Starting phenix.real_space_refine on Thu Feb 13 18:51:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7na8_24268/02_2025/7na8_24268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7na8_24268/02_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_24268/02_2025/7na8_24268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7na8_24268/02_2025/7na8_24268.map" model { file = "/net/cci-nas-00/data/ceres_data/7na8_24268/02_2025/7na8_24268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7na8_24268/02_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-5592/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: 5.86, per 1000 atoms: 0.66 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: 2.73 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: 1.06 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: 2.60 Time building geometry restraints manager: 2.98 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: 2.150 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- 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 9080 Z= 0.408 Angle : 0.926 21.491 12299 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 *********************** 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 : 1.189 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 1.5237 time to fit residues: 210.7545 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 : 1.088 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086324 restraints weight = 14098.967| |-----------------------------------------------------------------------------| 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 9080 Z= 0.204 Angle : 0.587 6.464 12299 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 *********************** 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 : 0.936 Fit side-chains REVERT: B 214 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7935 (mmt90) REVERT: N 160 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8039 (tmm160) REVERT: N 218 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7646 (mtm180) outliers start: 10 outliers final: 4 residues processed: 119 average time/residue: 1.4116 time to fit residues: 178.2327 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 : 1.283 ------------------------------------------------------------------------------- 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: 0.7980 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.114802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087337 restraints weight = 14028.517| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.93 r_work: 0.3082 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9080 Z= 0.175 Angle : 0.532 6.660 12299 Z= 0.280 Chirality : 0.042 0.137 1391 Planarity : 0.004 0.044 1538 Dihedral : 6.389 71.261 1331 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.76 % Allowed : 11.71 % 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 (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: -0.05 (0.25), residues: 1102 helix: 1.01 (0.27), residues: 370 sheet: -0.34 (0.31), residues: 263 loop : -0.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 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 *********************** 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 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.982 Fit side-chains REVERT: A 313 ARG cc_start: 0.8491 (ptp-170) cc_final: 0.8224 (ptp-110) REVERT: A 318 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 341 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8408 (t0) REVERT: B 214 ARG cc_start: 0.8300 (mmt180) cc_final: 0.8001 (mmt90) REVERT: N 160 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.8035 (tmm160) REVERT: N 218 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7672 (mtm180) REVERT: R 87 PHE cc_start: 0.7993 (t80) cc_final: 0.7709 (t80) outliers start: 17 outliers final: 6 residues processed: 118 average time/residue: 1.3787 time to fit residues: 172.6899 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 218 ARG Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.0030 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.113900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086050 restraints weight = 13842.133| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.98 r_work: 0.3058 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9080 Z= 0.218 Angle : 0.551 7.768 12299 Z= 0.288 Chirality : 0.042 0.143 1391 Planarity : 0.003 0.039 1538 Dihedral : 6.450 72.559 1331 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 14.20 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.25), residues: 1102 helix: 1.18 (0.27), residues: 370 sheet: -0.31 (0.31), residues: 263 loop : -0.58 (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 0.023 0.001 PHE R 54 TYR 0.024 0.002 TYR R 284 ARG 0.001 0.000 ARG B 197 *********************** 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 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.995 Fit side-chains REVERT: A 313 ARG cc_start: 0.8469 (ptp-170) cc_final: 0.8135 (ptp-110) REVERT: A 318 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 341 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8436 (t0) REVERT: B 214 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8019 (mmt90) REVERT: N 160 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.8025 (tmm160) REVERT: N 218 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7676 (mtm180) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 1.3801 time to fit residues: 161.2514 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 38 MET 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=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: 0.6980 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 42 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 = 0.3605 r_free = 0.3605 target = 0.114695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087219 restraints weight = 13773.803| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.92 r_work: 0.3081 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9080 Z= 0.186 Angle : 0.530 7.132 12299 Z= 0.277 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.036 1538 Dihedral : 6.201 70.519 1331 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.66 % Allowed : 15.34 % Favored : 83.01 % 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: 0.20 (0.25), residues: 1102 helix: 1.36 (0.27), residues: 370 sheet: -0.26 (0.31), residues: 263 loop : -0.53 (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 0.017 0.001 PHE R 54 TYR 0.022 0.001 TYR A 296 ARG 0.001 0.000 ARG B 197 *********************** 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 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.972 Fit side-chains REVERT: A 271 LYS cc_start: 0.7026 (tmtt) cc_final: 0.6643 (ttpt) REVERT: A 341 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8406 (t0) REVERT: B 214 ARG cc_start: 0.8293 (mmt180) cc_final: 0.8025 (mmt90) REVERT: N 93 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8737 (ttp) REVERT: N 160 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7956 (tmm160) REVERT: R 87 PHE cc_start: 0.8079 (t80) cc_final: 0.7746 (t80) outliers start: 16 outliers final: 7 residues processed: 110 average time/residue: 1.4173 time to fit residues: 165.7855 Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 114 LEU Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 286 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.0070 chunk 21 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.116670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089318 restraints weight = 14083.521| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.03 r_work: 0.3100 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9080 Z= 0.149 Angle : 0.512 6.413 12299 Z= 0.267 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.034 1538 Dihedral : 5.869 68.333 1331 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 15.75 % 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: 0.35 (0.25), residues: 1102 helix: 1.56 (0.27), residues: 370 sheet: -0.25 (0.31), residues: 265 loop : -0.47 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 280 PHE 0.015 0.001 PHE R 54 TYR 0.025 0.001 TYR R 284 ARG 0.002 0.000 ARG R 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.043 Fit side-chains REVERT: A 21 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7774 (ttm-80) REVERT: A 271 LYS cc_start: 0.6922 (tmtt) cc_final: 0.6587 (ttpt) REVERT: A 341 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8443 (t0) REVERT: G 46 LYS cc_start: 0.8598 (mmpt) cc_final: 0.7770 (mppt) REVERT: N 93 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8672 (ttp) REVERT: N 144 THR cc_start: 0.7526 (m) cc_final: 0.7269 (t) REVERT: N 160 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7791 (mtm110) REVERT: R 87 PHE cc_start: 0.8030 (t80) cc_final: 0.7733 (t80) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 1.4701 time to fit residues: 180.9211 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 189 SER 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: 0.0870 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.115000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087191 restraints weight = 13867.001| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.98 r_work: 0.3079 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9080 Z= 0.192 Angle : 0.533 9.060 12299 Z= 0.275 Chirality : 0.041 0.136 1391 Planarity : 0.003 0.033 1538 Dihedral : 5.982 69.572 1331 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.18 % Allowed : 16.06 % 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 (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: 0.38 (0.25), residues: 1102 helix: 1.60 (0.27), residues: 370 sheet: -0.26 (0.31), residues: 265 loop : -0.46 (0.28), residues: 467 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 0.015 0.001 PHE R 54 TYR 0.024 0.001 TYR A 296 ARG 0.007 0.000 ARG B 197 *********************** 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 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.833 Fit side-chains REVERT: A 21 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7726 (ttm-80) REVERT: A 271 LYS cc_start: 0.6926 (tmtt) cc_final: 0.6613 (ttpt) REVERT: A 341 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8393 (t0) REVERT: B 214 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8063 (mmt90) REVERT: N 93 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8755 (ttp) REVERT: N 144 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7211 (t) REVERT: N 160 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7710 (mtm110) REVERT: R 87 PHE cc_start: 0.8013 (t80) cc_final: 0.7758 (t80) outliers start: 21 outliers final: 10 residues processed: 113 average time/residue: 1.4883 time to fit residues: 177.6947 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 : 1.034 ------------------------------------------------------------------------------- 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 61 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085540 restraints weight = 14090.034| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.00 r_work: 0.3050 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9080 Z= 0.249 Angle : 0.573 8.131 12299 Z= 0.297 Chirality : 0.043 0.136 1391 Planarity : 0.003 0.035 1538 Dihedral : 6.248 70.092 1331 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 17.10 % 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: 0.32 (0.25), residues: 1102 helix: 1.51 (0.27), residues: 370 sheet: -0.27 (0.31), residues: 265 loop : -0.46 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS N 35 PHE 0.013 0.001 PHE R 309 TYR 0.028 0.001 TYR A 296 ARG 0.003 0.000 ARG G 13 *********************** 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 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.969 Fit side-chains REVERT: A 271 LYS cc_start: 0.6977 (tmtt) cc_final: 0.6669 (ttpt) REVERT: A 341 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8553 (t0) REVERT: B 214 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8144 (mpt180) REVERT: G 24 ASN cc_start: 0.7810 (p0) cc_final: 0.7529 (p0) REVERT: N 144 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7259 (t) REVERT: N 160 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7766 (mtm110) REVERT: R 87 PHE cc_start: 0.7985 (t80) cc_final: 0.7669 (t80) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 1.4236 time to fit residues: 170.4863 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 146 LEU 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 211 THR 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: 0.8980 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 82 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.116226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088084 restraints weight = 13815.124| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.07 r_work: 0.3088 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9080 Z= 0.154 Angle : 0.534 8.200 12299 Z= 0.276 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.843 66.401 1331 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.55 % Allowed : 17.72 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.27), residues: 370 sheet: -0.27 (0.31), residues: 265 loop : -0.46 (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 0.021 0.001 TYR A 296 ARG 0.005 0.000 ARG A 21 *********************** 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 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.070 Fit side-chains REVERT: A 271 LYS cc_start: 0.6759 (tmtt) cc_final: 0.6522 (ttpt) REVERT: A 341 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8399 (t0) REVERT: B 214 ARG cc_start: 0.8397 (mmt180) cc_final: 0.8089 (mmp80) REVERT: N 93 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8681 (ttp) REVERT: N 144 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7169 (t) REVERT: N 160 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7742 (mtm110) REVERT: R 87 PHE cc_start: 0.8063 (t80) cc_final: 0.7769 (t80) outliers start: 15 outliers final: 8 residues processed: 112 average time/residue: 1.4284 time to fit residues: 169.9326 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain 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 22 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088557 restraints weight = 13804.740| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.07 r_work: 0.3094 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9080 Z= 0.159 Angle : 0.549 8.469 12299 Z= 0.282 Chirality : 0.041 0.137 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.706 66.091 1331 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.14 % Allowed : 18.45 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.25), residues: 1102 helix: 1.81 (0.28), residues: 364 sheet: -0.29 (0.31), residues: 266 loop : -0.43 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 280 PHE 0.029 0.001 PHE R 54 TYR 0.021 0.001 TYR A 296 ARG 0.006 0.000 ARG A 21 ********************** 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 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.118 Fit side-chains REVERT: A 271 LYS cc_start: 0.6689 (tmtt) cc_final: 0.6470 (ttpt) REVERT: A 273 LEU cc_start: 0.7522 (tp) cc_final: 0.7295 (tp) REVERT: A 341 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8441 (t0) REVERT: N 93 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8703 (ttp) REVERT: N 144 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7114 (t) REVERT: N 160 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7786 (mtm110) REVERT: R 87 PHE cc_start: 0.8055 (t80) cc_final: 0.7771 (t80) REVERT: R 325 ILE cc_start: 0.7866 (tt) cc_final: 0.7611 (tp) outliers start: 11 outliers final: 7 residues processed: 111 average time/residue: 1.4560 time to fit residues: 171.7443 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain 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 286 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.0170 chunk 109 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 overall best weight: 0.2716 ------------------------------------------------------------------------------- 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 R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090851 restraints weight = 13812.780| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.09 r_work: 0.3133 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9080 Z= 0.139 Angle : 0.534 9.448 12299 Z= 0.273 Chirality : 0.040 0.136 1391 Planarity : 0.003 0.036 1538 Dihedral : 5.371 64.363 1331 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.93 % Allowed : 18.45 % 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: 0.58 (0.26), residues: 1102 helix: 1.94 (0.28), residues: 363 sheet: -0.25 (0.31), residues: 264 loop : -0.38 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.000 HIS R 280 PHE 0.013 0.001 PHE R 309 TYR 0.016 0.001 TYR A 296 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6747.79 seconds wall clock time: 119 minutes 52.64 seconds (7192.64 seconds total)