.976A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.530A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1239 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: 1.58 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2259 1.33 - 1.46: 2385 1.46 - 1.58: 4650 1.58 - 1.71: 1 1.71 - 1.84: 100 Bond restraints: 9395 Sorted by residual: bond pdb=" C2 IX8 R 401 " pdb=" C25 IX8 R 401 " ideal model delta sigma weight residual 1.522 1.654 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C2 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.451 1.542 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C15 IX8 R 401 " pdb=" C16 IX8 R 401 " ideal model delta sigma weight residual 1.460 1.550 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C11 IX8 R 401 " pdb=" N10 IX8 R 401 " ideal model delta sigma weight residual 1.359 1.446 -0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12308 1.90 - 3.81: 318 3.81 - 5.71: 68 5.71 - 7.61: 22 7.61 - 9.52: 7 Bond angle restraints: 12723 Sorted by residual: angle pdb=" N THR A 329 " pdb=" CA THR A 329 " pdb=" C THR A 329 " ideal model delta sigma weight residual 111.36 119.06 -7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" N LYS A 330 " pdb=" CA LYS A 330 " pdb=" C LYS A 330 " ideal model delta sigma weight residual 113.37 120.42 -7.05 1.38e+00 5.25e-01 2.61e+01 angle pdb=" N HIS R 55 " pdb=" CA HIS R 55 " pdb=" C HIS R 55 " ideal model delta sigma weight residual 111.28 115.97 -4.69 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N HIS R 184 " pdb=" CA HIS R 184 " pdb=" C HIS R 184 " ideal model delta sigma weight residual 111.28 115.35 -4.07 1.09e+00 8.42e-01 1.39e+01 angle pdb=" C ILE R 169 " pdb=" N GLN R 170 " pdb=" CA GLN R 170 " ideal model delta sigma weight residual 122.68 127.90 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 12718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5159 17.76 - 35.51: 434 35.51 - 53.26: 68 53.26 - 71.02: 9 71.02 - 88.77: 6 Dihedral angle restraints: 5676 sinusoidal: 2341 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 57.87 35.13 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA ASN R 17 " pdb=" C ASN R 17 " pdb=" N CYS R 18 " pdb=" CA CYS R 18 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PHE R 197 " pdb=" C PHE R 197 " pdb=" N PHE R 198 " pdb=" CA PHE R 198 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 1424 0.259 - 0.518: 4 0.518 - 0.777: 0 0.777 - 1.036: 0 1.036 - 1.295: 1 Chirality restraints: 1429 Sorted by residual: chirality pdb=" C1 NAG R 405 " pdb=" ND2 ASN R 17 " pdb=" C2 NAG R 405 " pdb=" O5 NAG R 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C2 IX8 R 401 " pdb=" C1 IX8 R 401 " pdb=" C25 IX8 R 401 " pdb=" N3 IX8 R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.87 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1426 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 405 " -0.314 2.00e-02 2.50e+03 2.66e-01 8.81e+02 pdb=" C7 NAG R 405 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG R 405 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG R 405 " 0.459 2.00e-02 2.50e+03 pdb=" O7 NAG R 405 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO S 75 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 17 " -0.025 2.00e-02 2.50e+03 2.65e-02 8.78e+00 pdb=" CG ASN R 17 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN R 17 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN R 17 " 0.042 2.00e-02 2.50e+03 pdb=" C1 NAG R 405 " -0.032 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 175 2.68 - 3.23: 8234 3.23 - 3.79: 15201 3.79 - 4.34: 20936 4.34 - 4.90: 34502 Nonbonded interactions: 79048 Sorted by model distance: nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.120 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O1 NIO R 403 " model vdw 2.283 3.040 ... (remaining 79043 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.040 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.005 0.132 9401 Z= 0.247 Angle : 0.798 16.998 12736 Z= 0.411 Chirality : 0.063 1.295 1429 Planarity : 0.009 0.266 1596 Dihedral : 13.098 88.774 3505 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.04 (0.24), residues: 1137 helix: 0.56 (0.25), residues: 388 sheet: 0.09 (0.30), residues: 280 loop : -0.45 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 202 TYR 0.023 0.002 TYR S 190 PHE 0.027 0.002 PHE R 52 TRP 0.011 0.001 TRP R 59 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9395) covalent geometry : angle 0.78263 (12723) SS BOND : bond 0.00537 ( 5) SS BOND : angle 1.31663 ( 10) hydrogen bonds : bond 0.17861 ( 443) hydrogen bonds : angle 6.92944 ( 1239) link_NAG-ASN : bond 0.06219 ( 1) link_NAG-ASN : angle 9.87574 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.376 Fit side-chains REVERT: A 8 GLU cc_start: 0.7017 (mt-10) cc_final: 0.5788 (mt-10) REVERT: A 21 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7357 (ttp-170) REVERT: A 208 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7623 (ttm110) REVERT: A 330 LYS cc_start: 0.7276 (mttt) cc_final: 0.6958 (mtpp) REVERT: B 42 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6836 (tpt170) REVERT: S 238 THR cc_start: 0.8179 (m) cc_final: 0.7722 (p) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.6196 time to fit residues: 113.5150 Evaluate side-chains 127 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN S 186 GLN R 112 GLN R 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126970 restraints weight = 8968.828| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.95 r_work: 0.3155 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9401 Z= 0.147 Angle : 0.566 6.754 12736 Z= 0.301 Chirality : 0.042 0.190 1429 Planarity : 0.004 0.076 1596 Dihedral : 5.935 51.080 1413 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 8.54 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.70 (0.25), residues: 1137 helix: 1.54 (0.26), residues: 390 sheet: 0.18 (0.29), residues: 284 loop : -0.17 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 72 TYR 0.031 0.002 TYR S 190 PHE 0.012 0.002 PHE R 117 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9395) covalent geometry : angle 0.56412 (12723) SS BOND : bond 0.00677 ( 5) SS BOND : angle 1.48985 ( 10) hydrogen bonds : bond 0.04349 ( 443) hydrogen bonds : angle 4.77764 ( 1239) link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 1.02382 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.357 Fit side-chains REVERT: A 21 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7561 (mtm-85) REVERT: A 198 MET cc_start: 0.8861 (ttp) cc_final: 0.8631 (ttp) REVERT: A 275 GLU cc_start: 0.7631 (pp20) cc_final: 0.7124 (pp20) REVERT: A 330 LYS cc_start: 0.7263 (mttt) cc_final: 0.6426 (mtpp) REVERT: B 42 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6787 (tpt170) REVERT: B 197 ARG cc_start: 0.8373 (mmm160) cc_final: 0.8097 (mmm160) REVERT: S 80 PHE cc_start: 0.8663 (m-80) cc_final: 0.8394 (m-80) REVERT: S 113 GLN cc_start: 0.7476 (pm20) cc_final: 0.7050 (tp40) REVERT: S 238 THR cc_start: 0.8760 (m) cc_final: 0.8391 (p) REVERT: R 60 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7327 (mttp) REVERT: R 136 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8417 (tp) outliers start: 17 outliers final: 6 residues processed: 153 average time/residue: 0.6588 time to fit residues: 107.2012 Evaluate side-chains 132 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 294 ASN B 259 GLN B 340 ASN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128879 restraints weight = 9048.164| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.91 r_work: 0.3176 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9401 Z= 0.109 Angle : 0.490 6.408 12736 Z= 0.262 Chirality : 0.041 0.170 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.758 62.373 1413 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.71 % Allowed : 11.56 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.96 (0.26), residues: 1137 helix: 1.90 (0.27), residues: 393 sheet: 0.26 (0.29), residues: 291 loop : -0.14 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 129 TYR 0.026 0.001 TYR S 190 PHE 0.010 0.001 PHE R 117 TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9395) covalent geometry : angle 0.48933 (12723) SS BOND : bond 0.00409 ( 5) SS BOND : angle 0.97487 ( 10) hydrogen bonds : bond 0.03935 ( 443) hydrogen bonds : angle 4.44414 ( 1239) link_NAG-ASN : bond 0.00310 ( 1) link_NAG-ASN : angle 0.39649 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.358 Fit side-chains REVERT: A 21 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7715 (mtm110) REVERT: A 208 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7779 (ttp80) REVERT: A 275 GLU cc_start: 0.7621 (pp20) cc_final: 0.7156 (pp20) REVERT: A 330 LYS cc_start: 0.7494 (mttt) cc_final: 0.6671 (mtpp) REVERT: S 77 ASN cc_start: 0.8197 (m-40) cc_final: 0.7883 (m110) REVERT: S 113 GLN cc_start: 0.7685 (pm20) cc_final: 0.7404 (mm-40) REVERT: S 238 THR cc_start: 0.8802 (m) cc_final: 0.8474 (p) REVERT: R 136 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8479 (tp) REVERT: R 150 LEU cc_start: 0.8353 (mp) cc_final: 0.8142 (mm) outliers start: 17 outliers final: 6 residues processed: 145 average time/residue: 0.6942 time to fit residues: 106.8229 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 104 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129619 restraints weight = 9094.290| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.90 r_work: 0.3183 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9401 Z= 0.102 Angle : 0.474 6.432 12736 Z= 0.252 Chirality : 0.040 0.167 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.583 65.632 1413 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.81 % Allowed : 13.07 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.15 (0.26), residues: 1137 helix: 2.24 (0.27), residues: 388 sheet: 0.25 (0.29), residues: 293 loop : -0.11 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 202 TYR 0.025 0.001 TYR S 190 PHE 0.009 0.001 PHE A 189 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9395) covalent geometry : angle 0.47344 (12723) SS BOND : bond 0.00415 ( 5) SS BOND : angle 0.83039 ( 10) hydrogen bonds : bond 0.03584 ( 443) hydrogen bonds : angle 4.28198 ( 1239) link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 0.81255 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.369 Fit side-chains REVERT: A 21 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7754 (mtm110) REVERT: A 208 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7702 (ttp80) REVERT: A 275 GLU cc_start: 0.7770 (pp20) cc_final: 0.7347 (pp20) REVERT: A 330 LYS cc_start: 0.7599 (mttt) cc_final: 0.6772 (mtpp) REVERT: B 42 ARG cc_start: 0.7231 (tpt170) cc_final: 0.6880 (tpt170) REVERT: B 44 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: S 77 ASN cc_start: 0.8272 (m-40) cc_final: 0.7935 (m110) REVERT: S 113 GLN cc_start: 0.7794 (pm20) cc_final: 0.7505 (mm-40) REVERT: S 238 THR cc_start: 0.8766 (m) cc_final: 0.8472 (p) REVERT: R 60 LYS cc_start: 0.7639 (mttp) cc_final: 0.7397 (mtpt) REVERT: R 136 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8518 (tp) REVERT: R 150 LEU cc_start: 0.8382 (mp) cc_final: 0.8178 (mm) outliers start: 18 outliers final: 6 residues processed: 142 average time/residue: 0.7087 time to fit residues: 106.6232 Evaluate side-chains 138 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 179 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124478 restraints weight = 8990.382| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.88 r_work: 0.3110 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9401 Z= 0.143 Angle : 0.524 6.428 12736 Z= 0.277 Chirality : 0.042 0.194 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.817 73.603 1413 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.11 % Allowed : 14.27 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1137 helix: 2.20 (0.27), residues: 389 sheet: 0.20 (0.29), residues: 294 loop : -0.11 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 180 TYR 0.029 0.001 TYR S 190 PHE 0.014 0.001 PHE R 117 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9395) covalent geometry : angle 0.52168 (12723) SS BOND : bond 0.00570 ( 5) SS BOND : angle 1.84885 ( 10) hydrogen bonds : bond 0.03955 ( 443) hydrogen bonds : angle 4.44860 ( 1239) link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 0.94581 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.325 Fit side-chains REVERT: A 21 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7774 (mtm110) REVERT: A 46 LYS cc_start: 0.6204 (mttp) cc_final: 0.5861 (mttt) REVERT: A 53 MET cc_start: 0.6914 (mmm) cc_final: 0.5341 (mmt) REVERT: A 208 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7819 (ttp80) REVERT: A 275 GLU cc_start: 0.7731 (pp20) cc_final: 0.7289 (pp20) REVERT: A 330 LYS cc_start: 0.7516 (mttt) cc_final: 0.6492 (mtpp) REVERT: B 44 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: B 268 ASN cc_start: 0.7709 (t0) cc_final: 0.7325 (p0) REVERT: S 77 ASN cc_start: 0.8416 (m-40) cc_final: 0.8130 (m110) REVERT: S 113 GLN cc_start: 0.7888 (pm20) cc_final: 0.7659 (mm-40) REVERT: S 238 THR cc_start: 0.8805 (m) cc_final: 0.8511 (p) REVERT: R 60 LYS cc_start: 0.7655 (mttp) cc_final: 0.7422 (mtpt) REVERT: R 85 ASP cc_start: 0.8356 (t0) cc_final: 0.8148 (t0) REVERT: R 136 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (tp) REVERT: R 150 LEU cc_start: 0.8375 (mp) cc_final: 0.8169 (mm) REVERT: R 164 LYS cc_start: 0.7141 (mppt) cc_final: 0.6653 (mtmm) REVERT: R 167 MET cc_start: 0.8213 (mmp) cc_final: 0.7473 (mmp) REVERT: R 186 PHE cc_start: 0.7511 (m-80) cc_final: 0.6270 (t80) REVERT: R 225 LYS cc_start: 0.7845 (mttt) cc_final: 0.7533 (mtpt) outliers start: 21 outliers final: 12 residues processed: 150 average time/residue: 0.7235 time to fit residues: 114.7425 Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 340 ASN S 179 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126571 restraints weight = 9086.748| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.89 r_work: 0.3142 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9401 Z= 0.113 Angle : 0.486 6.349 12736 Z= 0.259 Chirality : 0.041 0.176 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.803 84.326 1413 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.41 % Allowed : 14.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.16 (0.26), residues: 1137 helix: 2.26 (0.27), residues: 389 sheet: 0.24 (0.29), residues: 291 loop : -0.10 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 180 TYR 0.028 0.001 TYR S 190 PHE 0.011 0.001 PHE R 277 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9395) covalent geometry : angle 0.48398 (12723) SS BOND : bond 0.00559 ( 5) SS BOND : angle 1.31213 ( 10) hydrogen bonds : bond 0.03692 ( 443) hydrogen bonds : angle 4.34666 ( 1239) link_NAG-ASN : bond 0.00069 ( 1) link_NAG-ASN : angle 1.26808 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.272 Fit side-chains REVERT: A 21 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7747 (mtm110) REVERT: A 46 LYS cc_start: 0.6292 (mttp) cc_final: 0.5960 (mttt) REVERT: A 53 MET cc_start: 0.6807 (mmm) cc_final: 0.5392 (mmt) REVERT: A 208 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.7827 (ttp80) REVERT: A 275 GLU cc_start: 0.7753 (pp20) cc_final: 0.7297 (pp20) REVERT: A 330 LYS cc_start: 0.7550 (mttt) cc_final: 0.6534 (mtpp) REVERT: B 38 ASP cc_start: 0.7422 (m-30) cc_final: 0.7111 (OUTLIER) REVERT: B 42 ARG cc_start: 0.7215 (tpt170) cc_final: 0.6895 (tpt170) REVERT: B 268 ASN cc_start: 0.7671 (t0) cc_final: 0.7298 (p0) REVERT: S 77 ASN cc_start: 0.8359 (m-40) cc_final: 0.8097 (m110) REVERT: S 238 THR cc_start: 0.8761 (m) cc_final: 0.8505 (p) REVERT: R 85 ASP cc_start: 0.8376 (t0) cc_final: 0.8156 (t0) REVERT: R 136 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8544 (tp) REVERT: R 150 LEU cc_start: 0.8372 (mp) cc_final: 0.8168 (mm) REVERT: R 164 LYS cc_start: 0.7175 (mppt) cc_final: 0.6688 (mtmm) REVERT: R 225 LYS cc_start: 0.7761 (mttt) cc_final: 0.7493 (mtpt) REVERT: R 238 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8062 (mp) outliers start: 24 outliers final: 11 residues processed: 151 average time/residue: 0.7005 time to fit residues: 111.7735 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127732 restraints weight = 9083.221| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.88 r_work: 0.3156 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9401 Z= 0.108 Angle : 0.485 6.403 12736 Z= 0.259 Chirality : 0.041 0.173 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.637 84.037 1413 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.21 % Allowed : 15.38 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.18 (0.26), residues: 1137 helix: 2.31 (0.27), residues: 389 sheet: 0.23 (0.29), residues: 291 loop : -0.11 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 202 TYR 0.027 0.001 TYR S 190 PHE 0.010 0.001 PHE R 277 TRP 0.009 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9395) covalent geometry : angle 0.48334 (12723) SS BOND : bond 0.00514 ( 5) SS BOND : angle 1.12452 ( 10) hydrogen bonds : bond 0.03614 ( 443) hydrogen bonds : angle 4.30356 ( 1239) link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.27011 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.249 Fit side-chains REVERT: A 21 ARG cc_start: 0.8191 (ttm110) cc_final: 0.7718 (mtm110) REVERT: A 46 LYS cc_start: 0.6313 (mttp) cc_final: 0.5833 (mttt) REVERT: A 53 MET cc_start: 0.6731 (mmm) cc_final: 0.5406 (mmt) REVERT: A 208 ARG cc_start: 0.8102 (ttp-110) cc_final: 0.7818 (ttp80) REVERT: A 275 GLU cc_start: 0.7701 (pp20) cc_final: 0.7236 (pp20) REVERT: A 330 LYS cc_start: 0.7534 (mttt) cc_final: 0.6613 (mtpp) REVERT: B 38 ASP cc_start: 0.7373 (m-30) cc_final: 0.7087 (OUTLIER) REVERT: B 42 ARG cc_start: 0.7238 (tpt170) cc_final: 0.6935 (tpt170) REVERT: B 223 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 268 ASN cc_start: 0.7719 (t0) cc_final: 0.7381 (p0) REVERT: S 190 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6401 (p90) REVERT: S 202 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.7990 (ptt-90) REVERT: S 238 THR cc_start: 0.8745 (m) cc_final: 0.8508 (p) REVERT: R 85 ASP cc_start: 0.8353 (t0) cc_final: 0.8131 (t0) REVERT: R 164 LYS cc_start: 0.7157 (mppt) cc_final: 0.6675 (mtmm) REVERT: R 225 LYS cc_start: 0.7733 (mttt) cc_final: 0.7461 (mtpt) outliers start: 22 outliers final: 12 residues processed: 148 average time/residue: 0.7134 time to fit residues: 111.5229 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 36 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.163765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125340 restraints weight = 9006.179| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3125 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9401 Z= 0.128 Angle : 0.510 6.854 12736 Z= 0.272 Chirality : 0.042 0.189 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.479 74.539 1413 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 16.48 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.16 (0.26), residues: 1137 helix: 2.30 (0.27), residues: 389 sheet: 0.21 (0.29), residues: 293 loop : -0.12 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 216 TYR 0.029 0.001 TYR S 190 PHE 0.013 0.001 PHE R 277 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9395) covalent geometry : angle 0.50912 (12723) SS BOND : bond 0.00528 ( 5) SS BOND : angle 1.14872 ( 10) hydrogen bonds : bond 0.03783 ( 443) hydrogen bonds : angle 4.38887 ( 1239) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.24375 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.369 Fit side-chains REVERT: A 21 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7698 (mtm110) REVERT: A 46 LYS cc_start: 0.6463 (mttp) cc_final: 0.5980 (mttt) REVERT: A 53 MET cc_start: 0.6800 (mmm) cc_final: 0.5457 (mmt) REVERT: A 208 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7829 (ttp80) REVERT: A 275 GLU cc_start: 0.7699 (pp20) cc_final: 0.7228 (pp20) REVERT: A 330 LYS cc_start: 0.7577 (mttt) cc_final: 0.6674 (mtpp) REVERT: B 38 ASP cc_start: 0.7439 (m-30) cc_final: 0.7132 (OUTLIER) REVERT: B 42 ARG cc_start: 0.7235 (tpt170) cc_final: 0.6927 (tpt170) REVERT: B 196 THR cc_start: 0.7740 (p) cc_final: 0.7397 (p) REVERT: B 223 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 268 ASN cc_start: 0.7755 (t0) cc_final: 0.7385 (p0) REVERT: S 18 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8163 (tpp-160) REVERT: S 190 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.6462 (p90) REVERT: S 202 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.8053 (ptt-90) REVERT: S 238 THR cc_start: 0.8765 (m) cc_final: 0.8534 (p) REVERT: R 85 ASP cc_start: 0.8333 (t0) cc_final: 0.8113 (t0) REVERT: R 164 LYS cc_start: 0.7178 (mppt) cc_final: 0.6715 (mtmm) REVERT: R 225 LYS cc_start: 0.7733 (mttt) cc_final: 0.7481 (mtpt) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.7178 time to fit residues: 113.1194 Evaluate side-chains 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 0.0270 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124460 restraints weight = 8990.187| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.86 r_work: 0.3116 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9401 Z= 0.135 Angle : 0.522 7.480 12736 Z= 0.277 Chirality : 0.042 0.190 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.376 67.040 1413 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 16.68 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1137 helix: 2.22 (0.27), residues: 389 sheet: 0.14 (0.30), residues: 294 loop : -0.12 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 216 TYR 0.029 0.001 TYR S 190 PHE 0.014 0.001 PHE R 277 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9395) covalent geometry : angle 0.52074 (12723) SS BOND : bond 0.00537 ( 5) SS BOND : angle 1.10419 ( 10) hydrogen bonds : bond 0.03880 ( 443) hydrogen bonds : angle 4.44245 ( 1239) link_NAG-ASN : bond 0.00065 ( 1) link_NAG-ASN : angle 1.21768 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.491 Fit side-chains REVERT: A 21 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7729 (mtm110) REVERT: A 46 LYS cc_start: 0.6525 (mttp) cc_final: 0.6057 (mttt) REVERT: A 53 MET cc_start: 0.6806 (mmm) cc_final: 0.5447 (mmt) REVERT: A 208 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7831 (ttp80) REVERT: A 275 GLU cc_start: 0.7709 (pp20) cc_final: 0.7238 (pp20) REVERT: A 330 LYS cc_start: 0.7589 (mttt) cc_final: 0.6719 (mtpp) REVERT: B 42 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6937 (tpt170) REVERT: B 196 THR cc_start: 0.7755 (p) cc_final: 0.7430 (p) REVERT: B 223 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8623 (p) REVERT: B 268 ASN cc_start: 0.7748 (t0) cc_final: 0.7378 (p0) REVERT: S 190 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.6465 (p90) REVERT: S 202 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.8044 (ptt-90) REVERT: S 238 THR cc_start: 0.8766 (m) cc_final: 0.8531 (p) REVERT: R 85 ASP cc_start: 0.8333 (t0) cc_final: 0.8118 (t0) REVERT: R 138 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7690 (mmtp) REVERT: R 164 LYS cc_start: 0.7243 (mppt) cc_final: 0.6770 (mtmm) REVERT: R 225 LYS cc_start: 0.7747 (mttt) cc_final: 0.7496 (mtpt) outliers start: 16 outliers final: 11 residues processed: 144 average time/residue: 0.7228 time to fit residues: 110.1180 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.162586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123641 restraints weight = 9029.447| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.90 r_work: 0.3105 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9401 Z= 0.142 Angle : 0.537 8.980 12736 Z= 0.284 Chirality : 0.042 0.193 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.323 62.481 1413 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 16.88 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.02 (0.26), residues: 1137 helix: 2.14 (0.26), residues: 389 sheet: 0.12 (0.30), residues: 294 loop : -0.15 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 216 TYR 0.030 0.001 TYR S 190 PHE 0.014 0.001 PHE R 277 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9395) covalent geometry : angle 0.53582 (12723) SS BOND : bond 0.00537 ( 5) SS BOND : angle 1.12279 ( 10) hydrogen bonds : bond 0.03964 ( 443) hydrogen bonds : angle 4.50607 ( 1239) link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 1.22674 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.395 Fit side-chains REVERT: A 21 ARG cc_start: 0.8186 (ttm110) cc_final: 0.7726 (mtm110) REVERT: A 46 LYS cc_start: 0.6648 (mttp) cc_final: 0.6168 (mttt) REVERT: A 53 MET cc_start: 0.6889 (mmm) cc_final: 0.5445 (mmt) REVERT: A 208 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7856 (ttp80) REVERT: A 275 GLU cc_start: 0.7705 (pp20) cc_final: 0.7229 (pp20) REVERT: A 330 LYS cc_start: 0.7591 (mttt) cc_final: 0.6738 (mtpp) REVERT: B 196 THR cc_start: 0.7764 (p) cc_final: 0.7452 (p) REVERT: B 268 ASN cc_start: 0.7759 (t0) cc_final: 0.7359 (p0) REVERT: S 190 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6477 (p90) REVERT: S 202 ARG cc_start: 0.8284 (ptt-90) cc_final: 0.8056 (ptt-90) REVERT: S 238 THR cc_start: 0.8770 (m) cc_final: 0.8533 (p) REVERT: R 85 ASP cc_start: 0.8315 (t0) cc_final: 0.8103 (t0) REVERT: R 138 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7810 (mmtp) REVERT: R 164 LYS cc_start: 0.7235 (mppt) cc_final: 0.6794 (mtmm) REVERT: R 225 LYS cc_start: 0.7744 (mttt) cc_final: 0.7485 (mtpt) REVERT: R 238 ILE cc_start: 0.8275 (mt) cc_final: 0.8074 (mp) outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 0.7421 time to fit residues: 107.4542 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 136 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN R 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122263 restraints weight = 8910.648| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.87 r_work: 0.3094 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9401 Z= 0.155 Angle : 0.559 9.247 12736 Z= 0.293 Chirality : 0.043 0.198 1429 Planarity : 0.004 0.066 1596 Dihedral : 5.383 61.457 1413 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 17.29 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 1.02 (0.26), residues: 1137 helix: 2.19 (0.26), residues: 382 sheet: 0.11 (0.30), residues: 294 loop : -0.15 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 180 TYR 0.031 0.002 TYR S 190 PHE 0.016 0.001 PHE R 277 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9395) covalent geometry : angle 0.55764 (12723) SS BOND : bond 0.00547 ( 5) SS BOND : angle 1.14731 ( 10) hydrogen bonds : bond 0.04079 ( 443) hydrogen bonds : angle 4.56679 ( 1239) link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 1.17253 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4640.94 seconds wall clock time: 79 minutes 47.29 seconds (4787.29 seconds total)