Starting phenix.real_space_refine on Tue Feb 11 19:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.map" model { file = "/net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unu_42417/02_2025/8unu_42417.cif" } resolution = 3.5 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= 0.023 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 39 5.16 5 C 4192 2.51 5 N 1117 2.21 5 O 1163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6514 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1685 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 124 Conformer: "B" Number of residues, atoms: 225, 1685 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 124 bond proxies already assigned to first conformer: 1702 Chain: "B" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2401 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 132 Chain: "G" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 325 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2044 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 128 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.50, per 1000 atoms: 0.84 Number of scatterers: 6514 At special positions: 0 Unit cell: (83.2992, 133.626, 98.9178, 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 39 16.00 P 3 15.00 O 1163 8.00 N 1117 7.00 C 4192 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=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 48.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.847A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.946A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.954A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.642A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.115A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.606A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.569A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.590A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.655A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.535A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.700A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.548A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.109A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.974A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.847A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.734A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.904A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.879A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.389A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.870A 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 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 7.191A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.625A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.358A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.784A 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: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.823A 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: 7.155A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.511A 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: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.382A 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: 3.616A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.288A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 351 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: 1.88 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1172 1.33 - 1.45: 1782 1.45 - 1.57: 3642 1.57 - 1.70: 6 1.70 - 1.82: 52 Bond restraints: 6654 Sorted by residual: bond pdb=" N VAL A 57 " pdb=" CA VAL A 57 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.20e-02 6.94e+03 1.28e+01 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.37e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N ILE A 372 " pdb=" CA ILE A 372 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.19e+00 bond pdb=" N ILE R 58 " pdb=" CA ILE R 58 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 ... (remaining 6649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8721 2.04 - 4.08: 325 4.08 - 6.12: 43 6.12 - 8.16: 7 8.16 - 10.20: 8 Bond angle restraints: 9104 Sorted by residual: angle pdb=" N GLN A 59 " pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 111.28 104.89 6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" C PRO G 60 " ideal model delta sigma weight residual 113.53 105.84 7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" N LYS A 233 " pdb=" CA LYS A 233 " pdb=" C LYS A 233 " ideal model delta sigma weight residual 113.72 106.74 6.98 1.30e+00 5.92e-01 2.88e+01 angle pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sigma weight residual 113.80 118.67 -4.87 1.00e+00 1.00e+00 2.38e+01 angle pdb=" N THR A 350 " pdb=" CA THR A 350 " pdb=" C THR A 350 " ideal model delta sigma weight residual 111.40 117.32 -5.92 1.22e+00 6.72e-01 2.35e+01 ... (remaining 9099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 3767 34.96 - 69.92: 59 69.92 - 104.88: 7 104.88 - 139.83: 0 139.83 - 174.79: 2 Dihedral angle restraints: 3835 sinusoidal: 1235 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 172.56 -79.56 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -162.99 76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -105.52 174.79 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 3832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 913 0.068 - 0.135: 152 0.135 - 0.203: 28 0.203 - 0.271: 1 0.271 - 0.339: 1 Chirality restraints: 1095 Sorted by residual: chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE R 233 " pdb=" N ILE R 233 " pdb=" C ILE R 233 " pdb=" CB ILE R 233 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 1092 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C ASP A 223 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP A 223 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 224 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 368 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP A 368 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP A 368 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 320 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR A 320 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 320 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 321 " -0.011 2.00e-02 2.50e+03 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 997 2.76 - 3.30: 6082 3.30 - 3.83: 10137 3.83 - 4.37: 11092 4.37 - 4.90: 20448 Nonbonded interactions: 48756 Sorted by model distance: nonbonded pdb=" CD LYS A 233 " pdb=" CE MET B 188 " model vdw 2.227 3.860 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU A 209 " pdb=" CE1 PHE A 222 " model vdw 2.256 3.340 nonbonded pdb=" OD2 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.332 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.333 3.040 ... (remaining 48751 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.054 6654 Z= 0.362 Angle : 0.832 10.201 9104 Z= 0.553 Chirality : 0.053 0.339 1095 Planarity : 0.004 0.078 1135 Dihedral : 14.141 174.793 2137 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.50 % Allowed : 1.85 % Favored : 97.65 % 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: 1.67 (0.30), residues: 869 helix: 2.61 (0.28), residues: 382 sheet: 0.94 (0.43), residues: 166 loop : -0.70 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 173 HIS 0.004 0.001 HIS B 183 PHE 0.021 0.001 PHE A 212 TYR 0.008 0.001 TYR A 318 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.695 Fit side-chains REVERT: A 53 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7698 (ptpt) REVERT: A 211 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7314 (mmtt) outliers start: 3 outliers final: 2 residues processed: 109 average time/residue: 0.1643 time to fit residues: 24.6386 Evaluate side-chains 80 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN R 65 GLN R 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101494 restraints weight = 37837.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106611 restraints weight = 14008.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109395 restraints weight = 6277.639| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6654 Z= 0.237 Angle : 0.517 6.947 9104 Z= 0.281 Chirality : 0.042 0.148 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.754 177.939 974 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 8.39 % Favored : 90.10 % 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: 1.72 (0.29), residues: 869 helix: 2.62 (0.27), residues: 398 sheet: 0.61 (0.40), residues: 179 loop : -0.63 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.001 PHE B 241 TYR 0.013 0.001 TYR B 289 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7667 (ptpt) REVERT: R 82 MET cc_start: 0.7510 (tmm) cc_final: 0.6996 (ttt) outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 0.1453 time to fit residues: 18.8199 Evaluate side-chains 80 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103313 restraints weight = 40764.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108616 restraints weight = 14066.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111846 restraints weight = 6439.811| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6654 Z= 0.144 Angle : 0.451 6.892 9104 Z= 0.241 Chirality : 0.040 0.140 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.481 172.380 972 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.17 % Allowed : 10.57 % Favored : 88.26 % 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: 1.79 (0.29), residues: 869 helix: 2.69 (0.27), residues: 397 sheet: 0.71 (0.41), residues: 176 loop : -0.62 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.011 0.001 TYR R 316 ARG 0.001 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7680 (ptpp) REVERT: A 390 GLN cc_start: 0.8253 (tp40) cc_final: 0.8037 (tp-100) REVERT: B 291 ASP cc_start: 0.8226 (t70) cc_final: 0.7974 (t0) REVERT: R 82 MET cc_start: 0.7496 (tmm) cc_final: 0.6962 (ttt) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1487 time to fit residues: 19.2922 Evaluate side-chains 81 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098380 restraints weight = 40974.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103013 restraints weight = 13565.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107232 restraints weight = 6471.263| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6654 Z= 0.238 Angle : 0.497 7.636 9104 Z= 0.268 Chirality : 0.041 0.146 1095 Planarity : 0.003 0.041 1135 Dihedral : 8.443 167.550 971 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.68 % Allowed : 12.08 % Favored : 86.24 % 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: 1.59 (0.30), residues: 869 helix: 2.52 (0.27), residues: 399 sheet: 0.45 (0.40), residues: 179 loop : -0.65 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.001 PHE B 241 TYR 0.008 0.001 TYR A 37 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.687 Fit side-chains REVERT: A 53 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7950 (ptpt) REVERT: A 211 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7211 (mmtt) REVERT: B 105 TYR cc_start: 0.9112 (t80) cc_final: 0.8886 (t80) REVERT: B 291 ASP cc_start: 0.8368 (t70) cc_final: 0.8100 (t0) REVERT: R 82 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6953 (ttm) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.1692 time to fit residues: 21.2163 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101631 restraints weight = 38586.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107003 restraints weight = 13068.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110139 restraints weight = 6068.142| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6654 Z= 0.131 Angle : 0.455 8.106 9104 Z= 0.240 Chirality : 0.039 0.136 1095 Planarity : 0.003 0.041 1135 Dihedral : 8.275 166.114 971 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.34 % Allowed : 13.93 % Favored : 84.73 % 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: 1.78 (0.30), residues: 869 helix: 2.77 (0.27), residues: 392 sheet: 0.50 (0.40), residues: 181 loop : -0.59 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.019 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.714 Fit side-chains REVERT: A 53 LYS cc_start: 0.8237 (ptpt) cc_final: 0.7954 (ptpt) REVERT: B 291 ASP cc_start: 0.8335 (t70) cc_final: 0.8074 (t0) outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 0.1587 time to fit residues: 20.7992 Evaluate side-chains 86 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.0170 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099688 restraints weight = 35248.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104271 restraints weight = 11618.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107401 restraints weight = 6615.250| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6654 Z= 0.180 Angle : 0.470 7.270 9104 Z= 0.250 Chirality : 0.040 0.140 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.263 164.311 971 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.35 % Allowed : 13.42 % Favored : 84.23 % 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: 1.63 (0.30), residues: 869 helix: 2.59 (0.27), residues: 399 sheet: 0.44 (0.40), residues: 177 loop : -0.64 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.009 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.024 0.001 TYR R 308 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.772 Fit side-chains REVERT: A 53 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7999 (ptpt) REVERT: B 291 ASP cc_start: 0.8440 (t70) cc_final: 0.8128 (t0) REVERT: R 82 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6959 (ttm) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.1622 time to fit residues: 20.8298 Evaluate side-chains 91 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.0000 chunk 21 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099774 restraints weight = 48761.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105424 restraints weight = 15127.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109743 restraints weight = 6339.010| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.140 Angle : 0.454 6.831 9104 Z= 0.241 Chirality : 0.039 0.146 1095 Planarity : 0.003 0.040 1135 Dihedral : 8.188 163.098 971 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 14.09 % Favored : 83.39 % 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: 1.66 (0.30), residues: 869 helix: 2.68 (0.27), residues: 395 sheet: 0.46 (0.40), residues: 177 loop : -0.68 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.007 0.001 HIS R 296 PHE 0.010 0.001 PHE B 241 TYR 0.021 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.712 Fit side-chains REVERT: A 53 LYS cc_start: 0.8283 (ptpt) cc_final: 0.8024 (ptpt) REVERT: B 291 ASP cc_start: 0.8340 (t70) cc_final: 0.8095 (t0) REVERT: R 82 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7046 (ttm) REVERT: R 144 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7715 (tt) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.1533 time to fit residues: 20.3218 Evaluate side-chains 92 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 40 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 70 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102650 restraints weight = 40926.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107374 restraints weight = 13053.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111776 restraints weight = 6292.517| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6654 Z= 0.123 Angle : 0.451 7.652 9104 Z= 0.236 Chirality : 0.039 0.137 1095 Planarity : 0.002 0.039 1135 Dihedral : 8.047 160.526 971 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.18 % Allowed : 14.26 % Favored : 83.56 % 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: 1.87 (0.30), residues: 869 helix: 2.87 (0.27), residues: 392 sheet: 0.55 (0.40), residues: 175 loop : -0.57 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.015 0.001 TYR R 308 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.710 Fit side-chains REVERT: A 53 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7978 (ptpt) REVERT: R 82 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7042 (ttm) REVERT: R 144 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7682 (tt) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.1508 time to fit residues: 21.6422 Evaluate side-chains 95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102605 restraints weight = 26064.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106700 restraints weight = 10230.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109551 restraints weight = 6016.431| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6654 Z= 0.129 Angle : 0.454 6.894 9104 Z= 0.241 Chirality : 0.039 0.138 1095 Planarity : 0.002 0.039 1135 Dihedral : 8.021 159.635 971 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.01 % Allowed : 15.10 % Favored : 82.89 % 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: 1.78 (0.30), residues: 869 helix: 2.72 (0.27), residues: 399 sheet: 0.58 (0.40), residues: 175 loop : -0.63 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.005 0.001 HIS R 296 PHE 0.011 0.001 PHE A 212 TYR 0.017 0.001 TYR A 37 ARG 0.001 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.843 Fit side-chains REVERT: A 53 LYS cc_start: 0.8277 (ptpt) cc_final: 0.8020 (ptpt) REVERT: B 59 TYR cc_start: 0.8429 (m-80) cc_final: 0.7602 (m-80) REVERT: R 82 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6964 (ttm) REVERT: R 144 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7646 (tt) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.1572 time to fit residues: 20.9223 Evaluate side-chains 95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101704 restraints weight = 42002.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106394 restraints weight = 12826.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110499 restraints weight = 6223.970| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6654 Z= 0.158 Angle : 0.469 6.908 9104 Z= 0.249 Chirality : 0.039 0.139 1095 Planarity : 0.003 0.039 1135 Dihedral : 8.023 158.854 971 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.01 % Allowed : 15.10 % Favored : 82.89 % 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: 1.76 (0.30), residues: 869 helix: 2.71 (0.27), residues: 399 sheet: 0.55 (0.39), residues: 175 loop : -0.63 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.709 Fit side-chains REVERT: A 53 LYS cc_start: 0.8259 (ptpt) cc_final: 0.8004 (ptpt) REVERT: B 59 TYR cc_start: 0.8463 (m-80) cc_final: 0.7652 (m-80) REVERT: R 82 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7011 (ttm) REVERT: R 144 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7710 (tt) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1498 time to fit residues: 19.7437 Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 0.0670 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101125 restraints weight = 43897.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105590 restraints weight = 13014.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109838 restraints weight = 6414.036| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6654 Z= 0.174 Angle : 0.480 7.902 9104 Z= 0.252 Chirality : 0.040 0.165 1095 Planarity : 0.003 0.039 1135 Dihedral : 8.029 158.375 971 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.35 % Allowed : 15.27 % Favored : 82.38 % 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: 1.71 (0.30), residues: 869 helix: 2.71 (0.27), residues: 395 sheet: 0.52 (0.39), residues: 175 loop : -0.67 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE B 241 TYR 0.019 0.001 TYR R 308 ARG 0.001 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.75 seconds wall clock time: 43 minutes 8.82 seconds (2588.82 seconds total)