Starting phenix.real_space_refine on Tue Feb 3 22:03:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odl_70366/02_2026/9odl_70366.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 4572 2.51 5 N 1235 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7165 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2373 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 17, 'GLN:plan1': 6, 'ARG:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 174 Chain: "G" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 319 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2378 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 4, 'TRANS': 341} Unresolved non-hydrogen bonds: 399 Unresolved non-hydrogen angles: 475 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 12, 'ARG:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 5, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 234 Chain: "R" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2032 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 2, 'ARG:plan': 6, 'TYR:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 109 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EIG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.25 Number of scatterers: 7165 At special positions: 0 Unit cell: (85.44, 92.16, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 3 15.00 Mg 1 11.99 O 1305 8.00 N 1235 7.00 C 4572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 310.4 milliseconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 50.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.673A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.942A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 97 through 111 removed outlier: 4.282A pdb=" N VAL A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.698A pdb=" N ILE A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.626A pdb=" N GLU A 207 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 4.170A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.836A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.631A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.866A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.066A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'R' and resid 66 through 96 Processing helix chain 'R' and resid 101 through 131 Proline residue: R 122 - end of helix removed outlier: 3.737A pdb=" N TYR R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 171 removed outlier: 3.654A pdb=" N CYS R 140 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE R 155 " --> pdb=" O MET R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 Processing helix chain 'R' and resid 180 through 205 removed outlier: 3.954A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 228 through 242 removed outlier: 3.635A pdb=" N ILE R 242 " --> pdb=" O ILE R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 260 Processing helix chain 'R' and resid 269 through 307 removed outlier: 3.525A pdb=" N ARG R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 295 - end of helix removed outlier: 3.632A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 338 removed outlier: 4.138A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS R 330 " --> pdb=" O TYR R 326 " (cutoff:3.500A) Proline residue: R 333 - end of helix removed outlier: 3.532A pdb=" N PHE R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.737A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.864A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.591A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.033A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.627A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.647A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.232A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 34 through 37 removed outlier: 5.832A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.734A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 206 through 207 removed outlier: 3.610A pdb=" N THR R 218 " --> pdb=" O THR R 207 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1160 1.30 - 1.43: 1950 1.43 - 1.56: 4131 1.56 - 1.68: 5 1.68 - 1.81: 66 Bond restraints: 7312 Sorted by residual: bond pdb=" C08 EIG R 501 " pdb=" C10 EIG R 501 " ideal model delta sigma weight residual 1.541 1.314 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.14e-02 7.69e+03 7.05e+00 bond pdb=" N ARG A 208 " pdb=" CA ARG A 208 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 6.91e+00 bond pdb=" N LEU B 300 " pdb=" CA LEU B 300 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.82e+00 bond pdb=" C05 EIG R 501 " pdb=" C07 EIG R 501 " ideal model delta sigma weight residual 1.401 1.449 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 7307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 10012 4.40 - 8.79: 22 8.79 - 13.19: 1 13.19 - 17.59: 1 17.59 - 21.98: 1 Bond angle restraints: 10037 Sorted by residual: angle pdb=" C12 EIG R 501 " pdb=" C08 EIG R 501 " pdb=" N01 EIG R 501 " ideal model delta sigma weight residual 113.08 91.10 21.98 3.00e+00 1.11e-01 5.37e+01 angle pdb=" C10 EIG R 501 " pdb=" C08 EIG R 501 " pdb=" N01 EIG R 501 " ideal model delta sigma weight residual 112.49 128.43 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" N ASP B 27 " pdb=" CA ASP B 27 " pdb=" C ASP B 27 " ideal model delta sigma weight residual 114.56 110.20 4.36 1.27e+00 6.20e-01 1.18e+01 angle pdb=" CA PRO R 122 " pdb=" N PRO R 122 " pdb=" CD PRO R 122 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" N ILE A 49 " pdb=" CA ILE A 49 " pdb=" C ILE A 49 " ideal model delta sigma weight residual 112.98 108.87 4.11 1.25e+00 6.40e-01 1.08e+01 ... (remaining 10032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.91: 4073 29.91 - 59.82: 182 59.82 - 89.72: 8 89.72 - 119.63: 2 119.63 - 149.54: 2 Dihedral angle restraints: 4267 sinusoidal: 1273 harmonic: 2994 Sorted by residual: dihedral pdb=" O5' GTP A 402 " pdb=" O3A GTP A 402 " pdb=" PA GTP A 402 " pdb=" PB GTP A 402 " ideal model delta sinusoidal sigma weight residual 274.12 124.59 149.54 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C8 GTP A 402 " pdb=" C1' GTP A 402 " pdb=" N9 GTP A 402 " pdb=" O4' GTP A 402 " ideal model delta sinusoidal sigma weight residual 104.59 -43.92 148.51 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O3B GTP A 402 " pdb=" O3A GTP A 402 " pdb=" PB GTP A 402 " pdb=" PA GTP A 402 " ideal model delta sinusoidal sigma weight residual -68.92 -179.84 110.92 1 2.00e+01 2.50e-03 3.26e+01 ... (remaining 4264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1163 0.094 - 0.188: 51 0.188 - 0.281: 0 0.281 - 0.375: 0 0.375 - 0.469: 3 Chirality restraints: 1217 Sorted by residual: chirality pdb=" C10 EIG R 501 " pdb=" C08 EIG R 501 " pdb=" C13 EIG R 501 " pdb=" N02 EIG R 501 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C08 EIG R 501 " pdb=" C09 EIG R 501 " pdb=" C10 EIG R 501 " pdb=" C12 EIG R 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.36 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C14 EIG R 501 " pdb=" C13 EIG R 501 " pdb=" C15 EIG R 501 " pdb=" C17 EIG R 501 " both_signs ideal model delta sigma weight residual False -2.26 -2.65 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1214 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " 0.418 9.50e-02 1.11e+02 1.87e-01 2.15e+01 pdb=" NE ARG A 208 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 121 " -0.067 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO R 122 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO R 122 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 122 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 133 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO R 134 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO R 134 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 134 " -0.042 5.00e-02 4.00e+02 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 21 2.52 - 3.11: 5344 3.11 - 3.71: 10903 3.71 - 4.30: 13717 4.30 - 4.90: 23618 Nonbonded interactions: 53603 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O3G GTP A 402 " model vdw 1.924 2.170 nonbonded pdb="MG MG A 401 " pdb=" O2B GTP A 402 " model vdw 1.962 2.170 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.240 3.040 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.258 3.120 nonbonded pdb=" O GLU A 28 " pdb=" NH1 ARG A 32 " model vdw 2.268 3.120 ... (remaining 53598 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 group one per residue 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: 5.230 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.004 0.227 7313 Z= 0.228 Angle : 0.709 21.983 10039 Z= 0.399 Chirality : 0.046 0.469 1217 Planarity : 0.007 0.187 1276 Dihedral : 16.050 149.538 2322 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.50 % Allowed : 21.37 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.28), residues: 1013 helix: 2.49 (0.24), residues: 456 sheet: -1.86 (0.40), residues: 165 loop : -1.56 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.018 0.001 TYR A 146 PHE 0.031 0.002 PHE R 108 TRP 0.026 0.001 TRP B 339 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7312) covalent geometry : angle 0.70945 (10037) SS BOND : bond 0.00144 ( 1) SS BOND : angle 0.72169 ( 2) hydrogen bonds : bond 0.16343 ( 410) hydrogen bonds : angle 5.27952 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 101 average time/residue: 0.0961 time to fit residues: 13.1663 Evaluate side-chains 96 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 304 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 225 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086038 restraints weight = 14862.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.089026 restraints weight = 8008.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090987 restraints weight = 5570.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.092231 restraints weight = 4466.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093123 restraints weight = 3881.657| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7313 Z= 0.123 Angle : 0.484 5.436 10039 Z= 0.262 Chirality : 0.040 0.126 1217 Planarity : 0.004 0.071 1276 Dihedral : 9.682 155.482 1157 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.67 % Allowed : 20.53 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.28), residues: 1013 helix: 2.60 (0.24), residues: 479 sheet: -2.04 (0.35), residues: 201 loop : -1.39 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.013 0.001 TYR A 302 PHE 0.023 0.001 PHE R 108 TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7312) covalent geometry : angle 0.48436 (10037) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.60895 ( 2) hydrogen bonds : bond 0.04375 ( 410) hydrogen bonds : angle 3.98263 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.8435 (m100) cc_final: 0.8122 (m100) REVERT: A 61 TYR cc_start: 0.7358 (m-80) cc_final: 0.7119 (m-80) REVERT: A 197 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8988 (ttmm) REVERT: R 164 ASP cc_start: 0.9295 (t0) cc_final: 0.9086 (t0) outliers start: 10 outliers final: 7 residues processed: 102 average time/residue: 0.0774 time to fit residues: 11.1396 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 0.4980 chunk 40 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087538 restraints weight = 14730.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.090532 restraints weight = 7921.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092420 restraints weight = 5494.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093755 restraints weight = 4412.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094240 restraints weight = 3813.259| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7313 Z= 0.099 Angle : 0.453 5.405 10039 Z= 0.241 Chirality : 0.039 0.133 1217 Planarity : 0.003 0.062 1276 Dihedral : 8.893 160.361 1152 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.34 % Allowed : 19.87 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.28), residues: 1013 helix: 2.94 (0.23), residues: 471 sheet: -1.71 (0.37), residues: 194 loop : -1.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.010 0.001 TYR R 252 PHE 0.020 0.001 PHE R 108 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 7312) covalent geometry : angle 0.45286 (10037) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.40525 ( 2) hydrogen bonds : bond 0.03690 ( 410) hydrogen bonds : angle 3.61344 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8387 (tt0) cc_final: 0.8018 (tt0) outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 0.0690 time to fit residues: 11.2744 Evaluate side-chains 100 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 331 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086600 restraints weight = 15003.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.089567 restraints weight = 8160.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091425 restraints weight = 5719.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092778 restraints weight = 4625.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093460 restraints weight = 4004.972| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7313 Z= 0.108 Angle : 0.456 5.392 10039 Z= 0.243 Chirality : 0.040 0.140 1217 Planarity : 0.003 0.057 1276 Dihedral : 8.758 158.252 1152 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.34 % Allowed : 21.04 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 1013 helix: 3.01 (0.23), residues: 472 sheet: -1.58 (0.37), residues: 199 loop : -1.41 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 95 TYR 0.013 0.001 TYR R 91 PHE 0.021 0.001 PHE R 108 TRP 0.011 0.001 TRP R 293 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7312) covalent geometry : angle 0.45576 (10037) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.47038 ( 2) hydrogen bonds : bond 0.03720 ( 410) hydrogen bonds : angle 3.56150 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7831 (ptp-110) cc_final: 0.7591 (ptp90) REVERT: R 151 MET cc_start: 0.8816 (ttm) cc_final: 0.8571 (ttm) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.0737 time to fit residues: 11.1355 Evaluate side-chains 104 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.086271 restraints weight = 15134.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089161 restraints weight = 8191.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091137 restraints weight = 5742.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092271 restraints weight = 4599.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093093 restraints weight = 4025.500| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 7313 Z= 0.120 Angle : 0.466 5.425 10039 Z= 0.249 Chirality : 0.040 0.137 1217 Planarity : 0.003 0.056 1276 Dihedral : 8.643 150.861 1152 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.01 % Allowed : 21.87 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.28), residues: 1013 helix: 3.06 (0.23), residues: 472 sheet: -1.46 (0.38), residues: 199 loop : -1.40 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.010 0.001 TYR R 96 PHE 0.018 0.001 PHE R 108 TRP 0.014 0.001 TRP R 293 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7312) covalent geometry : angle 0.46585 (10037) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.53317 ( 2) hydrogen bonds : bond 0.03908 ( 410) hydrogen bonds : angle 3.56706 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 318 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8648 (mp) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.0666 time to fit residues: 10.6077 Evaluate side-chains 107 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS A 188 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083716 restraints weight = 15152.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086536 restraints weight = 8340.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088367 restraints weight = 5882.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089413 restraints weight = 4766.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.090193 restraints weight = 4208.633| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7313 Z= 0.167 Angle : 0.509 5.487 10039 Z= 0.273 Chirality : 0.041 0.133 1217 Planarity : 0.003 0.053 1276 Dihedral : 8.655 148.856 1152 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.01 % Allowed : 22.54 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.28), residues: 1013 helix: 2.94 (0.23), residues: 472 sheet: -1.57 (0.37), residues: 201 loop : -1.43 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.023 0.001 TYR R 336 PHE 0.022 0.001 PHE R 108 TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7312) covalent geometry : angle 0.50919 (10037) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.71403 ( 2) hydrogen bonds : bond 0.04601 ( 410) hydrogen bonds : angle 3.76461 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 0.0805 time to fit residues: 11.6908 Evaluate side-chains 101 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085033 restraints weight = 15226.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087915 restraints weight = 8222.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089821 restraints weight = 5748.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091046 restraints weight = 4597.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091656 restraints weight = 4006.975| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7313 Z= 0.125 Angle : 0.484 6.124 10039 Z= 0.257 Chirality : 0.040 0.133 1217 Planarity : 0.003 0.051 1276 Dihedral : 8.499 147.614 1152 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.17 % Allowed : 23.21 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.28), residues: 1013 helix: 2.94 (0.23), residues: 478 sheet: -1.50 (0.37), residues: 197 loop : -1.45 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.018 0.001 TYR R 336 PHE 0.020 0.001 PHE R 108 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7312) covalent geometry : angle 0.48387 (10037) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.51717 ( 2) hydrogen bonds : bond 0.04108 ( 410) hydrogen bonds : angle 3.59563 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8213 (tmtt) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.0803 time to fit residues: 12.1390 Evaluate side-chains 106 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084921 restraints weight = 15246.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087807 restraints weight = 8297.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089662 restraints weight = 5811.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090840 restraints weight = 4682.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091614 restraints weight = 4089.051| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7313 Z= 0.130 Angle : 0.486 6.236 10039 Z= 0.257 Chirality : 0.040 0.133 1217 Planarity : 0.003 0.051 1276 Dihedral : 8.475 147.074 1152 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.34 % Allowed : 23.21 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 1013 helix: 2.99 (0.23), residues: 478 sheet: -1.56 (0.37), residues: 199 loop : -1.43 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.017 0.001 TYR R 336 PHE 0.017 0.001 PHE R 108 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7312) covalent geometry : angle 0.48605 (10037) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.51780 ( 2) hydrogen bonds : bond 0.04028 ( 410) hydrogen bonds : angle 3.56035 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: A 54 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8270 (tmtt) REVERT: R 190 CYS cc_start: 0.8526 (m) cc_final: 0.8188 (m) outliers start: 20 outliers final: 18 residues processed: 108 average time/residue: 0.0798 time to fit residues: 11.9067 Evaluate side-chains 112 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085112 restraints weight = 15124.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087944 restraints weight = 8294.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089791 restraints weight = 5862.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090990 restraints weight = 4730.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091587 restraints weight = 4123.368| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7313 Z= 0.128 Angle : 0.484 6.187 10039 Z= 0.256 Chirality : 0.040 0.134 1217 Planarity : 0.003 0.050 1276 Dihedral : 8.421 147.136 1152 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.17 % Allowed : 23.21 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 1013 helix: 3.01 (0.23), residues: 478 sheet: -1.53 (0.37), residues: 197 loop : -1.47 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 277 TYR 0.016 0.001 TYR R 336 PHE 0.018 0.001 PHE R 108 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7312) covalent geometry : angle 0.48363 (10037) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.51108 ( 2) hydrogen bonds : bond 0.03973 ( 410) hydrogen bonds : angle 3.53825 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 48 ASP cc_start: 0.8723 (t0) cc_final: 0.8369 (m-30) REVERT: A 54 LYS cc_start: 0.8517 (tmtt) cc_final: 0.8282 (tmtt) REVERT: A 144 ARG cc_start: 0.8475 (tpt-90) cc_final: 0.8217 (tpt-90) REVERT: R 190 CYS cc_start: 0.8537 (m) cc_final: 0.8193 (m) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.0801 time to fit residues: 11.7706 Evaluate side-chains 110 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS A 188 HIS R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087722 restraints weight = 15111.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090623 restraints weight = 8117.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092578 restraints weight = 5662.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093825 restraints weight = 4513.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094531 restraints weight = 3905.209| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7313 Z= 0.097 Angle : 0.457 6.267 10039 Z= 0.239 Chirality : 0.039 0.132 1217 Planarity : 0.003 0.049 1276 Dihedral : 8.160 144.060 1152 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.67 % Allowed : 23.37 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.28), residues: 1013 helix: 3.14 (0.23), residues: 479 sheet: -1.46 (0.37), residues: 197 loop : -1.39 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 179 TYR 0.012 0.001 TYR R 336 PHE 0.011 0.001 PHE R 108 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7312) covalent geometry : angle 0.45698 (10037) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.36792 ( 2) hydrogen bonds : bond 0.03335 ( 410) hydrogen bonds : angle 3.32420 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 48 ASP cc_start: 0.8710 (t0) cc_final: 0.8440 (m-30) REVERT: A 54 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8308 (tmtt) REVERT: R 190 CYS cc_start: 0.8460 (m) cc_final: 0.8190 (m) outliers start: 16 outliers final: 15 residues processed: 114 average time/residue: 0.0715 time to fit residues: 11.5323 Evaluate side-chains 112 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 99 optimal weight: 0.0000 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 188 HIS ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087770 restraints weight = 15064.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090683 restraints weight = 8101.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092623 restraints weight = 5648.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093822 restraints weight = 4503.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094685 restraints weight = 3917.249| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7313 Z= 0.099 Angle : 0.462 6.574 10039 Z= 0.242 Chirality : 0.039 0.135 1217 Planarity : 0.003 0.049 1276 Dihedral : 8.148 142.712 1152 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.84 % Allowed : 23.87 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 1013 helix: 3.22 (0.23), residues: 474 sheet: -1.40 (0.37), residues: 197 loop : -1.37 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 179 TYR 0.011 0.001 TYR R 336 PHE 0.029 0.001 PHE R 320 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7312) covalent geometry : angle 0.46168 (10037) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.33136 ( 2) hydrogen bonds : bond 0.03338 ( 410) hydrogen bonds : angle 3.31084 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1428.52 seconds wall clock time: 25 minutes 17.79 seconds (1517.79 seconds total)