Starting phenix.real_space_refine on Fri Aug 22 18:13:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg6_29996/08_2025/8gg6_29996.cif" } resolution = 3.3 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= 0.024 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 45 5.16 5 C 4305 2.51 5 N 1156 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1796 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 12, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2437 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 332 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2109 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ARG:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 19 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 1.58, per 1000 atoms: 0.23 Number of scatterers: 6725 At special positions: 0 Unit cell: (85.9023, 133.626, 99.7855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 3 15.00 O 1216 8.00 N 1156 7.00 C 4305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.31 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 0.44 Conformation dependent library (CDL) restraints added in 275.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 46.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.777A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.754A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.704A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.600A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.763A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.546A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.958A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.560A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.939A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 34 through 61 removed outlier: 4.570A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 86 removed outlier: 3.865A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.587A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.884A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 186 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 removed outlier: 3.730A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 287 removed outlier: 3.808A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.502A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 322 removed outlier: 3.709A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.397A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.682A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.855A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.041A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.893A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.334A 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: 6.898A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.733A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.637A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1026 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: 0.80 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1268 1.33 - 1.45: 1765 1.45 - 1.57: 3766 1.57 - 1.69: 6 1.69 - 1.82: 62 Bond restraints: 6867 Sorted by residual: bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.18e-02 7.18e+03 1.18e+01 bond pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 1.527 1.495 0.032 1.02e-02 9.61e+03 9.81e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" CA ALA B 231 " pdb=" CB ALA B 231 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.72e-02 3.38e+03 6.98e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.573 -0.050 2.00e-02 2.50e+03 6.27e+00 ... (remaining 6862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 9177 1.58 - 3.15: 163 3.15 - 4.73: 29 4.73 - 6.31: 7 6.31 - 7.88: 4 Bond angle restraints: 9380 Sorted by residual: angle pdb=" N THR B 102 " pdb=" CA THR B 102 " pdb=" C THR B 102 " ideal model delta sigma weight residual 108.99 116.87 -7.88 1.57e+00 4.06e-01 2.52e+01 angle pdb=" N GLY A 355 " pdb=" CA GLY A 355 " pdb=" C GLY A 355 " ideal model delta sigma weight residual 115.36 108.83 6.53 1.33e+00 5.65e-01 2.41e+01 angle pdb=" N LEU R 115 " pdb=" CA LEU R 115 " pdb=" C LEU R 115 " ideal model delta sigma weight residual 111.28 115.81 -4.53 1.09e+00 8.42e-01 1.73e+01 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.28 115.02 -3.74 1.09e+00 8.42e-01 1.18e+01 angle pdb=" N ALA B 231 " pdb=" CA ALA B 231 " pdb=" C ALA B 231 " ideal model delta sigma weight residual 108.75 114.28 -5.53 1.71e+00 3.42e-01 1.05e+01 ... (remaining 9375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 3916 34.93 - 69.87: 73 69.87 - 104.80: 7 104.80 - 139.74: 0 139.74 - 174.67: 1 Dihedral angle restraints: 3997 sinusoidal: 1362 harmonic: 2635 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 86.20 174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 7.67 96.92 1 2.00e+01 2.50e-03 2.69e+01 dihedral pdb=" CG ARG B 219 " pdb=" CD ARG B 219 " pdb=" NE ARG B 219 " pdb=" CZ ARG B 219 " ideal model delta sinusoidal sigma weight residual -90.00 -46.92 -43.08 2 1.50e+01 4.44e-03 9.95e+00 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 695 0.031 - 0.062: 264 0.062 - 0.093: 103 0.093 - 0.125: 46 0.125 - 0.156: 3 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB THR R 56 " pdb=" CA THR R 56 " pdb=" OG1 THR R 56 " pdb=" CG2 THR R 56 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1108 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO G 53 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 113 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP R 113 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP R 113 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL R 114 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C SER A 349 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 350 " 0.014 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 810 2.75 - 3.29: 6213 3.29 - 3.83: 10503 3.83 - 4.36: 11720 4.36 - 4.90: 22076 Nonbonded interactions: 51322 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.277 3.040 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE2 GLU G 22 " model vdw 2.340 3.120 nonbonded pdb=" OE2 GLU R 187 " pdb=" OG1 THR R 189 " model vdw 2.344 3.040 ... (remaining 51317 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.005 0.280 6869 Z= 0.267 Angle : 0.606 25.181 9384 Z= 0.340 Chirality : 0.041 0.156 1111 Planarity : 0.004 0.083 1178 Dihedral : 15.251 174.672 2281 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.31 % Allowed : 11.98 % Favored : 87.71 % 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 aren not related in a simple way. whole: 0.67 (0.28), residues: 890 helix: 1.84 (0.28), residues: 366 sheet: 0.13 (0.39), residues: 170 loop : -0.87 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.012 0.001 TYR B 59 PHE 0.017 0.001 PHE A 238 TRP 0.010 0.001 TRP R 109 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6867) covalent geometry : angle 0.54786 ( 9380) SS BOND : bond 0.19800 ( 2) SS BOND : angle 12.61135 ( 4) hydrogen bonds : bond 0.21668 ( 350) hydrogen bonds : angle 6.25518 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.187 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.0683 time to fit residues: 8.6600 Evaluate side-chains 88 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.098682 restraints weight = 9288.226| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.23 r_work: 0.2965 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6869 Z= 0.128 Angle : 0.514 7.431 9384 Z= 0.281 Chirality : 0.042 0.139 1111 Planarity : 0.004 0.065 1178 Dihedral : 8.175 176.001 994 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 12.44 % Favored : 85.85 % 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 aren not related in a simple way. whole: 0.97 (0.28), residues: 890 helix: 1.98 (0.27), residues: 384 sheet: 0.50 (0.40), residues: 168 loop : -0.85 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.009 0.001 TYR A 253 PHE 0.015 0.001 PHE A 212 TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6867) covalent geometry : angle 0.51240 ( 9380) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.70760 ( 4) hydrogen bonds : bond 0.05497 ( 350) hydrogen bonds : angle 4.35263 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8355 (mptt) cc_final: 0.7883 (mptt) REVERT: A 220 HIS cc_start: 0.8190 (t70) cc_final: 0.7837 (t-90) REVERT: B 234 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8674 (t80) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.0707 time to fit residues: 9.0320 Evaluate side-chains 95 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105102 restraints weight = 9130.917| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.09 r_work: 0.2981 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6869 Z= 0.190 Angle : 0.563 7.779 9384 Z= 0.304 Chirality : 0.044 0.139 1111 Planarity : 0.004 0.062 1178 Dihedral : 8.254 176.272 994 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.95 % Allowed : 13.84 % Favored : 83.20 % 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 aren not related in a simple way. whole: 0.79 (0.28), residues: 890 helix: 1.83 (0.27), residues: 385 sheet: 0.23 (0.38), residues: 175 loop : -0.86 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.014 0.002 TYR A 253 PHE 0.018 0.002 PHE B 241 TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6867) covalent geometry : angle 0.56235 ( 9380) SS BOND : bond 0.00606 ( 2) SS BOND : angle 1.33587 ( 4) hydrogen bonds : bond 0.06136 ( 350) hydrogen bonds : angle 4.27311 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8037 (ppp) REVERT: R 234 ASP cc_start: 0.8932 (t0) cc_final: 0.8634 (t0) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.0718 time to fit residues: 9.7399 Evaluate side-chains 102 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.108023 restraints weight = 9226.245| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.12 r_work: 0.3035 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6869 Z= 0.105 Angle : 0.476 7.404 9384 Z= 0.258 Chirality : 0.041 0.133 1111 Planarity : 0.004 0.055 1178 Dihedral : 7.980 175.847 994 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.18 % Allowed : 15.09 % Favored : 82.74 % 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 aren not related in a simple way. whole: 0.99 (0.28), residues: 890 helix: 2.04 (0.27), residues: 385 sheet: 0.40 (0.39), residues: 174 loop : -0.86 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.007 0.001 TYR A 253 PHE 0.014 0.001 PHE B 241 TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6867) covalent geometry : angle 0.47573 ( 9380) SS BOND : bond 0.00316 ( 2) SS BOND : angle 1.00648 ( 4) hydrogen bonds : bond 0.04401 ( 350) hydrogen bonds : angle 3.97217 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8098 (t70) cc_final: 0.7751 (t-90) REVERT: B 59 TYR cc_start: 0.8404 (m-80) cc_final: 0.8140 (m-80) REVERT: B 234 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8695 (t80) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0725 time to fit residues: 10.0213 Evaluate side-chains 100 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 294 GLN R 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107574 restraints weight = 9248.139| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.12 r_work: 0.3033 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6869 Z= 0.101 Angle : 0.467 7.295 9384 Z= 0.251 Chirality : 0.041 0.132 1111 Planarity : 0.004 0.053 1178 Dihedral : 7.833 174.610 994 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.95 % Allowed : 14.93 % Favored : 82.12 % 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 aren not related in a simple way. whole: 1.04 (0.28), residues: 890 helix: 2.07 (0.27), residues: 391 sheet: 0.42 (0.39), residues: 173 loop : -0.86 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.006 0.001 TYR R 199 PHE 0.013 0.001 PHE A 222 TRP 0.006 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6867) covalent geometry : angle 0.46659 ( 9380) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.88843 ( 4) hydrogen bonds : bond 0.04135 ( 350) hydrogen bonds : angle 3.82107 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8116 (t70) cc_final: 0.7697 (t-90) REVERT: B 59 TYR cc_start: 0.8436 (m-80) cc_final: 0.8210 (m-80) REVERT: B 217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8069 (ppp) REVERT: B 234 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8701 (t80) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.0823 time to fit residues: 11.5529 Evaluate side-chains 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 87 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110009 restraints weight = 9146.655| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.10 r_work: 0.3050 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6869 Z= 0.096 Angle : 0.459 7.188 9384 Z= 0.247 Chirality : 0.041 0.130 1111 Planarity : 0.004 0.051 1178 Dihedral : 7.736 173.737 994 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.11 % Allowed : 14.93 % Favored : 81.96 % 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 aren not related in a simple way. whole: 1.17 (0.28), residues: 890 helix: 2.20 (0.27), residues: 392 sheet: 0.68 (0.41), residues: 162 loop : -0.93 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.006 0.001 TYR R 199 PHE 0.013 0.001 PHE A 222 TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6867) covalent geometry : angle 0.45919 ( 9380) SS BOND : bond 0.00290 ( 2) SS BOND : angle 0.81607 ( 4) hydrogen bonds : bond 0.03820 ( 350) hydrogen bonds : angle 3.73268 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8078 (t70) cc_final: 0.7767 (t-90) REVERT: B 217 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8069 (ppp) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8773 (t80) REVERT: R 130 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8361 (t0) outliers start: 20 outliers final: 16 residues processed: 107 average time/residue: 0.0859 time to fit residues: 12.2159 Evaluate side-chains 112 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 52 optimal weight: 0.0570 chunk 74 optimal weight: 0.0270 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110859 restraints weight = 9173.283| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.11 r_work: 0.3082 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6869 Z= 0.093 Angle : 0.457 7.147 9384 Z= 0.245 Chirality : 0.041 0.134 1111 Planarity : 0.004 0.049 1178 Dihedral : 7.659 172.932 994 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.95 % Allowed : 15.40 % Favored : 81.65 % 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 aren not related in a simple way. whole: 1.25 (0.28), residues: 890 helix: 2.31 (0.27), residues: 392 sheet: 0.61 (0.40), residues: 168 loop : -0.91 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.005 0.001 TYR A 339 PHE 0.014 0.001 PHE A 222 TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 6867) covalent geometry : angle 0.45671 ( 9380) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.80833 ( 4) hydrogen bonds : bond 0.03619 ( 350) hydrogen bonds : angle 3.66426 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8080 (t70) cc_final: 0.7736 (t-90) REVERT: B 217 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8068 (ppp) REVERT: B 234 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8692 (t80) REVERT: R 130 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (t0) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.0910 time to fit residues: 12.5277 Evaluate side-chains 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109364 restraints weight = 9174.036| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.11 r_work: 0.3043 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6869 Z= 0.104 Angle : 0.475 7.186 9384 Z= 0.255 Chirality : 0.041 0.136 1111 Planarity : 0.004 0.049 1178 Dihedral : 7.679 172.591 994 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.95 % Allowed : 15.86 % Favored : 81.18 % 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 aren not related in a simple way. whole: 1.24 (0.28), residues: 890 helix: 2.30 (0.26), residues: 392 sheet: 0.63 (0.40), residues: 168 loop : -0.93 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.006 0.001 TYR R 199 PHE 0.014 0.001 PHE A 222 TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6867) covalent geometry : angle 0.47436 ( 9380) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.81325 ( 4) hydrogen bonds : bond 0.03963 ( 350) hydrogen bonds : angle 3.68991 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8130 (t70) cc_final: 0.7791 (t-90) REVERT: B 217 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8036 (ppp) REVERT: B 234 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8767 (t80) REVERT: R 130 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (t0) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.0766 time to fit residues: 10.7046 Evaluate side-chains 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN R 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108740 restraints weight = 9177.103| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.12 r_work: 0.3034 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6869 Z= 0.110 Angle : 0.481 7.197 9384 Z= 0.258 Chirality : 0.041 0.136 1111 Planarity : 0.004 0.048 1178 Dihedral : 7.695 172.408 994 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.80 % Allowed : 16.17 % Favored : 81.03 % 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 aren not related in a simple way. whole: 1.22 (0.28), residues: 890 helix: 2.29 (0.26), residues: 392 sheet: 0.59 (0.40), residues: 168 loop : -0.93 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.008 0.001 TYR A 253 PHE 0.014 0.001 PHE A 222 TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6867) covalent geometry : angle 0.48114 ( 9380) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.83198 ( 4) hydrogen bonds : bond 0.04107 ( 350) hydrogen bonds : angle 3.72348 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8195 (t70) cc_final: 0.7843 (t-170) REVERT: B 175 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8133 (mm-40) REVERT: B 217 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8039 (ppp) REVERT: B 234 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8769 (t80) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.0758 time to fit residues: 10.5676 Evaluate side-chains 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 41 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110506 restraints weight = 9152.529| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.11 r_work: 0.3077 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6869 Z= 0.098 Angle : 0.469 7.156 9384 Z= 0.252 Chirality : 0.041 0.136 1111 Planarity : 0.004 0.048 1178 Dihedral : 7.647 171.890 994 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.64 % Allowed : 16.49 % Favored : 80.87 % 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 aren not related in a simple way. whole: 1.25 (0.28), residues: 890 helix: 2.34 (0.27), residues: 392 sheet: 0.69 (0.41), residues: 162 loop : -0.95 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.006 0.001 TYR R 308 PHE 0.014 0.001 PHE A 222 TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 6867) covalent geometry : angle 0.46875 ( 9380) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.77064 ( 4) hydrogen bonds : bond 0.03709 ( 350) hydrogen bonds : angle 3.68161 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8306 (mptt) cc_final: 0.8052 (mmtm) REVERT: B 217 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8028 (ppp) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8754 (t80) REVERT: R 130 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8268 (t0) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.0679 time to fit residues: 9.2283 Evaluate side-chains 108 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 303 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109066 restraints weight = 9133.968| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.11 r_work: 0.3039 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6869 Z= 0.110 Angle : 0.484 7.197 9384 Z= 0.259 Chirality : 0.042 0.136 1111 Planarity : 0.004 0.048 1178 Dihedral : 7.670 171.739 994 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.80 % Allowed : 16.17 % Favored : 81.03 % 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 aren not related in a simple way. whole: 1.23 (0.28), residues: 890 helix: 2.31 (0.26), residues: 392 sheet: 0.58 (0.40), residues: 169 loop : -0.93 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.008 0.001 TYR A 253 PHE 0.018 0.001 PHE A 222 TRP 0.011 0.001 TRP A 277 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6867) covalent geometry : angle 0.48373 ( 9380) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.80975 ( 4) hydrogen bonds : bond 0.04026 ( 350) hydrogen bonds : angle 3.72613 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.70 seconds wall clock time: 28 minutes 51.36 seconds (1731.36 seconds total)