Starting phenix.real_space_refine on Sat May 10 18:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gg6_29996/05_2025/8gg6_29996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gg6_29996/05_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_29996/05_2025/8gg6_29996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gg6_29996/05_2025/8gg6_29996.map" model { file = "/net/cci-nas-00/data/ceres_data/8gg6_29996/05_2025/8gg6_29996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gg6_29996/05_2025/8gg6_29996.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'GLU:plan': 12, 'ARG:plan': 7, 'ASN:plan1': 2, '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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 8, '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: {'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} 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: 4.65, per 1000 atoms: 0.69 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.78 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: 1.86 Time building geometry restraints manager: 2.09 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: 1.490 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.560 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (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 TRP 0.010 0.001 TRP R 109 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE A 238 TYR 0.012 0.001 TYR B 59 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.21668 ( 350) hydrogen bonds : angle 6.25518 ( 1026) SS BOND : bond 0.19800 ( 2) SS BOND : angle 12.61135 ( 4) covalent geometry : bond 0.00358 ( 6867) covalent geometry : angle 0.54786 ( 9380) *********************** 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 : 0.767 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.2006 time to fit residues: 25.2467 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 : 0.762 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.137976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109792 restraints weight = 9042.334| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.08 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6869 Z= 0.138 Angle : 0.523 7.472 9384 Z= 0.286 Chirality : 0.042 0.143 1111 Planarity : 0.004 0.065 1178 Dihedral : 8.210 175.988 994 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.87 % Allowed : 12.60 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.28), residues: 890 helix: 1.96 (0.27), residues: 384 sheet: 0.46 (0.40), residues: 168 loop : -0.86 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR A 253 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05743 ( 350) hydrogen bonds : angle 4.39407 ( 1026) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.64956 ( 4) covalent geometry : bond 0.00304 ( 6867) covalent geometry : angle 0.52152 ( 9380) *********************** 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 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8323 (mptt) cc_final: 0.7889 (mptt) REVERT: A 220 HIS cc_start: 0.8196 (t70) cc_final: 0.7830 (t-170) REVERT: A 339 TYR cc_start: 0.8927 (m-80) cc_final: 0.8714 (m-80) REVERT: B 234 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8594 (t80) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1945 time to fit residues: 25.2433 Evaluate side-chains 96 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 70 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.0370 chunk 30 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108947 restraints weight = 9129.850| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.11 r_work: 0.3052 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6869 Z= 0.105 Angle : 0.475 7.385 9384 Z= 0.258 Chirality : 0.041 0.136 1111 Planarity : 0.004 0.057 1178 Dihedral : 7.963 176.135 994 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.18 % Allowed : 13.69 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 890 helix: 2.09 (0.27), residues: 386 sheet: 0.60 (0.40), residues: 168 loop : -0.80 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE A 212 TYR 0.007 0.001 TYR A 253 ARG 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 350) hydrogen bonds : angle 4.04246 ( 1026) SS BOND : bond 0.00371 ( 2) SS BOND : angle 1.13859 ( 4) covalent geometry : bond 0.00218 ( 6867) covalent geometry : angle 0.47490 ( 9380) *********************** 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: 14 poor density : 95 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8322 (mptt) cc_final: 0.7797 (mptt) REVERT: A 220 HIS cc_start: 0.8243 (t70) cc_final: 0.7877 (t-90) REVERT: B 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8591 (t80) REVERT: R 234 ASP cc_start: 0.8896 (t0) cc_final: 0.8591 (t0) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1902 time to fit residues: 26.0248 Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 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 24 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113012 restraints weight = 9232.970| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.12 r_work: 0.3048 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6869 Z= 0.109 Angle : 0.475 7.357 9384 Z= 0.256 Chirality : 0.041 0.132 1111 Planarity : 0.004 0.054 1178 Dihedral : 7.873 175.440 994 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.49 % Allowed : 14.15 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 890 helix: 2.18 (0.27), residues: 385 sheet: 0.46 (0.39), residues: 175 loop : -0.81 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS B 142 PHE 0.019 0.001 PHE A 222 TYR 0.008 0.001 TYR A 253 ARG 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 350) hydrogen bonds : angle 3.93675 ( 1026) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.95686 ( 4) covalent geometry : bond 0.00237 ( 6867) covalent geometry : angle 0.47509 ( 9380) *********************** 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 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8374 (mptt) cc_final: 0.7939 (mmtm) REVERT: B 217 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8075 (ppp) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8597 (t80) REVERT: R 234 ASP cc_start: 0.8900 (t0) cc_final: 0.8582 (t0) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.1866 time to fit residues: 24.9623 Evaluate side-chains 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.134290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105455 restraints weight = 9229.621| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.13 r_work: 0.3021 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6869 Z= 0.130 Angle : 0.496 7.439 9384 Z= 0.267 Chirality : 0.042 0.134 1111 Planarity : 0.004 0.053 1178 Dihedral : 7.874 174.783 994 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.64 % Allowed : 14.93 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 890 helix: 2.17 (0.27), residues: 385 sheet: 0.49 (0.39), residues: 174 loop : -0.88 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.020 0.001 PHE A 222 TYR 0.010 0.001 TYR A 253 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 350) hydrogen bonds : angle 3.93822 ( 1026) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.90564 ( 4) covalent geometry : bond 0.00299 ( 6867) covalent geometry : angle 0.49535 ( 9380) *********************** 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 111 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8271 (t70) cc_final: 0.7877 (t-90) REVERT: B 59 TYR cc_start: 0.8444 (m-80) cc_final: 0.8185 (m-80) REVERT: B 217 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8068 (ppp) REVERT: B 234 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8633 (t80) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.1920 time to fit residues: 26.0755 Evaluate side-chains 102 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 214 VAL 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 R residue 80 LEU Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.132951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104123 restraints weight = 9173.696| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.11 r_work: 0.2981 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6869 Z= 0.149 Angle : 0.516 7.535 9384 Z= 0.278 Chirality : 0.043 0.136 1111 Planarity : 0.004 0.053 1178 Dihedral : 7.948 174.436 994 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.64 % Allowed : 15.55 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.28), residues: 890 helix: 2.08 (0.27), residues: 385 sheet: 0.45 (0.40), residues: 172 loop : -0.97 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS R 296 PHE 0.015 0.001 PHE B 241 TYR 0.012 0.001 TYR A 253 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 350) hydrogen bonds : angle 4.00786 ( 1026) SS BOND : bond 0.00468 ( 2) SS BOND : angle 0.99460 ( 4) covalent geometry : bond 0.00351 ( 6867) covalent geometry : angle 0.51615 ( 9380) *********************** 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 110 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8302 (mptt) cc_final: 0.7925 (mmtm) REVERT: B 217 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8045 (ppp) REVERT: B 234 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8655 (t80) outliers start: 17 outliers final: 14 residues processed: 103 average time/residue: 0.1916 time to fit residues: 26.4388 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 214 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105094 restraints weight = 9089.021| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.09 r_work: 0.3017 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6869 Z= 0.130 Angle : 0.500 7.435 9384 Z= 0.270 Chirality : 0.042 0.133 1111 Planarity : 0.004 0.051 1178 Dihedral : 7.906 174.112 994 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.80 % Allowed : 15.40 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 890 helix: 2.10 (0.27), residues: 385 sheet: 0.45 (0.39), residues: 172 loop : -0.98 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 277 HIS 0.004 0.001 HIS R 296 PHE 0.015 0.001 PHE B 241 TYR 0.010 0.001 TYR A 253 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 350) hydrogen bonds : angle 3.94051 ( 1026) SS BOND : bond 0.00397 ( 2) SS BOND : angle 0.95176 ( 4) covalent geometry : bond 0.00300 ( 6867) covalent geometry : angle 0.49958 ( 9380) *********************** 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 109 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8279 (mptt) cc_final: 0.7013 (mmtt) REVERT: A 220 HIS cc_start: 0.8310 (t70) cc_final: 0.7576 (t-90) REVERT: B 217 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8070 (ppp) REVERT: B 234 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8646 (t80) REVERT: R 130 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (t0) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.1968 time to fit residues: 26.2552 Evaluate side-chains 105 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 328 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.124454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.094182 restraints weight = 9184.104| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.21 r_work: 0.2903 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1508 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= 0.201 Angle : 0.570 7.717 9384 Z= 0.307 Chirality : 0.045 0.139 1111 Planarity : 0.004 0.052 1178 Dihedral : 8.067 173.685 994 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.80 % Allowed : 15.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.28), residues: 890 helix: 1.89 (0.26), residues: 385 sheet: 0.20 (0.39), residues: 175 loop : -1.02 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 277 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE B 241 TYR 0.015 0.002 TYR A 253 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05946 ( 350) hydrogen bonds : angle 4.13418 ( 1026) SS BOND : bond 0.00584 ( 2) SS BOND : angle 1.12772 ( 4) covalent geometry : bond 0.00494 ( 6867) covalent geometry : angle 0.56988 ( 9380) *********************** 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 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.8302 (mptt) cc_final: 0.7826 (mmtt) REVERT: B 217 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8110 (ppp) REVERT: R 130 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (t0) outliers start: 18 outliers final: 15 residues processed: 95 average time/residue: 0.1980 time to fit residues: 24.9186 Evaluate side-chains 103 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.134969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106382 restraints weight = 9178.080| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.11 r_work: 0.3011 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.033 6869 Z= 0.110 Angle : 0.484 7.290 9384 Z= 0.262 Chirality : 0.042 0.133 1111 Planarity : 0.004 0.049 1178 Dihedral : 7.870 173.348 994 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.49 % Allowed : 16.17 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.28), residues: 890 helix: 2.02 (0.27), residues: 391 sheet: 0.43 (0.40), residues: 166 loop : -1.04 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 277 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 350) hydrogen bonds : angle 3.90024 ( 1026) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.89368 ( 4) covalent geometry : bond 0.00236 ( 6867) covalent geometry : angle 0.48405 ( 9380) *********************** 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 106 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8074 (ppp) REVERT: B 234 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8737 (t80) REVERT: R 130 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (t0) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.1781 time to fit residues: 23.5601 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 : 0.698 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096146 restraints weight = 9262.712| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.25 r_work: 0.2925 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6869 Z= 0.138 Angle : 0.516 7.384 9384 Z= 0.278 Chirality : 0.043 0.138 1111 Planarity : 0.004 0.050 1178 Dihedral : 7.914 172.905 994 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 890 helix: 2.05 (0.26), residues: 385 sheet: 0.33 (0.39), residues: 172 loop : -1.03 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS R 296 PHE 0.015 0.001 PHE B 241 TYR 0.011 0.001 TYR A 253 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 350) hydrogen bonds : angle 3.93993 ( 1026) SS BOND : bond 0.00418 ( 2) SS BOND : angle 0.93408 ( 4) covalent geometry : bond 0.00322 ( 6867) covalent geometry : angle 0.51603 ( 9380) ********************** 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 107 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8173 (ppp) REVERT: B 234 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8655 (t80) REVERT: R 130 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8223 (t0) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1909 time to fit residues: 25.2796 Evaluate side-chains 104 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 328 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0010 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS 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 = 0.3514 r_free = 0.3514 target = 0.133789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103513 restraints weight = 9010.241| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.25 r_work: 0.2959 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6869 Z= 0.114 Angle : 0.491 7.259 9384 Z= 0.266 Chirality : 0.042 0.140 1111 Planarity : 0.004 0.049 1178 Dihedral : 7.837 172.745 994 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.28), residues: 890 helix: 2.06 (0.27), residues: 391 sheet: 0.38 (0.39), residues: 172 loop : -1.00 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 277 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 350) hydrogen bonds : angle 3.85579 ( 1026) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.81753 ( 4) covalent geometry : bond 0.00254 ( 6867) covalent geometry : angle 0.49116 ( 9380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.78 seconds wall clock time: 64 minutes 51.34 seconds (3891.34 seconds total)