Starting phenix.real_space_refine on Wed Apr 30 12:01:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6p_36010/04_2025/8j6p_36010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6p_36010/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6p_36010/04_2025/8j6p_36010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6p_36010/04_2025/8j6p_36010.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6p_36010/04_2025/8j6p_36010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6p_36010/04_2025/8j6p_36010.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.51, per 1000 atoms: 0.60 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.22 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: 2.71 Time building geometry restraints manager: 2.97 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: 0.820 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.260 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP R 59 HIS 0.005 0.001 HIS S 232 PHE 0.027 0.002 PHE R 52 TYR 0.023 0.002 TYR S 190 ARG 0.006 0.000 ARG S 202 Details of bonding type rmsd link_NAG-ASN : bond 0.06219 ( 1) link_NAG-ASN : angle 9.87574 ( 3) hydrogen bonds : bond 0.17861 ( 443) hydrogen bonds : angle 6.92944 ( 1239) SS BOND : bond 0.00537 ( 5) SS BOND : angle 1.31663 ( 10) covalent geometry : bond 0.00510 ( 9395) covalent geometry : angle 0.78263 (12723) *********************** 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 : 0.933 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: 1.2926 time to fit residues: 237.1985 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 : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.164596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124934 restraints weight = 8940.751| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.98 r_work: 0.3121 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2403 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= 0.171 Angle : 0.589 7.208 12736 Z= 0.314 Chirality : 0.043 0.202 1429 Planarity : 0.005 0.076 1596 Dihedral : 5.977 50.521 1413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 8.94 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1137 helix: 1.50 (0.26), residues: 389 sheet: 0.28 (0.30), residues: 291 loop : -0.20 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS S 232 PHE 0.014 0.002 PHE R 117 TYR 0.033 0.002 TYR S 190 ARG 0.007 0.001 ARG S 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 1.30907 ( 3) hydrogen bonds : bond 0.04491 ( 443) hydrogen bonds : angle 4.85676 ( 1239) SS BOND : bond 0.00893 ( 5) SS BOND : angle 1.53297 ( 10) covalent geometry : bond 0.00377 ( 9395) covalent geometry : angle 0.58753 (12723) *********************** 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 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.188 Fit side-chains REVERT: A 21 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7650 (mtm-85) REVERT: A 198 MET cc_start: 0.8910 (ttp) cc_final: 0.8685 (ttp) REVERT: A 275 GLU cc_start: 0.7738 (pp20) cc_final: 0.7221 (pp20) REVERT: A 330 LYS cc_start: 0.7324 (mttt) cc_final: 0.6495 (mtpp) REVERT: B 42 ARG cc_start: 0.7201 (tpt170) cc_final: 0.6763 (tpt170) REVERT: S 77 ASN cc_start: 0.8019 (m-40) cc_final: 0.7789 (m-40) REVERT: S 113 GLN cc_start: 0.7649 (pm20) cc_final: 0.7182 (tp40) REVERT: S 238 THR cc_start: 0.8790 (m) cc_final: 0.8435 (p) REVERT: R 60 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7384 (mttp) REVERT: R 101 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: R 136 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8434 (tp) outliers start: 17 outliers final: 6 residues processed: 141 average time/residue: 1.3955 time to fit residues: 209.4328 Evaluate side-chains 127 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 167 HIS S 186 GLN R 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119790 restraints weight = 9071.537| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.95 r_work: 0.3044 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9401 Z= 0.207 Angle : 0.601 7.010 12736 Z= 0.319 Chirality : 0.045 0.222 1429 Planarity : 0.005 0.069 1596 Dihedral : 6.336 70.039 1413 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.02 % Allowed : 10.75 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1137 helix: 1.63 (0.26), residues: 389 sheet: 0.09 (0.29), residues: 286 loop : -0.26 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS S 232 PHE 0.019 0.002 PHE R 277 TYR 0.034 0.002 TYR S 190 ARG 0.005 0.001 ARG S 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 1) link_NAG-ASN : angle 0.43421 ( 3) hydrogen bonds : bond 0.04809 ( 443) hydrogen bonds : angle 4.89828 ( 1239) SS BOND : bond 0.00498 ( 5) SS BOND : angle 1.37408 ( 10) covalent geometry : bond 0.00480 ( 9395) covalent geometry : angle 0.60016 (12723) *********************** 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 169 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.916 Fit side-chains REVERT: A 21 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7720 (mtm-85) REVERT: A 46 LYS cc_start: 0.6516 (mttp) cc_final: 0.6314 (mtmt) REVERT: A 208 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.8029 (ttp80) REVERT: A 275 GLU cc_start: 0.7765 (pp20) cc_final: 0.7244 (pp20) REVERT: A 305 CYS cc_start: 0.8015 (m) cc_final: 0.7702 (m) REVERT: A 330 LYS cc_start: 0.7479 (mttt) cc_final: 0.6456 (mtpp) REVERT: B 44 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: B 325 MET cc_start: 0.8905 (tpp) cc_final: 0.8705 (mmt) REVERT: S 76 LYS cc_start: 0.7235 (pttt) cc_final: 0.6883 (mttp) REVERT: S 238 THR cc_start: 0.8858 (m) cc_final: 0.8564 (p) REVERT: R 138 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7809 (mmtp) REVERT: R 164 LYS cc_start: 0.7205 (mppt) cc_final: 0.6729 (mtmm) REVERT: R 186 PHE cc_start: 0.7574 (m-80) cc_final: 0.6300 (t80) REVERT: R 225 LYS cc_start: 0.7866 (mttt) cc_final: 0.7548 (mtpt) outliers start: 30 outliers final: 11 residues processed: 153 average time/residue: 1.9733 time to fit residues: 320.7953 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 B residue 276 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 340 ASN 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 = 0.3813 r_free = 0.3813 target = 0.162951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124110 restraints weight = 9005.602| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.88 r_work: 0.3111 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9401 Z= 0.118 Angle : 0.503 6.316 12736 Z= 0.269 Chirality : 0.041 0.181 1429 Planarity : 0.004 0.064 1596 Dihedral : 6.069 78.517 1413 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.41 % Allowed : 14.07 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1137 helix: 1.93 (0.27), residues: 390 sheet: 0.14 (0.29), residues: 283 loop : -0.22 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE A 196 TYR 0.029 0.001 TYR S 190 ARG 0.004 0.000 ARG R 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 0.87540 ( 3) hydrogen bonds : bond 0.03917 ( 443) hydrogen bonds : angle 4.57558 ( 1239) SS BOND : bond 0.00682 ( 5) SS BOND : angle 1.55066 ( 10) covalent geometry : bond 0.00257 ( 9395) covalent geometry : angle 0.50093 (12723) *********************** 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 166 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.050 Fit side-chains REVERT: A 21 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7772 (mtm-85) REVERT: A 46 LYS cc_start: 0.6413 (mttp) cc_final: 0.5928 (mttt) REVERT: A 208 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7939 (ttp80) REVERT: A 275 GLU cc_start: 0.7783 (pp20) cc_final: 0.7336 (pp20) REVERT: A 330 LYS cc_start: 0.7520 (mttt) cc_final: 0.6481 (mtpp) REVERT: B 268 ASN cc_start: 0.7710 (t0) cc_final: 0.7309 (p0) REVERT: G 52 THR cc_start: 0.7802 (m) cc_final: 0.7564 (p) REVERT: S 18 ARG cc_start: 0.8325 (tpp80) cc_final: 0.8047 (tpp-160) REVERT: S 76 LYS cc_start: 0.7099 (pttt) cc_final: 0.6688 (mttp) REVERT: S 238 THR cc_start: 0.8788 (m) cc_final: 0.8507 (p) REVERT: R 150 LEU cc_start: 0.8418 (mp) cc_final: 0.8183 (mm) REVERT: R 164 LYS cc_start: 0.7136 (mppt) cc_final: 0.6729 (mtmm) REVERT: R 186 PHE cc_start: 0.7490 (m-80) cc_final: 0.6252 (t80) REVERT: R 225 LYS cc_start: 0.7798 (mttt) cc_final: 0.7537 (mtpt) outliers start: 24 outliers final: 11 residues processed: 154 average time/residue: 1.4395 time to fit residues: 234.3748 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR 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 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.0470 chunk 72 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 77 ASN S 171 ASN 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 = 0.3820 r_free = 0.3820 target = 0.163663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125446 restraints weight = 8987.343| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.82 r_work: 0.3132 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3392 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= 0.115 Angle : 0.492 6.360 12736 Z= 0.263 Chirality : 0.041 0.178 1429 Planarity : 0.004 0.065 1596 Dihedral : 6.020 88.231 1413 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.31 % Allowed : 14.87 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1137 helix: 2.14 (0.27), residues: 387 sheet: 0.19 (0.29), residues: 292 loop : -0.19 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 117 TYR 0.027 0.001 TYR S 190 ARG 0.004 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.10892 ( 3) hydrogen bonds : bond 0.03801 ( 443) hydrogen bonds : angle 4.47774 ( 1239) SS BOND : bond 0.00547 ( 5) SS BOND : angle 1.16027 ( 10) covalent geometry : bond 0.00253 ( 9395) covalent geometry : angle 0.49040 (12723) *********************** 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 160 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.045 Fit side-chains REVERT: A 21 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7700 (mtm110) REVERT: A 46 LYS cc_start: 0.6471 (mttp) cc_final: 0.5926 (mttt) REVERT: A 208 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7900 (ttp80) REVERT: A 275 GLU cc_start: 0.7784 (pp20) cc_final: 0.7327 (pp20) REVERT: A 330 LYS cc_start: 0.7526 (mttt) cc_final: 0.6529 (mtpp) REVERT: B 42 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6819 (tpt170) REVERT: B 268 ASN cc_start: 0.7724 (t0) cc_final: 0.7327 (p0) REVERT: S 18 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8090 (tpp-160) REVERT: S 76 LYS cc_start: 0.7251 (pttt) cc_final: 0.6786 (mttp) REVERT: S 142 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: S 190 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6413 (p90) REVERT: S 238 THR cc_start: 0.8773 (m) cc_final: 0.8537 (p) REVERT: R 150 LEU cc_start: 0.8397 (mp) cc_final: 0.8174 (mm) REVERT: R 164 LYS cc_start: 0.7122 (mppt) cc_final: 0.6681 (mtmm) REVERT: R 186 PHE cc_start: 0.7470 (m-80) cc_final: 0.6266 (t80) REVERT: R 225 LYS cc_start: 0.7751 (mttt) cc_final: 0.7480 (mtpt) REVERT: R 238 ILE cc_start: 0.8222 (mt) cc_final: 0.8003 (mp) outliers start: 23 outliers final: 9 residues processed: 149 average time/residue: 1.4303 time to fit residues: 225.3892 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP 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 S residue 142 GLN 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 Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 142 GLN S 171 ASN S 186 GLN R 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119368 restraints weight = 8961.054| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.90 r_work: 0.3042 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9401 Z= 0.205 Angle : 0.583 6.803 12736 Z= 0.309 Chirality : 0.044 0.217 1429 Planarity : 0.004 0.068 1596 Dihedral : 6.188 79.405 1413 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.81 % Allowed : 15.28 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1137 helix: 1.99 (0.26), residues: 386 sheet: 0.10 (0.30), residues: 293 loop : -0.22 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.002 PHE R 277 TYR 0.033 0.002 TYR S 190 ARG 0.005 0.001 ARG S 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 0.81584 ( 3) hydrogen bonds : bond 0.04454 ( 443) hydrogen bonds : angle 4.77704 ( 1239) SS BOND : bond 0.00637 ( 5) SS BOND : angle 1.28681 ( 10) covalent geometry : bond 0.00477 ( 9395) covalent geometry : angle 0.58220 (12723) *********************** 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 165 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.057 Fit side-chains REVERT: A 21 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7763 (mtm-85) REVERT: A 46 LYS cc_start: 0.6906 (mttp) cc_final: 0.6211 (mttt) REVERT: A 208 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7821 (ttp80) REVERT: A 275 GLU cc_start: 0.7669 (pp20) cc_final: 0.7205 (pp20) REVERT: A 330 LYS cc_start: 0.7560 (mttt) cc_final: 0.6496 (mtpp) REVERT: B 259 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: B 268 ASN cc_start: 0.7775 (t0) cc_final: 0.7350 (p0) REVERT: S 76 LYS cc_start: 0.7321 (pttt) cc_final: 0.6936 (mttp) REVERT: S 142 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: S 190 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.6506 (p90) REVERT: S 238 THR cc_start: 0.8816 (m) cc_final: 0.8545 (p) REVERT: R 150 LEU cc_start: 0.8415 (mp) cc_final: 0.8172 (mm) REVERT: R 164 LYS cc_start: 0.7149 (mppt) cc_final: 0.6670 (mtmm) REVERT: R 186 PHE cc_start: 0.7592 (m-80) cc_final: 0.6311 (t80) REVERT: R 225 LYS cc_start: 0.7715 (mttt) cc_final: 0.7467 (mtpt) outliers start: 28 outliers final: 13 residues processed: 152 average time/residue: 1.6913 time to fit residues: 271.0509 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR 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 259 GLN 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 142 GLN 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 Chi-restraints excluded: chain R residue 192 MET 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 42 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.161455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122909 restraints weight = 9045.521| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.83 r_work: 0.3093 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9401 Z= 0.126 Angle : 0.513 6.855 12736 Z= 0.274 Chirality : 0.042 0.189 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.789 69.533 1413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.61 % Allowed : 16.08 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1137 helix: 2.10 (0.27), residues: 387 sheet: 0.15 (0.30), residues: 291 loop : -0.20 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE R 277 TYR 0.030 0.001 TYR S 190 ARG 0.006 0.000 ARG S 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.09545 ( 3) hydrogen bonds : bond 0.03925 ( 443) hydrogen bonds : angle 4.56789 ( 1239) SS BOND : bond 0.00517 ( 5) SS BOND : angle 0.99372 ( 10) covalent geometry : bond 0.00279 ( 9395) covalent geometry : angle 0.51243 (12723) *********************** 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: 26 poor density : 134 time to evaluate : 0.947 Fit side-chains REVERT: A 21 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7734 (mtm110) REVERT: A 46 LYS cc_start: 0.6804 (mttp) cc_final: 0.6386 (mtmt) REVERT: A 208 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7796 (ttp80) REVERT: A 275 GLU cc_start: 0.7670 (pp20) cc_final: 0.7191 (pp20) REVERT: A 330 LYS cc_start: 0.7575 (mttt) cc_final: 0.6564 (mtpp) REVERT: B 259 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: B 268 ASN cc_start: 0.7740 (t0) cc_final: 0.7348 (p0) REVERT: S 76 LYS cc_start: 0.7359 (pttt) cc_final: 0.6925 (mttp) REVERT: S 142 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: S 190 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.6458 (p90) REVERT: S 202 ARG cc_start: 0.8208 (ptt-90) cc_final: 0.7992 (ptt-90) REVERT: S 238 THR cc_start: 0.8808 (m) cc_final: 0.8546 (p) REVERT: R 150 LEU cc_start: 0.8401 (mp) cc_final: 0.8179 (mm) REVERT: R 164 LYS cc_start: 0.7101 (mppt) cc_final: 0.6658 (mtmm) REVERT: R 186 PHE cc_start: 0.7541 (m-80) cc_final: 0.6287 (t80) REVERT: R 225 LYS cc_start: 0.7671 (mttt) cc_final: 0.7432 (mtpt) REVERT: R 238 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7999 (mp) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 1.5041 time to fit residues: 230.9073 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP 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 259 GLN 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 142 GLN 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 Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 43 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.123723 restraints weight = 9110.464| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.83 r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9401 Z= 0.124 Angle : 0.510 7.337 12736 Z= 0.271 Chirality : 0.041 0.188 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.505 60.980 1413 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.41 % Allowed : 16.18 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1137 helix: 2.16 (0.27), residues: 387 sheet: 0.20 (0.30), residues: 292 loop : -0.19 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE R 277 TYR 0.029 0.001 TYR S 190 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 1.24338 ( 3) hydrogen bonds : bond 0.03846 ( 443) hydrogen bonds : angle 4.49486 ( 1239) SS BOND : bond 0.00506 ( 5) SS BOND : angle 1.00956 ( 10) covalent geometry : bond 0.00277 ( 9395) covalent geometry : angle 0.50940 (12723) *********************** 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 155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 3.490 Fit side-chains REVERT: A 21 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7707 (mtm110) REVERT: A 46 LYS cc_start: 0.6858 (mttp) cc_final: 0.6407 (mtmt) REVERT: A 208 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7916 (ttp80) REVERT: A 275 GLU cc_start: 0.7657 (pp20) cc_final: 0.7154 (pp20) REVERT: A 330 LYS cc_start: 0.7601 (mttt) cc_final: 0.6671 (mtpp) REVERT: B 42 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6843 (tpt170) REVERT: B 268 ASN cc_start: 0.7745 (t0) cc_final: 0.7359 (p0) REVERT: S 76 LYS cc_start: 0.7245 (pttt) cc_final: 0.6832 (mttp) REVERT: S 190 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.6435 (p90) REVERT: S 238 THR cc_start: 0.8800 (m) cc_final: 0.8541 (p) REVERT: R 150 LEU cc_start: 0.8410 (mp) cc_final: 0.8193 (mm) REVERT: R 164 LYS cc_start: 0.7118 (mppt) cc_final: 0.6663 (mtmm) REVERT: R 186 PHE cc_start: 0.7575 (m-80) cc_final: 0.6321 (t80) REVERT: R 238 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8009 (mp) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 2.5684 time to fit residues: 386.5129 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 : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP 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 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 Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124789 restraints weight = 8978.788| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.87 r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3686 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= 0.114 Angle : 0.505 8.417 12736 Z= 0.267 Chirality : 0.041 0.180 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.365 58.244 1413 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.21 % Allowed : 16.58 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1137 helix: 2.20 (0.27), residues: 387 sheet: 0.20 (0.30), residues: 293 loop : -0.15 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 276 TYR 0.028 0.001 TYR S 190 ARG 0.007 0.000 ARG S 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00016 ( 1) link_NAG-ASN : angle 1.37247 ( 3) hydrogen bonds : bond 0.03741 ( 443) hydrogen bonds : angle 4.42942 ( 1239) SS BOND : bond 0.00481 ( 5) SS BOND : angle 0.95448 ( 10) covalent geometry : bond 0.00249 ( 9395) covalent geometry : angle 0.50400 (12723) *********************** 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 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.072 Fit side-chains REVERT: A 21 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7709 (mtm110) REVERT: A 46 LYS cc_start: 0.6801 (mttp) cc_final: 0.6337 (mtmt) REVERT: A 208 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7900 (ttp80) REVERT: A 275 GLU cc_start: 0.7673 (pp20) cc_final: 0.7169 (pp20) REVERT: A 330 LYS cc_start: 0.7601 (mttt) cc_final: 0.6675 (mtpp) REVERT: B 42 ARG cc_start: 0.7198 (tpt170) cc_final: 0.6839 (tpt170) REVERT: B 268 ASN cc_start: 0.7767 (t0) cc_final: 0.7338 (p0) REVERT: S 190 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.6411 (p90) REVERT: S 238 THR cc_start: 0.8779 (m) cc_final: 0.8544 (p) REVERT: R 150 LEU cc_start: 0.8424 (mp) cc_final: 0.8194 (mm) REVERT: R 164 LYS cc_start: 0.7150 (mppt) cc_final: 0.6702 (mtmm) REVERT: R 225 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7680 (mtpt) REVERT: R 238 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8005 (mp) outliers start: 22 outliers final: 12 residues processed: 139 average time/residue: 1.7470 time to fit residues: 257.9617 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 38 ASP 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 B residue 276 VAL 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 Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 52 optimal weight: 0.0000 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123338 restraints weight = 9170.288| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.11 r_work: 0.3164 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3713 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= 0.108 Angle : 0.493 7.058 12736 Z= 0.264 Chirality : 0.041 0.174 1429 Planarity : 0.004 0.063 1596 Dihedral : 5.205 57.040 1413 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 17.19 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1137 helix: 2.26 (0.27), residues: 387 sheet: 0.23 (0.30), residues: 291 loop : -0.12 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 276 TYR 0.027 0.001 TYR S 190 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 1.39942 ( 3) hydrogen bonds : bond 0.03675 ( 443) hydrogen bonds : angle 4.38678 ( 1239) SS BOND : bond 0.00487 ( 5) SS BOND : angle 0.88578 ( 10) covalent geometry : bond 0.00234 ( 9395) covalent geometry : angle 0.49201 (12723) ********************** 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 155 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.963 Fit side-chains REVERT: A 21 ARG cc_start: 0.7584 (ttm110) cc_final: 0.6909 (mtm110) REVERT: A 46 LYS cc_start: 0.6516 (mttp) cc_final: 0.6034 (mtmt) REVERT: A 208 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7394 (ttp80) REVERT: A 275 GLU cc_start: 0.7490 (pp20) cc_final: 0.7022 (pp20) REVERT: A 330 LYS cc_start: 0.7215 (mttt) cc_final: 0.6260 (mtpp) REVERT: B 42 ARG cc_start: 0.7077 (tpt170) cc_final: 0.6724 (tpt170) REVERT: B 258 ASP cc_start: 0.7908 (t0) cc_final: 0.7686 (t0) REVERT: B 259 GLN cc_start: 0.7875 (mt0) cc_final: 0.7661 (mt0) REVERT: B 268 ASN cc_start: 0.7541 (t0) cc_final: 0.6882 (p0) REVERT: S 18 ARG cc_start: 0.8179 (tpp-160) cc_final: 0.7970 (tpp80) REVERT: S 190 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.5996 (p90) REVERT: S 238 THR cc_start: 0.8658 (m) cc_final: 0.8291 (p) REVERT: R 150 LEU cc_start: 0.8024 (mp) cc_final: 0.7745 (mm) REVERT: R 164 LYS cc_start: 0.6915 (mppt) cc_final: 0.6340 (mtmm) REVERT: R 238 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7547 (mp) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 1.4535 time to fit residues: 224.4357 Evaluate side-chains 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 38 ASP 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 B residue 276 VAL 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 Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122734 restraints weight = 9049.987| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.11 r_work: 0.3155 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3777 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= 0.115 Angle : 0.501 7.263 12736 Z= 0.268 Chirality : 0.041 0.180 1429 Planarity : 0.004 0.063 1596 Dihedral : 5.121 55.687 1413 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.31 % Allowed : 18.09 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1137 helix: 2.29 (0.27), residues: 387 sheet: 0.22 (0.30), residues: 293 loop : -0.14 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.009 0.001 PHE B 151 TYR 0.028 0.001 TYR S 190 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.36125 ( 3) hydrogen bonds : bond 0.03750 ( 443) hydrogen bonds : angle 4.39590 ( 1239) SS BOND : bond 0.00478 ( 5) SS BOND : angle 0.88788 ( 10) covalent geometry : bond 0.00253 ( 9395) covalent geometry : angle 0.50069 (12723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10023.00 seconds wall clock time: 176 minutes 2.07 seconds (10562.07 seconds total)