Starting phenix.real_space_refine on Thu Jul 2 16:19:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.cif" model { file = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na8_24268/07_2026/7na8_24268.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.074 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 63 5.16 5 C 5687 2.51 5 N 1502 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2285 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'1KD': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.04, per 1000 atoms: 0.23 Number of scatterers: 8888 At special positions: 0 Unit cell: (90.034, 122.248, 126.378, 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 63 16.00 O 1636 8.00 N 1502 7.00 C 5687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 458.3 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.945A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.658A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.003A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.530A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.861A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.503A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 4.068A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.570A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 4.196A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'R' and resid 42 through 71 removed outlier: 3.568A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.570A pdb=" N ARG R 75 " --> pdb=" O ARG R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 78 through 101 Proline residue: R 97 - end of helix removed outlier: 3.590A pdb=" N VAL R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 105 removed outlier: 3.645A pdb=" N GLN R 105 " --> pdb=" O ARG R 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 102 through 105' Processing helix chain 'R' and resid 114 through 147 removed outlier: 3.819A pdb=" N LEU R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU R 124 " --> pdb=" O GLN R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 155 Processing helix chain 'R' and resid 157 through 175 removed outlier: 4.010A pdb=" N LYS R 161 " --> pdb=" O LYS R 157 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 162 " --> pdb=" O GLY R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 192 through 196 removed outlier: 3.588A pdb=" N THR R 195 " --> pdb=" O PRO R 192 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN R 196 " --> pdb=" O TRP R 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 192 through 196' Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.698A pdb=" N VAL R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 243 removed outlier: 3.850A pdb=" N TRP R 215 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix removed outlier: 4.010A pdb=" N VAL R 230 " --> pdb=" O PHE R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 319 removed outlier: 4.122A pdb=" N ILE R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR R 303 " --> pdb=" O GLN R 299 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA R 316 " --> pdb=" O PHE R 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 324 removed outlier: 3.625A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN R 324 " --> pdb=" O PRO R 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 319 through 324' Processing helix chain 'R' and resid 327 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.071A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.561A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.561A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.505A 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: 6.227A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.535A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.653A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.973A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.698A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.241A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 140 through 141 removed outlier: 3.552A pdb=" N ALA N 211 " --> pdb=" O SER N 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 146 through 148 removed outlier: 6.305A pdb=" N VAL N 147 " --> pdb=" O GLU N 246 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY N 225 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU N 174 " --> pdb=" O TYR N 190 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR N 190 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP N 176 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 182 through 184 removed outlier: 3.623A pdb=" N ARG R 199 " --> pdb=" O GLY R 183 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1424 1.29 - 1.42: 2422 1.42 - 1.56: 5143 1.56 - 1.69: 1 1.69 - 1.82: 90 Bond restraints: 9080 Sorted by residual: bond pdb=" N PRO R 278 " pdb=" CD PRO R 278 " ideal model delta sigma weight residual 1.473 1.194 0.279 1.40e-02 5.10e+03 3.97e+02 bond pdb=" N PRO R 39 " pdb=" CD PRO R 39 " ideal model delta sigma weight residual 1.473 1.343 0.130 1.40e-02 5.10e+03 8.57e+01 bond pdb=" CA SER R 308 " pdb=" CB SER R 308 " ideal model delta sigma weight residual 1.529 1.418 0.111 1.64e-02 3.72e+03 4.55e+01 bond pdb=" CA ASN A 294 " pdb=" C ASN A 294 " ideal model delta sigma weight residual 1.527 1.602 -0.075 1.19e-02 7.06e+03 3.97e+01 bond pdb=" C PHE N 32 " pdb=" O PHE N 32 " ideal model delta sigma weight residual 1.236 1.163 0.073 1.21e-02 6.83e+03 3.64e+01 ... (remaining 9075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 12215 4.30 - 8.60: 74 8.60 - 12.89: 6 12.89 - 17.19: 1 17.19 - 21.49: 3 Bond angle restraints: 12299 Sorted by residual: angle pdb=" N THR A 295 " pdb=" CA THR A 295 " pdb=" C THR A 295 " ideal model delta sigma weight residual 110.14 96.39 13.75 1.55e+00 4.16e-01 7.87e+01 angle pdb=" C PHE R 279 " pdb=" CA PHE R 279 " pdb=" CB PHE R 279 " ideal model delta sigma weight residual 110.96 99.63 11.33 1.54e+00 4.22e-01 5.41e+01 angle pdb=" C22 1KD R 401 " pdb=" C23 1KD R 401 " pdb=" C26 1KD R 401 " ideal model delta sigma weight residual 109.58 131.07 -21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C LYS N 244 " pdb=" CA LYS N 244 " pdb=" CB LYS N 244 " ideal model delta sigma weight residual 109.75 98.13 11.62 1.65e+00 3.67e-01 4.96e+01 angle pdb=" C24 1KD R 401 " pdb=" C23 1KD R 401 " pdb=" C26 1KD R 401 " ideal model delta sigma weight residual 113.62 92.66 20.96 3.00e+00 1.11e-01 4.88e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 5082 23.74 - 47.47: 272 47.47 - 71.21: 28 71.21 - 94.94: 10 94.94 - 118.68: 1 Dihedral angle restraints: 5393 sinusoidal: 2140 harmonic: 3253 Sorted by residual: dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -162.31 76.31 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" C ASN R 305 " pdb=" N ASN R 305 " pdb=" CA ASN R 305 " pdb=" CB ASN R 305 " ideal model delta harmonic sigma weight residual -122.60 -143.14 20.54 0 2.50e+00 1.60e-01 6.75e+01 dihedral pdb=" C LYS N 244 " pdb=" N LYS N 244 " pdb=" CA LYS N 244 " pdb=" CB LYS N 244 " ideal model delta harmonic sigma weight residual -122.60 -104.95 -17.65 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1365 0.145 - 0.289: 17 0.289 - 0.434: 8 0.434 - 0.579: 0 0.579 - 0.724: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASN R 305 " pdb=" N ASN R 305 " pdb=" C ASN R 305 " pdb=" CB ASN R 305 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA PHE R 279 " pdb=" N PHE R 279 " pdb=" C PHE R 279 " pdb=" CB PHE R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU R 42 " pdb=" N LEU R 42 " pdb=" C LEU R 42 " pdb=" CB LEU R 42 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1388 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 112 " -0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C GLY R 112 " 0.091 2.00e-02 2.50e+03 pdb=" O GLY R 112 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP R 113 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 221 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ALA N 221 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA N 221 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU N 222 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 115 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C LEU R 115 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU R 115 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS R 116 " 0.020 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 186 2.67 - 3.23: 8373 3.23 - 3.78: 13811 3.78 - 4.34: 20368 4.34 - 4.90: 33297 Nonbonded interactions: 76035 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.212 3.040 nonbonded pdb=" O PHE R 286 " pdb=" OG SER R 287 " model vdw 2.252 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.266 3.040 ... (remaining 76030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.590 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.007 0.279 9083 Z= 0.422 Angle : 0.929 21.491 12305 Z= 0.560 Chirality : 0.060 0.724 1391 Planarity : 0.005 0.056 1538 Dihedral : 14.638 118.678 3282 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.31 % Allowed : 1.14 % Favored : 98.55 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.24), residues: 1102 helix: -0.42 (0.27), residues: 385 sheet: -0.53 (0.30), residues: 281 loop : -0.83 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 202 TYR 0.022 0.002 TYR R 284 PHE 0.023 0.002 PHE R 279 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.42 ( 9080) covalent geometry : angle 0.92642 / 0.56 (12299) SS BOND : bond 0.05065 / 2.53 ( 3) SS BOND : angle 3.30775 / 1.34 ( 6) hydrogen bonds : bond 0.16434 / 10.80 ( 426) hydrogen bonds : angle 6.72310 / 4.69 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.356 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.7181 time to fit residues: 99.1597 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain R residue 219 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085800 restraints weight = 14308.282| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.15 r_work: 0.3067 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9083 Z= 0.152 Angle : 0.584 6.353 12305 Z= 0.308 Chirality : 0.043 0.139 1391 Planarity : 0.004 0.048 1538 Dihedral : 7.642 111.449 1269 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.93 % Allowed : 9.74 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1102 helix: 0.61 (0.27), residues: 370 sheet: -0.42 (0.30), residues: 267 loop : -0.57 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.022 0.002 TYR R 284 PHE 0.026 0.001 PHE R 54 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9080) covalent geometry : angle 0.58323 / 0.31 (12299) SS BOND : bond 0.00165 / 0.08 ( 3) SS BOND : angle 1.18073 / 0.62 ( 6) hydrogen bonds : bond 0.04035 / 2.61 ( 426) hydrogen bonds : angle 4.99800 / 3.45 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.209 Fit side-chains REVERT: B 214 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7936 (mmt90) REVERT: N 160 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8039 (tmm160) REVERT: N 218 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7645 (mtm180) outliers start: 9 outliers final: 4 residues processed: 117 average time/residue: 0.5606 time to fit residues: 69.5073 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 294 ASN G 17 GLN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087452 restraints weight = 13846.472| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.92 r_work: 0.3084 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9083 Z= 0.117 Angle : 0.531 6.600 12305 Z= 0.279 Chirality : 0.042 0.137 1391 Planarity : 0.004 0.044 1538 Dihedral : 6.867 110.978 1267 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.66 % Allowed : 12.02 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1102 helix: 1.01 (0.27), residues: 369 sheet: -0.32 (0.31), residues: 263 loop : -0.57 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.014 0.001 TYR R 313 PHE 0.010 0.001 PHE R 309 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9080) covalent geometry : angle 0.53102 / 0.28 (12299) SS BOND : bond 0.00159 / 0.08 ( 3) SS BOND : angle 0.88886 / 0.47 ( 6) hydrogen bonds : bond 0.03593 / 2.30 ( 426) hydrogen bonds : angle 4.67903 / 3.21 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.339 Fit side-chains REVERT: A 313 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8238 (ptp-110) REVERT: A 318 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: A 341 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8408 (t0) REVERT: B 214 ARG cc_start: 0.8301 (mmt180) cc_final: 0.8030 (mmt90) REVERT: N 160 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.8024 (tmm160) REVERT: N 218 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7657 (mtm180) outliers start: 16 outliers final: 6 residues processed: 116 average time/residue: 0.6289 time to fit residues: 77.4400 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 85 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 294 ASN N 183 GLN R 110 ASN R 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089048 restraints weight = 14271.532| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.04 r_work: 0.3093 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9083 Z= 0.108 Angle : 0.521 8.083 12305 Z= 0.272 Chirality : 0.041 0.144 1391 Planarity : 0.003 0.039 1538 Dihedral : 6.556 110.605 1267 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 14.30 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1102 helix: 1.31 (0.28), residues: 370 sheet: -0.25 (0.31), residues: 263 loop : -0.55 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.024 0.001 TYR R 284 PHE 0.024 0.001 PHE R 54 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9080) covalent geometry : angle 0.52128 / 0.27 (12299) SS BOND : bond 0.00157 / 0.08 ( 3) SS BOND : angle 0.82836 / 0.43 ( 6) hydrogen bonds : bond 0.03347 / 2.14 ( 426) hydrogen bonds : angle 4.47407 / 3.06 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.348 Fit side-chains REVERT: A 21 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7759 (ttm-80) REVERT: A 271 LYS cc_start: 0.6947 (tmtt) cc_final: 0.6573 (ttpt) REVERT: A 313 ARG cc_start: 0.8470 (ptp-170) cc_final: 0.8165 (ptp-110) REVERT: A 341 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8422 (t0) REVERT: B 214 ARG cc_start: 0.8288 (mmt180) cc_final: 0.7979 (mmt90) REVERT: N 93 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8705 (ttp) REVERT: N 160 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7770 (mtm110) REVERT: R 87 PHE cc_start: 0.8050 (t80) cc_final: 0.7766 (t80) outliers start: 13 outliers final: 5 residues processed: 121 average time/residue: 0.6747 time to fit residues: 86.4861 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087764 restraints weight = 13874.471| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.08 r_work: 0.3084 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9083 Z= 0.114 Angle : 0.517 7.114 12305 Z= 0.270 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.037 1538 Dihedral : 6.538 110.569 1267 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 15.44 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1102 helix: 1.48 (0.27), residues: 370 sheet: -0.24 (0.31), residues: 265 loop : -0.48 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.021 0.001 TYR A 296 PHE 0.012 0.001 PHE R 309 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9080) covalent geometry : angle 0.51717 / 0.27 (12299) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 0.87697 / 0.47 ( 6) hydrogen bonds : bond 0.03315 / 2.11 ( 426) hydrogen bonds : angle 4.40937 / 3.01 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.367 Fit side-chains REVERT: A 21 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7765 (ttm-80) REVERT: A 271 LYS cc_start: 0.6980 (tmtt) cc_final: 0.6638 (ttpt) REVERT: A 313 ARG cc_start: 0.8458 (ptp-170) cc_final: 0.8141 (ptp-110) REVERT: A 341 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8454 (t0) REVERT: B 214 ARG cc_start: 0.8305 (mmt180) cc_final: 0.8060 (mmt90) REVERT: N 93 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8710 (ttp) REVERT: N 144 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7260 (t) REVERT: N 160 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7795 (mtm110) REVERT: R 87 PHE cc_start: 0.8072 (t80) cc_final: 0.7775 (t80) outliers start: 17 outliers final: 8 residues processed: 114 average time/residue: 0.6599 time to fit residues: 79.8783 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087091 restraints weight = 13975.340| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.93 r_work: 0.3080 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9083 Z= 0.136 Angle : 0.539 8.742 12305 Z= 0.280 Chirality : 0.042 0.135 1391 Planarity : 0.003 0.034 1538 Dihedral : 6.669 110.714 1267 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.87 % Allowed : 15.65 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1102 helix: 1.49 (0.27), residues: 370 sheet: -0.25 (0.31), residues: 265 loop : -0.47 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 202 TYR 0.024 0.001 TYR A 296 PHE 0.025 0.001 PHE R 54 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9080) covalent geometry : angle 0.53914 / 0.28 (12299) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 0.85779 / 0.45 ( 6) hydrogen bonds : bond 0.03403 / 2.17 ( 426) hydrogen bonds : angle 4.45153 / 3.04 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.368 Fit side-chains REVERT: A 21 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7780 (ttm-80) REVERT: A 271 LYS cc_start: 0.7032 (tmtt) cc_final: 0.6700 (ttpt) REVERT: A 341 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8419 (t0) REVERT: N 93 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8738 (ttp) REVERT: N 144 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7281 (t) REVERT: N 160 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7718 (mtm110) REVERT: R 87 PHE cc_start: 0.8079 (t80) cc_final: 0.7752 (t80) outliers start: 18 outliers final: 8 residues processed: 114 average time/residue: 0.7024 time to fit residues: 84.7689 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.0030 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS N 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087724 restraints weight = 13942.116| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.08 r_work: 0.3081 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9083 Z= 0.111 Angle : 0.518 7.926 12305 Z= 0.268 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.034 1538 Dihedral : 6.454 110.835 1267 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 16.79 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1102 helix: 1.61 (0.27), residues: 370 sheet: -0.30 (0.31), residues: 267 loop : -0.40 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.025 0.001 TYR R 284 PHE 0.013 0.001 PHE R 309 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9080) covalent geometry : angle 0.51787 / 0.27 (12299) SS BOND : bond 0.00183 / 0.09 ( 3) SS BOND : angle 0.68686 / 0.32 ( 6) hydrogen bonds : bond 0.03246 / 2.07 ( 426) hydrogen bonds : angle 4.35711 / 2.98 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.391 Fit side-chains REVERT: A 271 LYS cc_start: 0.6833 (tmtt) cc_final: 0.6541 (ttpt) REVERT: A 341 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8448 (t0) REVERT: B 214 ARG cc_start: 0.8421 (mmt180) cc_final: 0.8113 (mmt90) REVERT: N 93 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8719 (ttp) REVERT: N 144 THR cc_start: 0.7517 (m) cc_final: 0.7214 (t) REVERT: N 160 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.7788 (mtm110) REVERT: R 87 PHE cc_start: 0.8073 (t80) cc_final: 0.7785 (t80) outliers start: 15 outliers final: 8 residues processed: 116 average time/residue: 0.6823 time to fit residues: 83.9155 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS N 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087889 restraints weight = 14119.838| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.03 r_work: 0.3075 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9083 Z= 0.127 Angle : 0.543 7.683 12305 Z= 0.282 Chirality : 0.041 0.135 1391 Planarity : 0.003 0.033 1538 Dihedral : 6.548 111.022 1267 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.66 % Allowed : 17.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1102 helix: 1.62 (0.27), residues: 370 sheet: -0.21 (0.31), residues: 265 loop : -0.41 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.024 0.001 TYR A 296 PHE 0.022 0.001 PHE R 54 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9080) covalent geometry : angle 0.54336 / 0.28 (12299) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 0.77187 / 0.38 ( 6) hydrogen bonds : bond 0.03304 / 2.10 ( 426) hydrogen bonds : angle 4.37161 / 2.99 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.367 Fit side-chains REVERT: A 271 LYS cc_start: 0.6884 (tmtt) cc_final: 0.6465 (ttpt) REVERT: A 273 LEU cc_start: 0.7501 (tp) cc_final: 0.7284 (tp) REVERT: A 341 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8419 (t0) REVERT: B 214 ARG cc_start: 0.8426 (mmt180) cc_final: 0.8109 (mpt180) REVERT: N 93 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8717 (ttp) REVERT: N 144 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7204 (t) REVERT: N 160 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7742 (mtm110) REVERT: R 87 PHE cc_start: 0.8068 (t80) cc_final: 0.7789 (t80) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 0.6952 time to fit residues: 83.8215 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087375 restraints weight = 13767.034| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.07 r_work: 0.3075 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9083 Z= 0.122 Angle : 0.543 8.023 12305 Z= 0.280 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.038 1538 Dihedral : 6.513 111.316 1267 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 18.03 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.25), residues: 1102 helix: 1.73 (0.28), residues: 363 sheet: -0.22 (0.31), residues: 265 loop : -0.39 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.025 0.001 TYR A 296 PHE 0.013 0.001 PHE R 309 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9080) covalent geometry : angle 0.54249 / 0.28 (12299) SS BOND : bond 0.00151 / 0.07 ( 3) SS BOND : angle 0.66225 / 0.29 ( 6) hydrogen bonds : bond 0.03261 / 2.07 ( 426) hydrogen bonds : angle 4.34418 / 2.97 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.261 Fit side-chains REVERT: A 271 LYS cc_start: 0.6669 (tmtt) cc_final: 0.6457 (ttpt) REVERT: A 273 LEU cc_start: 0.7519 (tp) cc_final: 0.7269 (tp) REVERT: A 341 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 214 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8075 (mpt180) REVERT: G 46 LYS cc_start: 0.8563 (mmpt) cc_final: 0.7778 (mppt) REVERT: N 93 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8699 (ttp) REVERT: N 144 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7171 (t) REVERT: N 160 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7733 (mtm110) REVERT: R 87 PHE cc_start: 0.8064 (t80) cc_final: 0.7773 (t80) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.5844 time to fit residues: 67.5197 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.112985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084818 restraints weight = 13887.739| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.98 r_work: 0.3033 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9083 Z= 0.190 Angle : 0.609 8.616 12305 Z= 0.314 Chirality : 0.044 0.136 1391 Planarity : 0.004 0.037 1538 Dihedral : 7.030 111.656 1267 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.45 % Allowed : 18.45 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1102 helix: 1.41 (0.27), residues: 371 sheet: -0.24 (0.32), residues: 265 loop : -0.44 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.034 0.002 TYR A 296 PHE 0.015 0.001 PHE R 54 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 9080) covalent geometry : angle 0.60927 / 0.31 (12299) SS BOND : bond 0.00128 / 0.06 ( 3) SS BOND : angle 0.81542 / 0.40 ( 6) hydrogen bonds : bond 0.03645 / 2.31 ( 426) hydrogen bonds : angle 4.56577 / 3.13 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.409 Fit side-chains REVERT: A 271 LYS cc_start: 0.6849 (tmtt) cc_final: 0.6639 (ttpt) REVERT: A 341 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (t0) REVERT: B 130 GLN cc_start: 0.8085 (mp10) cc_final: 0.7661 (mp10) REVERT: B 214 ARG cc_start: 0.8434 (mmt180) cc_final: 0.8115 (mpt180) REVERT: N 147 VAL cc_start: 0.6934 (m) cc_final: 0.6715 (p) REVERT: N 160 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7760 (mtm110) REVERT: R 319 ASN cc_start: 0.8216 (m-40) cc_final: 0.7878 (m-40) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.6846 time to fit residues: 76.8276 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS G 17 GLN ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087386 restraints weight = 13649.135| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.07 r_work: 0.3075 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9083 Z= 0.118 Angle : 0.550 8.449 12305 Z= 0.283 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.038 1538 Dihedral : 6.580 112.205 1267 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 18.24 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1102 helix: 1.53 (0.28), residues: 371 sheet: -0.28 (0.32), residues: 265 loop : -0.43 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.024 0.001 TYR A 296 PHE 0.013 0.001 PHE R 309 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9080) covalent geometry : angle 0.55005 / 0.28 (12299) SS BOND : bond 0.00165 / 0.08 ( 3) SS BOND : angle 0.59301 / 0.22 ( 6) hydrogen bonds : bond 0.03235 / 2.05 ( 426) hydrogen bonds : angle 4.37938 / 3.00 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.00 seconds wall clock time: 62 minutes 8.95 seconds (3728.95 seconds total)