Starting phenix.real_space_refine on Fri Mar 14 03:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6p_36010/03_2025/8j6p_36010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6p_36010/03_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_36010/03_2025/8j6p_36010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6p_36010/03_2025/8j6p_36010.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6p_36010/03_2025/8j6p_36010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6p_36010/03_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-5624/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: 5.55, 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 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: 1.10 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: 2.86 Time building geometry restraints manager: 3.08 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: 0.700 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.950 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:15.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- 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 9395 Z= 0.319 Angle : 0.783 9.515 12723 Z= 0.407 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 *********************** 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 : 0.965 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: 1.1978 time to fit residues: 219.9327 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 : 0.973 ------------------------------------------------------------------------------- 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 9395 Z= 0.248 Angle : 0.588 7.208 12723 Z= 0.313 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 *********************** 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 : 1.098 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: 1.4947 time to fit residues: 224.2719 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 : 1.115 ------------------------------------------------------------------------------- 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 9395 Z= 0.315 Angle : 0.600 7.010 12723 Z= 0.318 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 *********************** 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 : 0.951 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: 1.5593 time to fit residues: 251.4873 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 : 0.977 ------------------------------------------------------------------------------- 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 9395 Z= 0.167 Angle : 0.501 6.316 12723 Z= 0.268 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 *********************** 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 : 1.109 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: 1.7235 time to fit residues: 281.3734 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 : 1.222 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.160237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121228 restraints weight = 8959.303| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.85 r_work: 0.3073 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9395 Z= 0.244 Angle : 0.541 6.406 12723 Z= 0.288 Chirality : 0.043 0.202 1429 Planarity : 0.004 0.066 1596 Dihedral : 6.303 89.125 1413 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.91 % Allowed : 14.17 % 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 (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: 0.89 (0.26), residues: 1137 helix: 1.94 (0.26), residues: 392 sheet: 0.12 (0.30), residues: 293 loop : -0.19 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 277 TYR 0.031 0.002 TYR S 190 ARG 0.004 0.000 ARG B 219 *********************** 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 161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.074 Fit side-chains REVERT: A 21 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7769 (mtm-85) REVERT: A 46 LYS cc_start: 0.6748 (mttp) cc_final: 0.6095 (mttt) REVERT: A 208 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.8012 (ttp80) REVERT: A 275 GLU cc_start: 0.7803 (pp20) cc_final: 0.7344 (pp20) REVERT: A 330 LYS cc_start: 0.7542 (mttt) cc_final: 0.6493 (mtpp) REVERT: B 197 ARG cc_start: 0.8745 (mmt-90) cc_final: 0.8161 (mmm160) REVERT: B 259 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: B 268 ASN cc_start: 0.7718 (t0) cc_final: 0.7288 (p0) REVERT: G 52 THR cc_start: 0.7848 (m) cc_final: 0.7615 (p) REVERT: S 19 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8021 (tttt) REVERT: S 76 LYS cc_start: 0.7266 (pttt) cc_final: 0.6887 (mttp) REVERT: S 190 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6521 (p90) REVERT: S 202 ARG cc_start: 0.8267 (ptt-90) cc_final: 0.8055 (ptt-90) REVERT: S 238 THR cc_start: 0.8816 (m) cc_final: 0.8562 (p) REVERT: R 150 LEU cc_start: 0.8419 (mp) cc_final: 0.8181 (mm) REVERT: R 164 LYS cc_start: 0.7166 (mppt) cc_final: 0.6711 (mtmm) REVERT: R 186 PHE cc_start: 0.7542 (m-80) cc_final: 0.6305 (t80) REVERT: R 225 LYS cc_start: 0.7796 (mttt) cc_final: 0.7474 (mtpt) REVERT: R 238 ILE cc_start: 0.8271 (mt) cc_final: 0.8035 (mp) outliers start: 29 outliers final: 12 residues processed: 149 average time/residue: 1.5934 time to fit residues: 250.9141 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 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 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 19 LYS 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 216 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 179 GLN 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 = 0.158527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119427 restraints weight = 8948.036| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.85 r_work: 0.3046 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9395 Z= 0.297 Angle : 0.575 6.709 12723 Z= 0.305 Chirality : 0.044 0.216 1429 Planarity : 0.004 0.067 1596 Dihedral : 6.156 76.795 1413 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.71 % Allowed : 15.58 % 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 (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: 0.83 (0.26), residues: 1137 helix: 1.86 (0.26), residues: 392 sheet: 0.09 (0.30), residues: 293 loop : -0.20 (0.31), residues: 452 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 0.018 0.002 PHE R 277 TYR 0.033 0.002 TYR S 190 ARG 0.004 0.000 ARG B 219 *********************** 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 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.313 Fit side-chains REVERT: A 21 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7728 (mtm110) REVERT: A 46 LYS cc_start: 0.6871 (mttp) cc_final: 0.6126 (mttt) REVERT: A 208 ARG cc_start: 0.8301 (ttp-110) cc_final: 0.7852 (ttp80) REVERT: A 275 GLU cc_start: 0.7676 (pp20) cc_final: 0.7152 (pp20) REVERT: A 330 LYS cc_start: 0.7568 (mttt) cc_final: 0.6487 (mtpp) REVERT: B 268 ASN cc_start: 0.7756 (t0) cc_final: 0.7328 (p0) REVERT: G 52 THR cc_start: 0.7830 (m) cc_final: 0.7583 (p) REVERT: S 19 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8012 (tttt) REVERT: S 76 LYS cc_start: 0.7356 (pttt) cc_final: 0.6967 (mttp) REVERT: S 142 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8552 (mt0) REVERT: S 190 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.6481 (p90) REVERT: S 238 THR cc_start: 0.8821 (m) cc_final: 0.8549 (p) REVERT: R 150 LEU cc_start: 0.8418 (mp) cc_final: 0.8172 (mm) REVERT: R 164 LYS cc_start: 0.7192 (mppt) cc_final: 0.6704 (mtmm) REVERT: R 186 PHE cc_start: 0.7637 (m-80) cc_final: 0.6325 (t80) REVERT: R 225 LYS cc_start: 0.7716 (mttt) cc_final: 0.7465 (mtpt) REVERT: R 227 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7299 (mttp) outliers start: 27 outliers final: 13 residues processed: 144 average time/residue: 1.5676 time to fit residues: 238.0578 Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 19 LYS 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 216 ARG Chi-restraints excluded: chain R residue 227 LYS 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: 6.9990 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.160869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122118 restraints weight = 9040.853| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.92 r_work: 0.3079 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9395 Z= 0.197 Angle : 0.522 6.405 12723 Z= 0.279 Chirality : 0.042 0.194 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.824 68.363 1413 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.61 % Allowed : 15.58 % Favored : 81.81 % 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: 0.93 (0.26), residues: 1137 helix: 2.01 (0.26), residues: 392 sheet: 0.10 (0.30), residues: 294 loop : -0.18 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE R 277 TYR 0.031 0.001 TYR S 190 ARG 0.006 0.000 ARG B 219 *********************** 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 158 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 1.071 Fit side-chains REVERT: A 21 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7724 (mtm110) REVERT: A 46 LYS cc_start: 0.6838 (mttp) cc_final: 0.6341 (mtmt) REVERT: A 208 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7823 (ttp80) REVERT: A 275 GLU cc_start: 0.7668 (pp20) cc_final: 0.7188 (pp20) REVERT: A 305 CYS cc_start: 0.8061 (m) cc_final: 0.7662 (m) REVERT: A 330 LYS cc_start: 0.7588 (mttt) cc_final: 0.6561 (mtpp) REVERT: B 259 GLN cc_start: 0.8127 (mt0) cc_final: 0.7900 (mt0) REVERT: B 268 ASN cc_start: 0.7744 (t0) cc_final: 0.7312 (p0) REVERT: G 52 THR cc_start: 0.7798 (m) cc_final: 0.7597 (p) REVERT: S 19 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: S 76 LYS cc_start: 0.7405 (pttt) cc_final: 0.6951 (mttp) REVERT: S 190 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.6477 (p90) REVERT: S 238 THR cc_start: 0.8821 (m) cc_final: 0.8563 (p) REVERT: R 138 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7837 (mmtp) REVERT: R 150 LEU cc_start: 0.8409 (mp) cc_final: 0.8183 (mm) REVERT: R 164 LYS cc_start: 0.7169 (mppt) cc_final: 0.6692 (mtmm) REVERT: R 186 PHE cc_start: 0.7570 (m-80) cc_final: 0.6299 (t80) REVERT: R 225 LYS cc_start: 0.7677 (mttt) cc_final: 0.7430 (mtpt) REVERT: R 238 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7995 (mp) outliers start: 26 outliers final: 13 residues processed: 143 average time/residue: 1.4516 time to fit residues: 219.6762 Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 19 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.160125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121312 restraints weight = 9099.930| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.91 r_work: 0.3069 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9395 Z= 0.224 Angle : 0.538 6.512 12723 Z= 0.286 Chirality : 0.042 0.202 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.745 63.449 1413 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 15.38 % 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: 0.97 (0.26), residues: 1137 helix: 2.10 (0.26), residues: 386 sheet: 0.15 (0.30), residues: 295 loop : -0.19 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 277 TYR 0.031 0.002 TYR S 190 ARG 0.008 0.000 ARG S 202 *********************** 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 159 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.038 Fit side-chains REVERT: A 21 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7737 (mtm110) REVERT: A 46 LYS cc_start: 0.6840 (mttp) cc_final: 0.6324 (mtmt) REVERT: A 208 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7827 (ttp80) REVERT: A 275 GLU cc_start: 0.7676 (pp20) cc_final: 0.7190 (pp20) REVERT: A 305 CYS cc_start: 0.8007 (m) cc_final: 0.7656 (m) REVERT: A 330 LYS cc_start: 0.7619 (mttt) cc_final: 0.6675 (mtpp) REVERT: B 259 GLN cc_start: 0.8136 (mt0) cc_final: 0.7905 (mt0) REVERT: B 268 ASN cc_start: 0.7771 (t0) cc_final: 0.7331 (p0) REVERT: S 19 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8023 (tttt) REVERT: S 76 LYS cc_start: 0.7383 (pttt) cc_final: 0.6969 (mttp) REVERT: S 190 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.6499 (p90) REVERT: S 238 THR cc_start: 0.8828 (m) cc_final: 0.8572 (p) REVERT: R 150 LEU cc_start: 0.8424 (mp) cc_final: 0.8202 (mm) REVERT: R 164 LYS cc_start: 0.7195 (mppt) cc_final: 0.6703 (mtmm) REVERT: R 186 PHE cc_start: 0.7665 (m-80) cc_final: 0.6381 (t80) REVERT: R 225 LYS cc_start: 0.7690 (mttt) cc_final: 0.7437 (mtpt) REVERT: R 238 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8008 (mp) outliers start: 27 outliers final: 13 residues processed: 145 average time/residue: 1.4206 time to fit residues: 218.0709 Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 19 LYS 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: 0.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 chunk 107 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.161554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123219 restraints weight = 8978.420| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.82 r_work: 0.3096 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9395 Z= 0.180 Angle : 0.507 6.842 12723 Z= 0.272 Chirality : 0.042 0.187 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.562 59.745 1413 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 16.68 % 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: 1.09 (0.26), residues: 1137 helix: 2.23 (0.27), residues: 387 sheet: 0.21 (0.30), residues: 293 loop : -0.16 (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 0.011 0.001 PHE R 277 TYR 0.029 0.001 TYR S 190 ARG 0.008 0.000 ARG B 219 *********************** 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 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.068 Fit side-chains REVERT: A 21 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7688 (mtm110) REVERT: A 46 LYS cc_start: 0.6899 (mttp) cc_final: 0.6360 (mtmt) REVERT: A 208 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7797 (ttp80) REVERT: A 275 GLU cc_start: 0.7665 (pp20) cc_final: 0.7163 (pp20) REVERT: A 305 CYS cc_start: 0.7995 (m) cc_final: 0.7623 (m) REVERT: A 330 LYS cc_start: 0.7611 (mttt) cc_final: 0.6692 (mtpp) REVERT: B 42 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6802 (tpt170) REVERT: B 268 ASN cc_start: 0.7749 (t0) cc_final: 0.7341 (p0) REVERT: S 19 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8020 (tttt) REVERT: S 76 LYS cc_start: 0.7270 (pttt) cc_final: 0.6881 (mttp) REVERT: S 190 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6429 (p90) REVERT: S 202 ARG cc_start: 0.8195 (ptt-90) cc_final: 0.7919 (ptt-90) REVERT: S 238 THR cc_start: 0.8813 (m) cc_final: 0.8549 (p) REVERT: R 150 LEU cc_start: 0.8409 (mp) cc_final: 0.8189 (mm) REVERT: R 164 LYS cc_start: 0.7182 (mppt) cc_final: 0.6695 (mtmm) REVERT: R 186 PHE cc_start: 0.7686 (m-80) cc_final: 0.6406 (t80) REVERT: R 225 LYS cc_start: 0.7670 (mttt) cc_final: 0.7430 (mtpt) REVERT: R 238 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8001 (mp) outliers start: 20 outliers final: 12 residues processed: 146 average time/residue: 1.4570 time to fit residues: 226.1427 Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 117 LEU 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: 3.9990 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 259 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 = 0.3778 r_free = 0.3778 target = 0.159817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121275 restraints weight = 9092.838| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.86 r_work: 0.3069 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9395 Z= 0.239 Angle : 0.543 7.643 12723 Z= 0.290 Chirality : 0.043 0.204 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.633 59.004 1413 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.51 % Allowed : 17.49 % 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 (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: 1.01 (0.26), residues: 1137 helix: 2.12 (0.26), residues: 388 sheet: 0.15 (0.30), residues: 294 loop : -0.16 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 277 TYR 0.032 0.002 TYR S 190 ARG 0.007 0.000 ARG B 219 ********************** 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 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.023 Fit side-chains REVERT: A 21 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7694 (mtm110) REVERT: A 46 LYS cc_start: 0.6890 (mttp) cc_final: 0.6352 (mtmt) REVERT: A 208 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7816 (ttp80) REVERT: A 275 GLU cc_start: 0.7682 (pp20) cc_final: 0.7177 (pp20) REVERT: A 305 CYS cc_start: 0.7994 (m) cc_final: 0.7646 (m) REVERT: A 330 LYS cc_start: 0.7626 (mttt) cc_final: 0.6666 (mtpp) REVERT: B 42 ARG cc_start: 0.7145 (tpt170) cc_final: 0.6772 (tpt170) REVERT: B 268 ASN cc_start: 0.7797 (t0) cc_final: 0.7339 (p0) REVERT: S 19 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8017 (tttt) REVERT: S 76 LYS cc_start: 0.7367 (pttt) cc_final: 0.6954 (mttp) REVERT: S 190 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.6465 (p90) REVERT: S 238 THR cc_start: 0.8831 (m) cc_final: 0.8570 (p) REVERT: R 150 LEU cc_start: 0.8427 (mp) cc_final: 0.8199 (mm) REVERT: R 164 LYS cc_start: 0.7196 (mppt) cc_final: 0.6707 (mtmm) REVERT: R 186 PHE cc_start: 0.7745 (m-80) cc_final: 0.6445 (t80) REVERT: R 225 LYS cc_start: 0.7683 (mttt) cc_final: 0.7434 (mtpt) REVERT: R 238 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8015 (mp) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 2.2579 time to fit residues: 332.1007 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 VAL Chi-restraints excluded: chain S residue 19 LYS 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.161477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123195 restraints weight = 9010.758| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9395 Z= 0.187 Angle : 0.515 7.242 12723 Z= 0.276 Chirality : 0.042 0.188 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.448 59.097 1413 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 17.49 % Favored : 80.90 % 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: 2.24 (0.27), residues: 387 sheet: 0.15 (0.30), residues: 294 loop : -0.14 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE R 277 TYR 0.029 0.001 TYR S 190 ARG 0.008 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9599.28 seconds wall clock time: 169 minutes 52.61 seconds (10192.61 seconds total)