Starting phenix.real_space_refine on Tue Mar 3 23:29:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7na8_24268/03_2026/7na8_24268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na8_24268/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2026/7na8_24268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2026/7na8_24268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2026/7na8_24268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na8_24268/03_2026/7na8_24268.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-5986/lib/python3.9/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: 2.51, per 1000 atoms: 0.28 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: 0.59 Conformation dependent library (CDL) restraints added in 341.0 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: 0.31 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: 1.43 Time building geometry restraints manager: 0.87 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: 5132 23.74 - 47.47: 279 47.47 - 71.21: 33 71.21 - 94.94: 10 94.94 - 118.68: 3 Dihedral angle restraints: 5457 sinusoidal: 2204 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 5454 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: 0.010 Normalize map: mean=0, sd=1: 2.860 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.090 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 15.005 118.678 3346 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 covalent geometry : bond 0.00680 ( 9080) covalent geometry : angle 0.92642 (12299) SS BOND : bond 0.05065 ( 3) SS BOND : angle 3.30775 ( 6) hydrogen bonds : bond 0.16434 ( 426) hydrogen bonds : angle 6.72310 ( 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 : 0.310 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.7652 time to fit residues: 105.4497 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 : 0.344 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085915 restraints weight = 14294.497| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.15 r_work: 0.3065 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1228 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= 0.154 Angle : 0.587 6.324 12305 Z= 0.308 Chirality : 0.043 0.139 1391 Planarity : 0.004 0.048 1538 Dihedral : 7.220 75.097 1333 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.04 % Allowed : 9.64 % 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: -0.28 (0.25), residues: 1102 helix: 0.62 (0.27), residues: 370 sheet: -0.42 (0.30), residues: 267 loop : -0.56 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.021 0.001 TYR R 284 PHE 0.026 0.001 PHE R 54 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9080) covalent geometry : angle 0.58659 (12299) SS BOND : bond 0.00222 ( 3) SS BOND : angle 1.16832 ( 6) hydrogen bonds : bond 0.03969 ( 426) hydrogen bonds : angle 4.96828 ( 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 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.363 Fit side-chains REVERT: B 214 ARG cc_start: 0.8273 (mmt180) cc_final: 0.7937 (mmt90) REVERT: N 160 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8040 (tmm160) REVERT: N 218 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7658 (mtm180) outliers start: 10 outliers final: 4 residues processed: 117 average time/residue: 0.6778 time to fit residues: 83.7888 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS G 17 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 = 0.3597 r_free = 0.3597 target = 0.114119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086665 restraints weight = 13852.272| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.92 r_work: 0.3072 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9083 Z= 0.133 Angle : 0.539 6.661 12305 Z= 0.284 Chirality : 0.042 0.137 1391 Planarity : 0.004 0.044 1538 Dihedral : 6.458 71.462 1331 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.66 % Allowed : 11.81 % Favored : 86.53 % 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: -0.06 (0.25), residues: 1102 helix: 0.99 (0.27), residues: 370 sheet: -0.33 (0.31), residues: 263 loop : -0.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 13 TYR 0.014 0.001 TYR R 313 PHE 0.011 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 covalent geometry : bond 0.00302 ( 9080) covalent geometry : angle 0.53892 (12299) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.99568 ( 6) hydrogen bonds : bond 0.03659 ( 426) hydrogen bonds : angle 4.69721 ( 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 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.355 Fit side-chains REVERT: A 313 ARG cc_start: 0.8483 (ptp-170) cc_final: 0.8205 (ptp-110) REVERT: A 318 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 214 ARG cc_start: 0.8305 (mmt180) cc_final: 0.8012 (mmt90) REVERT: B 215 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8289 (mt-10) REVERT: N 160 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8036 (tmm160) REVERT: R 87 PHE cc_start: 0.8004 (t80) cc_final: 0.7719 (t80) outliers start: 16 outliers final: 6 residues processed: 115 average time/residue: 0.6413 time to fit residues: 78.1271 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER 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: 1.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS R 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086539 restraints weight = 14006.687| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3066 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9083 Z= 0.133 Angle : 0.540 7.883 12305 Z= 0.283 Chirality : 0.042 0.144 1391 Planarity : 0.003 0.039 1538 Dihedral : 6.314 71.275 1331 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.35 % Allowed : 14.92 % Favored : 83.73 % 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: 0.09 (0.25), residues: 1102 helix: 1.20 (0.27), residues: 370 sheet: -0.27 (0.31), residues: 263 loop : -0.57 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.023 0.001 TYR R 284 PHE 0.023 0.001 PHE R 54 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9080) covalent geometry : angle 0.53968 (12299) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.91436 ( 6) hydrogen bonds : bond 0.03518 ( 426) hydrogen bonds : angle 4.59394 ( 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 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.362 Fit side-chains REVERT: A 271 LYS cc_start: 0.7123 (tmtt) cc_final: 0.6715 (ttpt) REVERT: A 313 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8152 (ptp-110) REVERT: A 318 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: A 341 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8677 (t0) REVERT: B 214 ARG cc_start: 0.8317 (mmt180) cc_final: 0.8052 (mmt90) REVERT: N 160 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.8036 (tmm160) REVERT: R 87 PHE cc_start: 0.8033 (t80) cc_final: 0.7692 (t80) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.6553 time to fit residues: 78.3593 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 85 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3619 r_free = 0.3619 target = 0.115771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087672 restraints weight = 13870.390| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.08 r_work: 0.3081 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9083 Z= 0.110 Angle : 0.525 9.180 12305 Z= 0.271 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.036 1538 Dihedral : 6.013 69.186 1331 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 15.34 % Favored : 83.11 % 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: 0.27 (0.25), residues: 1102 helix: 1.42 (0.27), residues: 370 sheet: -0.28 (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 B 197 TYR 0.023 0.001 TYR A 296 PHE 0.012 0.001 PHE R 309 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9080) covalent geometry : angle 0.52542 (12299) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.62897 ( 6) hydrogen bonds : bond 0.03317 ( 426) hydrogen bonds : angle 4.44141 ( 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 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.276 Fit side-chains REVERT: A 21 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7736 (ttm-80) REVERT: A 271 LYS cc_start: 0.6894 (tmtt) cc_final: 0.6576 (ttpt) REVERT: A 313 ARG cc_start: 0.8400 (ptp-170) cc_final: 0.8076 (ptp-110) REVERT: G 24 ASN cc_start: 0.7735 (p0) cc_final: 0.7532 (p0) REVERT: N 76 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7852 (pttm) REVERT: N 160 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7754 (mtm110) REVERT: N 244 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7763 (ttpp) REVERT: R 87 PHE cc_start: 0.8027 (t80) cc_final: 0.7744 (t80) outliers start: 15 outliers final: 6 residues processed: 114 average time/residue: 0.6879 time to fit residues: 82.5091 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain N residue 244 LYS 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: 2.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS N 183 GLN R 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087668 restraints weight = 13916.787| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.99 r_work: 0.3086 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9083 Z= 0.120 Angle : 0.537 8.703 12305 Z= 0.277 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.034 1538 Dihedral : 5.967 69.528 1331 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.76 % Allowed : 15.54 % Favored : 82.69 % 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 (0.25), residues: 1102 helix: 1.53 (0.27), residues: 370 sheet: -0.24 (0.32), residues: 265 loop : -0.45 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.022 0.001 TYR A 296 PHE 0.021 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 covalent geometry : bond 0.00272 ( 9080) covalent geometry : angle 0.53657 (12299) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.73166 ( 6) hydrogen bonds : bond 0.03319 ( 426) hydrogen bonds : angle 4.40734 ( 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 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.288 Fit side-chains REVERT: A 21 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7730 (ttm-80) REVERT: A 271 LYS cc_start: 0.6824 (tmtt) cc_final: 0.6515 (ttpt) REVERT: A 313 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8020 (ptp-110) REVERT: N 93 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8718 (ttp) REVERT: N 144 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7224 (t) REVERT: N 160 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7741 (mtm110) REVERT: R 87 PHE cc_start: 0.8012 (t80) cc_final: 0.7716 (t80) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 0.7423 time to fit residues: 87.5841 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 : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 38 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3623 r_free = 0.3623 target = 0.116117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087926 restraints weight = 13895.705| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.08 r_work: 0.3085 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9083 Z= 0.110 Angle : 0.522 7.939 12305 Z= 0.269 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.037 1538 Dihedral : 5.809 68.384 1331 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.76 % Allowed : 16.48 % Favored : 81.76 % 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: 0.42 (0.25), residues: 1102 helix: 1.64 (0.27), residues: 370 sheet: -0.23 (0.31), residues: 265 loop : -0.43 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 covalent geometry : bond 0.00248 ( 9080) covalent geometry : angle 0.52220 (12299) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.59515 ( 6) hydrogen bonds : bond 0.03243 ( 426) hydrogen bonds : angle 4.34280 ( 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: 17 poor density : 103 time to evaluate : 0.348 Fit side-chains REVERT: A 21 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7741 (ttm-80) REVERT: A 271 LYS cc_start: 0.6783 (tmtt) cc_final: 0.6497 (ttpt) REVERT: B 217 MET cc_start: 0.7437 (ppp) cc_final: 0.7216 (ppp) REVERT: G 46 LYS cc_start: 0.8541 (mmpt) cc_final: 0.7773 (mppt) REVERT: N 144 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7179 (t) REVERT: N 160 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7758 (mtm110) REVERT: R 87 PHE cc_start: 0.8033 (t80) cc_final: 0.7755 (t80) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.6805 time to fit residues: 81.3315 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 : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 61 MET 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 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 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: 0.9980 chunk 21 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3625 r_free = 0.3625 target = 0.116211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088176 restraints weight = 13836.661| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.07 r_work: 0.3087 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9083 Z= 0.112 Angle : 0.531 7.755 12305 Z= 0.274 Chirality : 0.041 0.135 1391 Planarity : 0.003 0.035 1538 Dihedral : 5.745 68.191 1331 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 17.31 % Favored : 81.35 % 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: 0.45 (0.25), residues: 1102 helix: 1.68 (0.27), residues: 370 sheet: -0.21 (0.31), residues: 265 loop : -0.44 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 13 TYR 0.021 0.001 TYR A 296 PHE 0.016 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 covalent geometry : bond 0.00254 ( 9080) covalent geometry : angle 0.53127 (12299) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.63442 ( 6) hydrogen bonds : bond 0.03207 ( 426) hydrogen bonds : angle 4.31180 ( 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 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.403 Fit side-chains REVERT: A 21 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7773 (ttm-80) REVERT: A 271 LYS cc_start: 0.6808 (tmtt) cc_final: 0.6434 (ttpt) REVERT: A 273 LEU cc_start: 0.7509 (tp) cc_final: 0.7300 (tp) REVERT: G 46 LYS cc_start: 0.8543 (mmpt) cc_final: 0.7796 (mppt) REVERT: N 93 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8704 (ttp) REVERT: N 144 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7185 (t) REVERT: N 160 ARG cc_start: 0.8295 (ttp-110) cc_final: 0.7783 (mtm110) REVERT: R 87 PHE cc_start: 0.8052 (t80) cc_final: 0.7742 (t80) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.6838 time to fit residues: 82.4759 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 61 MET 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 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 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: 1.9990 chunk 104 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3590 r_free = 0.3590 target = 0.113628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085533 restraints weight = 13783.016| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.98 r_work: 0.3048 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9083 Z= 0.168 Angle : 0.579 8.006 12305 Z= 0.298 Chirality : 0.043 0.135 1391 Planarity : 0.003 0.036 1538 Dihedral : 6.227 70.583 1331 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.76 % Allowed : 18.03 % Favored : 80.21 % 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: 0.37 (0.25), residues: 1102 helix: 1.54 (0.27), residues: 370 sheet: -0.22 (0.32), residues: 265 loop : -0.44 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.030 0.002 TYR A 296 PHE 0.013 0.001 PHE R 309 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9080) covalent geometry : angle 0.57909 (12299) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.93734 ( 6) hydrogen bonds : bond 0.03554 ( 426) hydrogen bonds : angle 4.50327 ( 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 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.368 Fit side-chains REVERT: A 21 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7761 (ttm-80) REVERT: A 271 LYS cc_start: 0.6854 (tmtt) cc_final: 0.6650 (ttpt) REVERT: B 130 GLN cc_start: 0.8109 (mp10) cc_final: 0.7698 (mp10) REVERT: G 13 ARG cc_start: 0.6784 (mtm180) cc_final: 0.6575 (mtm-85) REVERT: N 93 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8729 (ttp) REVERT: N 144 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7236 (t) REVERT: N 147 VAL cc_start: 0.6946 (m) cc_final: 0.6713 (p) REVERT: N 160 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7788 (mtm110) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.6820 time to fit residues: 81.4390 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 29 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085326 restraints weight = 13851.342| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.98 r_work: 0.3046 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9083 Z= 0.177 Angle : 0.600 8.548 12305 Z= 0.308 Chirality : 0.043 0.136 1391 Planarity : 0.004 0.036 1538 Dihedral : 6.301 69.274 1331 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.35 % Allowed : 18.55 % 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: 0.33 (0.25), residues: 1102 helix: 1.50 (0.28), residues: 367 sheet: -0.21 (0.32), residues: 264 loop : -0.47 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.031 0.002 TYR A 296 PHE 0.016 0.001 PHE R 54 TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9080) covalent geometry : angle 0.59968 (12299) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.85284 ( 6) hydrogen bonds : bond 0.03566 ( 426) hydrogen bonds : angle 4.53938 ( 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 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.273 Fit side-chains REVERT: A 271 LYS cc_start: 0.6909 (tmtt) cc_final: 0.6670 (ttpt) REVERT: B 130 GLN cc_start: 0.8070 (mp10) cc_final: 0.7685 (mp10) REVERT: G 24 ASN cc_start: 0.7872 (p0) cc_final: 0.7566 (p0) REVERT: N 93 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8734 (ttp) REVERT: N 147 VAL cc_start: 0.6982 (m) cc_final: 0.6758 (p) REVERT: N 160 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7789 (mtm110) REVERT: R 319 ASN cc_start: 0.8223 (m-40) cc_final: 0.7889 (m-40) outliers start: 13 outliers final: 12 residues processed: 108 average time/residue: 0.7033 time to fit residues: 80.2236 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 29 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 50 CYS 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: 0.9980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087128 restraints weight = 13606.712| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.91 r_work: 0.3081 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9083 Z= 0.134 Angle : 0.566 9.509 12305 Z= 0.291 Chirality : 0.042 0.136 1391 Planarity : 0.003 0.036 1538 Dihedral : 6.060 66.548 1331 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.35 % Allowed : 18.45 % Favored : 80.21 % 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: 0.37 (0.25), residues: 1102 helix: 1.59 (0.28), residues: 367 sheet: -0.24 (0.32), residues: 264 loop : -0.46 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.027 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 covalent geometry : bond 0.00311 ( 9080) covalent geometry : angle 0.56555 (12299) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.67624 ( 6) hydrogen bonds : bond 0.03343 ( 426) hydrogen bonds : angle 4.43432 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.06 seconds wall clock time: 59 minutes 6.41 seconds (3546.41 seconds total)