Starting phenix.real_space_refine on Wed Apr 30 06:33:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7na8_24268/04_2025/7na8_24268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na8_24268/04_2025/7na8_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_24268/04_2025/7na8_24268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na8_24268/04_2025/7na8_24268.map" model { file = "/net/cci-nas-00/data/ceres_data/7na8_24268/04_2025/7na8_24268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na8_24268/04_2025/7na8_24268.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.30, per 1000 atoms: 0.71 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.82 Time building geometry restraints manager: 2.99 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: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- 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 : 7.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (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 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 280 PHE 0.023 0.002 PHE R 279 TYR 0.022 0.002 TYR R 284 ARG 0.005 0.000 ARG N 202 Details of bonding type rmsd hydrogen bonds : bond 0.16434 ( 426) hydrogen bonds : angle 6.72310 ( 1206) SS BOND : bond 0.05065 ( 3) SS BOND : angle 3.30775 ( 6) covalent geometry : bond 0.00680 ( 9080) covalent geometry : angle 0.92642 (12299) *********************** 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 : 1.043 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 1.5231 time to fit residues: 210.6434 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.114849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086324 restraints weight = 14098.977| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.13 r_work: 0.3075 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9083 Z= 0.140 Angle : 0.587 6.464 12305 Z= 0.307 Chirality : 0.043 0.139 1391 Planarity : 0.004 0.048 1538 Dihedral : 7.174 75.011 1331 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.04 % Allowed : 9.33 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1102 helix: 0.64 (0.27), residues: 370 sheet: -0.42 (0.30), residues: 268 loop : -0.56 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.026 0.001 PHE R 54 TYR 0.020 0.001 TYR R 284 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 426) hydrogen bonds : angle 4.97562 ( 1206) SS BOND : bond 0.00160 ( 3) SS BOND : angle 1.07381 ( 6) covalent geometry : bond 0.00316 ( 9080) covalent geometry : angle 0.58675 (12299) *********************** 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 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.054 Fit side-chains REVERT: B 214 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7936 (mmt90) REVERT: N 160 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8039 (tmm160) REVERT: N 218 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7644 (mtm180) outliers start: 10 outliers final: 4 residues processed: 119 average time/residue: 1.4225 time to fit residues: 179.5917 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 42 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 105 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 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 = 0.3594 r_free = 0.3594 target = 0.113944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086409 restraints weight = 14021.264| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.93 r_work: 0.3066 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9083 Z= 0.138 Angle : 0.545 6.670 12305 Z= 0.287 Chirality : 0.042 0.137 1391 Planarity : 0.004 0.044 1538 Dihedral : 6.503 72.102 1331 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.76 % Allowed : 12.02 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1102 helix: 0.96 (0.27), residues: 370 sheet: -0.36 (0.31), residues: 263 loop : -0.60 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 PHE 0.011 0.001 PHE R 309 TYR 0.013 0.001 TYR R 313 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 426) hydrogen bonds : angle 4.72632 ( 1206) SS BOND : bond 0.00149 ( 3) SS BOND : angle 1.02181 ( 6) covalent geometry : bond 0.00315 ( 9080) covalent geometry : angle 0.54486 (12299) *********************** 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: 17 poor density : 109 time to evaluate : 0.802 Fit side-chains REVERT: A 313 ARG cc_start: 0.8484 (ptp-170) cc_final: 0.8198 (ptp-110) REVERT: A 318 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: B 214 ARG cc_start: 0.8307 (mmt180) cc_final: 0.8003 (mmt90) REVERT: N 160 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.8041 (tmm160) REVERT: R 303 TYR cc_start: 0.6306 (m-80) cc_final: 0.6105 (m-80) outliers start: 17 outliers final: 6 residues processed: 116 average time/residue: 1.6844 time to fit residues: 207.6631 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 N 183 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 = 0.3607 r_free = 0.3607 target = 0.114908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.087274 restraints weight = 13857.661| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.98 r_work: 0.3080 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9083 Z= 0.121 Angle : 0.533 7.991 12305 Z= 0.279 Chirality : 0.041 0.149 1391 Planarity : 0.003 0.039 1538 Dihedral : 6.248 69.623 1331 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.35 % Allowed : 14.51 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1102 helix: 1.22 (0.27), residues: 370 sheet: -0.31 (0.31), residues: 263 loop : -0.55 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 PHE 0.022 0.001 PHE R 54 TYR 0.023 0.001 TYR R 284 ARG 0.001 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 426) hydrogen bonds : angle 4.55955 ( 1206) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.82698 ( 6) covalent geometry : bond 0.00272 ( 9080) covalent geometry : angle 0.53269 (12299) *********************** 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 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.363 Fit side-chains REVERT: A 271 LYS cc_start: 0.7088 (tmtt) cc_final: 0.6678 (ttpt) REVERT: A 313 ARG cc_start: 0.8457 (ptp-170) cc_final: 0.8141 (ptp-110) REVERT: A 318 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: A 341 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8417 (t0) REVERT: B 214 ARG cc_start: 0.8312 (mmt180) cc_final: 0.8044 (mmt90) REVERT: N 93 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (ttp) REVERT: N 160 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8039 (tmm160) REVERT: N 201 GLU cc_start: 0.8033 (tp30) cc_final: 0.7829 (tp30) REVERT: R 87 PHE cc_start: 0.8095 (t80) cc_final: 0.7761 (t80) outliers start: 13 outliers final: 6 residues processed: 115 average time/residue: 1.5441 time to fit residues: 188.2449 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.113592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085670 restraints weight = 13753.225| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.97 r_work: 0.3051 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9083 Z= 0.158 Angle : 0.556 7.295 12305 Z= 0.290 Chirality : 0.043 0.136 1391 Planarity : 0.004 0.037 1538 Dihedral : 6.405 71.550 1331 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.97 % Allowed : 14.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1102 helix: 1.25 (0.27), residues: 371 sheet: -0.29 (0.31), residues: 263 loop : -0.52 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.026 0.001 TYR A 296 ARG 0.001 0.000 ARG R 283 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 426) hydrogen bonds : angle 4.60200 ( 1206) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.91532 ( 6) covalent geometry : bond 0.00365 ( 9080) covalent geometry : angle 0.55626 (12299) *********************** 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 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.077 Fit side-chains REVERT: A 271 LYS cc_start: 0.7136 (tmtt) cc_final: 0.6724 (ttpt) REVERT: A 318 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: A 341 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8415 (t0) REVERT: B 214 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8054 (mmt90) REVERT: N 160 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7963 (tmm160) REVERT: N 201 GLU cc_start: 0.7991 (tp30) cc_final: 0.7790 (tp30) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 1.3875 time to fit residues: 166.6671 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 189 SER Chi-restraints excluded: chain N residue 76 LYS 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 65 MET Chi-restraints excluded: chain R residue 114 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086899 restraints weight = 13844.778| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.97 r_work: 0.3073 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1783 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= 0.127 Angle : 0.543 8.788 12305 Z= 0.281 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.035 1538 Dihedral : 6.136 69.009 1331 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.66 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1102 helix: 1.41 (0.27), residues: 370 sheet: -0.31 (0.31), residues: 265 loop : -0.48 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.022 0.001 PHE R 54 TYR 0.024 0.001 TYR A 296 ARG 0.002 0.000 ARG R 283 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 426) hydrogen bonds : angle 4.50651 ( 1206) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.65600 ( 6) covalent geometry : bond 0.00292 ( 9080) covalent geometry : angle 0.54255 (12299) *********************** 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 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.950 Fit side-chains REVERT: A 271 LYS cc_start: 0.6948 (tmtt) cc_final: 0.6595 (ttpt) REVERT: A 341 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8353 (t0) REVERT: N 93 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8722 (ttp) REVERT: N 144 THR cc_start: 0.7546 (m) cc_final: 0.7255 (t) REVERT: N 160 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7706 (mtm110) REVERT: N 201 GLU cc_start: 0.7957 (tp30) cc_final: 0.7736 (tp30) REVERT: R 87 PHE cc_start: 0.8043 (t80) cc_final: 0.7738 (t80) outliers start: 16 outliers final: 11 residues processed: 114 average time/residue: 1.4290 time to fit residues: 173.1539 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 : 1.045 ------------------------------------------------------------------------------- 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 29 THR 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 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 65 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.116881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089887 restraints weight = 14054.681| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2017 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= 0.103 Angle : 0.516 8.238 12305 Z= 0.267 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.033 1538 Dihedral : 5.760 66.472 1331 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.07 % Allowed : 16.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1102 helix: 1.63 (0.28), residues: 370 sheet: -0.25 (0.31), residues: 265 loop : -0.43 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.025 0.001 TYR R 284 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 426) hydrogen bonds : angle 4.33501 ( 1206) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.62381 ( 6) covalent geometry : bond 0.00227 ( 9080) covalent geometry : angle 0.51613 (12299) *********************** 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 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.919 Fit side-chains REVERT: A 271 LYS cc_start: 0.6734 (tmtt) cc_final: 0.6498 (ttpt) REVERT: A 341 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8405 (t0) REVERT: B 214 ARG cc_start: 0.8387 (mmt180) cc_final: 0.8073 (mmt90) REVERT: B 217 MET cc_start: 0.7491 (ppp) cc_final: 0.7160 (ppp) REVERT: G 46 LYS cc_start: 0.8597 (mmpt) cc_final: 0.7789 (mppt) REVERT: N 93 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8687 (ttp) REVERT: N 144 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7204 (t) REVERT: N 160 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7754 (mtm110) REVERT: N 201 GLU cc_start: 0.7939 (tp30) cc_final: 0.7736 (tp30) REVERT: R 87 PHE cc_start: 0.8030 (t80) cc_final: 0.7758 (t80) outliers start: 20 outliers final: 7 residues processed: 120 average time/residue: 1.4116 time to fit residues: 179.7304 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 : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 CYS Chi-restraints excluded: chain R residue 219 ILE 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 32 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087103 restraints weight = 14057.996| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.00 r_work: 0.3075 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9083 Z= 0.134 Angle : 0.550 7.903 12305 Z= 0.285 Chirality : 0.042 0.136 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.922 68.436 1331 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 17.41 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1102 helix: 1.61 (0.27), residues: 370 sheet: -0.25 (0.31), residues: 265 loop : -0.44 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.015 0.001 PHE R 54 TYR 0.024 0.001 TYR A 296 ARG 0.005 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 426) hydrogen bonds : angle 4.39371 ( 1206) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.72856 ( 6) covalent geometry : bond 0.00309 ( 9080) covalent geometry : angle 0.55038 (12299) *********************** 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 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.001 Fit side-chains REVERT: A 271 LYS cc_start: 0.6771 (tmtt) cc_final: 0.6555 (ttpt) REVERT: A 273 LEU cc_start: 0.7518 (tp) cc_final: 0.7314 (tp) REVERT: A 341 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8374 (t0) REVERT: B 214 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8115 (mmt90) REVERT: B 217 MET cc_start: 0.7589 (ppp) cc_final: 0.7168 (ppp) REVERT: N 93 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: N 144 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7193 (t) REVERT: N 160 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7706 (mtm110) REVERT: N 201 GLU cc_start: 0.7988 (tp30) cc_final: 0.7775 (tp30) REVERT: R 87 PHE cc_start: 0.8033 (t80) cc_final: 0.7736 (t80) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 1.3402 time to fit residues: 158.1237 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 65 MET Chi-restraints excluded: chain R residue 219 ILE 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 44 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 48 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.116289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088148 restraints weight = 13772.153| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.06 r_work: 0.3086 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9083 Z= 0.111 Angle : 0.533 7.878 12305 Z= 0.274 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.035 1538 Dihedral : 5.726 66.586 1331 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.24 % Allowed : 18.13 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1102 helix: 1.72 (0.28), residues: 367 sheet: -0.25 (0.31), residues: 265 loop : -0.44 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.021 0.001 TYR A 296 ARG 0.008 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 426) hydrogen bonds : angle 4.30440 ( 1206) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.62246 ( 6) covalent geometry : bond 0.00251 ( 9080) covalent geometry : angle 0.53248 (12299) *********************** 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 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.036 Fit side-chains REVERT: A 271 LYS cc_start: 0.6659 (tmtt) cc_final: 0.6357 (ttpt) REVERT: A 313 ARG cc_start: 0.8404 (ptp-170) cc_final: 0.8117 (ptp-110) REVERT: A 341 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8381 (t0) REVERT: B 214 ARG cc_start: 0.8365 (mmt180) cc_final: 0.8089 (mpt180) REVERT: N 93 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8602 (ttp) REVERT: N 144 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7186 (t) REVERT: N 160 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7752 (mtm110) REVERT: R 87 PHE cc_start: 0.7996 (t80) cc_final: 0.7702 (t80) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 1.3812 time to fit residues: 159.9026 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087096 restraints weight = 13816.252| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.99 r_work: 0.3075 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2042 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= 0.137 Angle : 0.568 8.445 12305 Z= 0.291 Chirality : 0.042 0.136 1391 Planarity : 0.004 0.035 1538 Dihedral : 5.905 68.466 1331 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1102 helix: 1.74 (0.28), residues: 360 sheet: -0.27 (0.31), residues: 265 loop : -0.40 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.020 0.001 PHE R 54 TYR 0.026 0.001 TYR A 296 ARG 0.009 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 426) hydrogen bonds : angle 4.37836 ( 1206) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.73134 ( 6) covalent geometry : bond 0.00317 ( 9080) covalent geometry : angle 0.56817 (12299) ********************** 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.975 Fit side-chains REVERT: A 271 LYS cc_start: 0.6666 (tmtt) cc_final: 0.6416 (ttpt) REVERT: A 313 ARG cc_start: 0.8395 (ptp-170) cc_final: 0.8104 (ptp-110) REVERT: A 341 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8354 (t0) REVERT: B 214 ARG cc_start: 0.8373 (mmt180) cc_final: 0.8077 (mmt90) REVERT: N 3 GLN cc_start: 0.8651 (tt0) cc_final: 0.8439 (tt0) REVERT: N 93 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8684 (ttp) REVERT: N 144 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7171 (t) REVERT: N 160 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7716 (mtm110) REVERT: R 87 PHE cc_start: 0.8019 (t80) cc_final: 0.7744 (t80) outliers start: 13 outliers final: 11 residues processed: 107 average time/residue: 1.4517 time to fit residues: 164.6695 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.0020 chunk 69 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN 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 = 0.3670 r_free = 0.3670 target = 0.119481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091536 restraints weight = 13810.645| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.08 r_work: 0.3143 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9083 Z= 0.095 Angle : 0.530 9.274 12305 Z= 0.271 Chirality : 0.040 0.138 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.335 63.771 1331 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.93 % Allowed : 18.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1102 helix: 1.88 (0.28), residues: 362 sheet: -0.21 (0.31), residues: 264 loop : -0.32 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.000 HIS R 280 PHE 0.012 0.001 PHE R 309 TYR 0.015 0.001 TYR A 296 ARG 0.009 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 426) hydrogen bonds : angle 4.15556 ( 1206) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.55914 ( 6) covalent geometry : bond 0.00206 ( 9080) covalent geometry : angle 0.53008 (12299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7604.09 seconds wall clock time: 132 minutes 34.56 seconds (7954.56 seconds total)