Starting phenix.real_space_refine on Fri Mar 6 06:12:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426.map" model { file = "/net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ste_25426/03_2026/7ste_25426_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 67 5.16 5 C 8982 2.51 5 N 2487 2.21 5 O 2701 1.98 5 H 14379 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28628 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5028 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5146 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5218 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5470 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7626 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 6 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.16 Number of scatterers: 28628 At special positions: 0 Unit cell: (113.988, 122.248, 123.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 67 16.00 P 11 15.00 Mg 1 11.99 O 2701 8.00 N 2487 7.00 C 8982 6.00 H 14379 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 615.9 milliseconds 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 7 sheets defined 67.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.691A pdb=" N TYR B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.804A pdb=" N VAL B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.989A pdb=" N ASP B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.674A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 276 removed outlier: 3.713A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.861A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 removed outlier: 4.171A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.889A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.591A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.854A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 70 through 81 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.626A pdb=" N ARG D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.521A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.518A pdb=" N ARG D 175 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 193 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.703A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.528A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.588A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.731A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.771A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.703A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.393A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.509A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.803A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.512A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 250' Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 292 removed outlier: 5.762A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N MET A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.740A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.539A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.601A pdb=" N LEU A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 5.297A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 410 removed outlier: 3.723A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.823A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 486 through 503 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 565 through 584 Processing sheet with id=AA1, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.205A pdb=" N LEU B 76 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 79 through 83 removed outlier: 5.927A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.069A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.274A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.747A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.150A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.372A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2397 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: 6.02 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14348 1.03 - 1.23: 33 1.23 - 1.42: 5817 1.42 - 1.62: 8566 1.62 - 1.81: 103 Bond restraints: 28867 Sorted by residual: bond pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.83e-02 2.99e+03 1.96e+00 bond pdb=" C4 ADP D 801 " pdb=" C5 ADP D 801 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 51874 1.61 - 3.21: 365 3.21 - 4.82: 61 4.82 - 6.43: 23 6.43 - 8.03: 1 Bond angle restraints: 52324 Sorted by residual: angle pdb=" C VAL B 228 " pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 126.32 134.35 -8.03 1.74e+00 3.30e-01 2.13e+01 angle pdb=" C ASP B 229 " pdb=" CA ASP B 229 " pdb=" CB ASP B 229 " ideal model delta sigma weight residual 110.04 105.42 4.62 1.51e+00 4.39e-01 9.36e+00 angle pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.83 105.64 6.19 2.67e+00 1.40e-01 5.37e+00 angle pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" O2' ATP A 801 " ideal model delta sigma weight residual 110.58 104.34 6.24 2.79e+00 1.28e-01 4.99e+00 angle pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 111.06 105.50 5.56 2.50e+00 1.60e-01 4.95e+00 ... (remaining 52319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 13156 34.52 - 69.05: 259 69.05 - 103.57: 10 103.57 - 138.09: 5 138.09 - 172.62: 4 Dihedral angle restraints: 13434 sinusoidal: 7530 harmonic: 5904 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 127.39 172.62 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 82.53 -142.53 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 13431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1994 0.059 - 0.117: 235 0.117 - 0.176: 20 0.176 - 0.235: 1 0.235 - 0.293: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2249 not shown) Planarity restraints: 4172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " -0.037 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO E 63 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 287 " 0.011 2.00e-02 2.50e+03 9.19e-03 2.53e+00 pdb=" CG TYR E 287 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR E 287 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 287 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 287 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 287 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR E 287 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR E 287 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR E 287 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 287 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 228 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C VAL B 228 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 228 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 229 " 0.009 2.00e-02 2.50e+03 ... (remaining 4169 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1524 2.20 - 2.80: 59738 2.80 - 3.40: 79489 3.40 - 4.00: 102140 4.00 - 4.60: 160883 Nonbonded interactions: 403774 Sorted by model distance: nonbonded pdb=" OE1 GLU B 301 " pdb=" HH TYR C 308 " model vdw 1.600 2.450 nonbonded pdb="HH22 ARG D 91 " pdb=" O SER D 119 " model vdw 1.626 2.450 nonbonded pdb=" O ASN A 383 " pdb=" HG1 THR A 386 " model vdw 1.627 2.450 nonbonded pdb=" H LYS D 71 " pdb=" O3B ADP D 801 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASP D 37 " pdb=" HZ1 LYS D 50 " model vdw 1.663 2.450 ... (remaining 403769 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.480 Find NCS groups from input model: 0.100 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.002 0.026 14488 Z= 0.087 Angle : 0.483 8.034 19588 Z= 0.238 Chirality : 0.037 0.293 2252 Planarity : 0.003 0.057 2476 Dihedral : 14.056 172.618 5543 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.21), residues: 1748 helix: 3.26 (0.16), residues: 1048 sheet: -0.05 (0.41), residues: 166 loop : 0.53 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 283 TYR 0.027 0.001 TYR E 287 PHE 0.009 0.001 PHE A 96 TRP 0.005 0.000 TRP A 66 HIS 0.005 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00176 (14488) covalent geometry : angle 0.48257 (19588) hydrogen bonds : bond 0.12093 ( 825) hydrogen bonds : angle 4.86956 ( 2397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7945 (mpp) cc_final: 0.7586 (mpp) REVERT: B 119 MET cc_start: 0.4585 (tmm) cc_final: 0.3585 (mtt) REVERT: E 72 VAL cc_start: 0.8831 (t) cc_final: 0.8487 (t) REVERT: E 74 GLN cc_start: 0.7855 (mp10) cc_final: 0.7567 (mp-120) REVERT: E 161 TYR cc_start: 0.6916 (m-80) cc_final: 0.6709 (m-80) REVERT: A 287 MET cc_start: 0.5507 (ptm) cc_final: 0.5291 (ptm) REVERT: A 497 TYR cc_start: 0.7584 (t80) cc_final: 0.7331 (t80) REVERT: A 500 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8100 (tmmt) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 1.4876 time to fit residues: 484.8305 Evaluate side-chains 160 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 177 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN D 196 ASN E 336 ASN A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.145160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084563 restraints weight = 69967.883| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.03 r_work: 0.2956 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14488 Z= 0.168 Angle : 0.580 7.737 19588 Z= 0.283 Chirality : 0.037 0.138 2252 Planarity : 0.004 0.067 2476 Dihedral : 10.375 170.180 1993 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.95 % Allowed : 9.23 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.21), residues: 1748 helix: 3.00 (0.16), residues: 1062 sheet: -0.03 (0.40), residues: 165 loop : 0.40 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 115 TYR 0.015 0.001 TYR B 186 PHE 0.014 0.001 PHE E 305 TRP 0.004 0.001 TRP E 4 HIS 0.006 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00382 (14488) covalent geometry : angle 0.58035 (19588) hydrogen bonds : bond 0.04073 ( 825) hydrogen bonds : angle 4.13762 ( 2397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8148 (mp0) REVERT: B 119 MET cc_start: 0.5841 (tmm) cc_final: 0.5035 (mtt) REVERT: C 94 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8569 (tmm-80) REVERT: D 207 GLN cc_start: 0.8981 (mp10) cc_final: 0.8373 (mp10) REVERT: D 227 ASP cc_start: 0.8523 (t0) cc_final: 0.8297 (t0) REVERT: E 72 VAL cc_start: 0.9091 (t) cc_final: 0.8803 (t) REVERT: E 74 GLN cc_start: 0.8184 (mp10) cc_final: 0.7766 (mp-120) REVERT: A 497 TYR cc_start: 0.8139 (t80) cc_final: 0.7781 (t80) REVERT: A 500 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7805 (tmmt) outliers start: 15 outliers final: 5 residues processed: 175 average time/residue: 1.3151 time to fit residues: 252.7845 Evaluate side-chains 144 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 95 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.081980 restraints weight = 69622.156| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.98 r_work: 0.2949 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14488 Z= 0.187 Angle : 0.563 8.273 19588 Z= 0.276 Chirality : 0.038 0.135 2252 Planarity : 0.004 0.060 2476 Dihedral : 10.169 165.615 1991 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.07 % Allowed : 9.86 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.21), residues: 1748 helix: 2.83 (0.16), residues: 1065 sheet: -0.10 (0.41), residues: 168 loop : 0.26 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 73 TYR 0.011 0.001 TYR D 286 PHE 0.016 0.001 PHE E 305 TRP 0.005 0.001 TRP E 259 HIS 0.008 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00428 (14488) covalent geometry : angle 0.56290 (19588) hydrogen bonds : bond 0.04154 ( 825) hydrogen bonds : angle 4.07923 ( 2397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8961 (tp) cc_final: 0.8727 (tp) REVERT: B 77 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8170 (mp0) REVERT: D 207 GLN cc_start: 0.9007 (mp10) cc_final: 0.8763 (mp10) REVERT: D 227 ASP cc_start: 0.8654 (t0) cc_final: 0.8443 (t0) REVERT: E 72 VAL cc_start: 0.9130 (t) cc_final: 0.8850 (t) REVERT: E 74 GLN cc_start: 0.8186 (mp10) cc_final: 0.7826 (mp-120) REVERT: E 112 LEU cc_start: 0.9067 (mm) cc_final: 0.8744 (mm) REVERT: A 497 TYR cc_start: 0.8176 (t80) cc_final: 0.7945 (t80) outliers start: 17 outliers final: 6 residues processed: 157 average time/residue: 1.3144 time to fit residues: 226.8852 Evaluate side-chains 141 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 35 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 172 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 34 GLN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS A 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080808 restraints weight = 69530.422| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.86 r_work: 0.2928 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14488 Z= 0.155 Angle : 0.543 7.488 19588 Z= 0.264 Chirality : 0.037 0.138 2252 Planarity : 0.004 0.056 2476 Dihedral : 10.004 166.549 1991 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.14 % Allowed : 10.75 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.21), residues: 1748 helix: 2.78 (0.16), residues: 1067 sheet: -0.14 (0.40), residues: 168 loop : 0.25 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 73 TYR 0.019 0.001 TYR B 186 PHE 0.014 0.001 PHE E 305 TRP 0.006 0.001 TRP C 256 HIS 0.007 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00356 (14488) covalent geometry : angle 0.54278 (19588) hydrogen bonds : bond 0.03834 ( 825) hydrogen bonds : angle 3.96772 ( 2397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.7832 (ttp) cc_final: 0.7272 (pp-130) REVERT: B 76 LEU cc_start: 0.8930 (tp) cc_final: 0.8715 (tp) REVERT: B 77 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8177 (mp0) REVERT: B 301 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8685 (mt-10) REVERT: C 81 GLU cc_start: 0.8432 (mp0) cc_final: 0.8195 (mp0) REVERT: C 94 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8617 (tmm-80) REVERT: D 207 GLN cc_start: 0.8979 (mp10) cc_final: 0.8750 (mp10) REVERT: E 74 GLN cc_start: 0.8183 (mp10) cc_final: 0.7845 (mp-120) REVERT: A 285 MET cc_start: 0.1848 (mmm) cc_final: 0.1618 (mmm) REVERT: A 497 TYR cc_start: 0.8218 (t80) cc_final: 0.7872 (t80) REVERT: A 500 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7929 (tmmt) outliers start: 18 outliers final: 6 residues processed: 152 average time/residue: 1.2820 time to fit residues: 214.9331 Evaluate side-chains 130 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C 124 ASN C 128 ASN A 341 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.140850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079563 restraints weight = 69785.080| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.90 r_work: 0.2912 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14488 Z= 0.173 Angle : 0.535 7.337 19588 Z= 0.262 Chirality : 0.037 0.134 2252 Planarity : 0.004 0.051 2476 Dihedral : 10.097 165.038 1991 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.26 % Allowed : 11.06 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.20), residues: 1748 helix: 2.74 (0.16), residues: 1068 sheet: -0.16 (0.42), residues: 150 loop : 0.12 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 73 TYR 0.011 0.001 TYR D 286 PHE 0.014 0.001 PHE E 305 TRP 0.006 0.001 TRP C 256 HIS 0.007 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00398 (14488) covalent geometry : angle 0.53472 (19588) hydrogen bonds : bond 0.03909 ( 825) hydrogen bonds : angle 3.95223 ( 2397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8927 (tp) cc_final: 0.8709 (tp) REVERT: B 77 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8222 (mp0) REVERT: B 301 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8692 (mt-10) REVERT: C 81 GLU cc_start: 0.8481 (mp0) cc_final: 0.8221 (mp0) REVERT: C 94 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8624 (tmm-80) REVERT: E 74 GLN cc_start: 0.8252 (mp10) cc_final: 0.7990 (mp-120) REVERT: A 285 MET cc_start: 0.1869 (mmm) cc_final: 0.1590 (mmm) REVERT: A 497 TYR cc_start: 0.8286 (t80) cc_final: 0.7936 (t80) REVERT: A 500 LYS cc_start: 0.8254 (mmtm) cc_final: 0.7944 (tmmt) outliers start: 20 outliers final: 8 residues processed: 138 average time/residue: 1.2585 time to fit residues: 191.9519 Evaluate side-chains 134 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 111 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 147 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077710 restraints weight = 69732.014| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.93 r_work: 0.2881 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14488 Z= 0.196 Angle : 0.551 7.234 19588 Z= 0.271 Chirality : 0.038 0.159 2252 Planarity : 0.004 0.047 2476 Dihedral : 10.360 168.870 1991 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.20 % Allowed : 12.07 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.20), residues: 1748 helix: 2.64 (0.16), residues: 1069 sheet: -0.15 (0.41), residues: 150 loop : 0.08 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 73 TYR 0.026 0.001 TYR B 186 PHE 0.016 0.001 PHE E 305 TRP 0.006 0.001 TRP E 259 HIS 0.008 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00452 (14488) covalent geometry : angle 0.55136 (19588) hydrogen bonds : bond 0.04103 ( 825) hydrogen bonds : angle 4.00258 ( 2397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.8134 (ttp) cc_final: 0.7683 (pp-130) REVERT: B 76 LEU cc_start: 0.8879 (tp) cc_final: 0.8655 (tp) REVERT: B 77 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8198 (mp0) REVERT: B 119 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.5156 (mmm) REVERT: B 186 TYR cc_start: 0.8739 (p90) cc_final: 0.8495 (p90) REVERT: B 301 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: C 81 GLU cc_start: 0.8600 (mp0) cc_final: 0.8284 (mp0) REVERT: E 74 GLN cc_start: 0.8318 (mp10) cc_final: 0.8030 (mp-120) REVERT: A 285 MET cc_start: 0.2281 (mmm) cc_final: 0.1967 (mmm) REVERT: A 351 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7740 (m90) REVERT: A 497 TYR cc_start: 0.8309 (t80) cc_final: 0.7944 (t80) REVERT: A 500 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7961 (tmmt) outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 1.2600 time to fit residues: 200.6154 Evaluate side-chains 138 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 139 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.139225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077390 restraints weight = 69575.232| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.94 r_work: 0.2876 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14488 Z= 0.185 Angle : 0.544 7.151 19588 Z= 0.267 Chirality : 0.037 0.143 2252 Planarity : 0.004 0.044 2476 Dihedral : 10.275 170.752 1991 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.20 % Allowed : 12.33 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.20), residues: 1748 helix: 2.61 (0.16), residues: 1069 sheet: -0.29 (0.39), residues: 169 loop : 0.14 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 73 TYR 0.015 0.001 TYR B 186 PHE 0.014 0.001 PHE E 305 TRP 0.006 0.001 TRP C 256 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00428 (14488) covalent geometry : angle 0.54364 (19588) hydrogen bonds : bond 0.04013 ( 825) hydrogen bonds : angle 3.96352 ( 2397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8868 (tp) cc_final: 0.8648 (tp) REVERT: B 77 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8208 (mp0) REVERT: B 301 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: C 81 GLU cc_start: 0.8552 (mp0) cc_final: 0.8303 (mp0) REVERT: E 74 GLN cc_start: 0.8309 (mp10) cc_final: 0.8031 (mp-120) REVERT: A 285 MET cc_start: 0.2391 (mmm) cc_final: 0.2082 (mmm) REVERT: A 351 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7909 (m90) REVERT: A 500 LYS cc_start: 0.8365 (mmtm) cc_final: 0.8053 (tmmt) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 1.3227 time to fit residues: 208.5494 Evaluate side-chains 140 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 86 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 118 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 GLN A 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079536 restraints weight = 69372.571| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.99 r_work: 0.2905 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14488 Z= 0.112 Angle : 0.536 7.290 19588 Z= 0.260 Chirality : 0.036 0.142 2252 Planarity : 0.003 0.047 2476 Dihedral : 10.124 170.635 1991 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.82 % Allowed : 12.96 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.21), residues: 1748 helix: 2.74 (0.16), residues: 1069 sheet: -0.17 (0.41), residues: 149 loop : 0.13 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 73 TYR 0.010 0.001 TYR A 497 PHE 0.013 0.001 PHE C 111 TRP 0.008 0.001 TRP C 256 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00257 (14488) covalent geometry : angle 0.53551 (19588) hydrogen bonds : bond 0.03529 ( 825) hydrogen bonds : angle 3.85703 ( 2397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.8101 (ttp) cc_final: 0.7625 (pp-130) REVERT: B 76 LEU cc_start: 0.8886 (tp) cc_final: 0.8680 (tp) REVERT: B 77 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8256 (mp0) REVERT: B 186 TYR cc_start: 0.8690 (p90) cc_final: 0.8476 (p90) REVERT: B 301 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8658 (mt-10) REVERT: C 81 GLU cc_start: 0.8546 (mp0) cc_final: 0.8291 (mp0) REVERT: C 94 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8651 (tmm-80) REVERT: E 74 GLN cc_start: 0.8304 (mp10) cc_final: 0.8021 (mp-120) REVERT: A 285 MET cc_start: 0.2364 (mmm) cc_final: 0.2053 (mmm) REVERT: A 351 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7830 (m90) REVERT: A 500 LYS cc_start: 0.8334 (mmtm) cc_final: 0.8036 (tmmt) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 1.2773 time to fit residues: 197.5820 Evaluate side-chains 136 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.139162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077635 restraints weight = 69518.966| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.84 r_work: 0.2879 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14488 Z= 0.186 Angle : 0.556 9.075 19588 Z= 0.271 Chirality : 0.037 0.141 2252 Planarity : 0.004 0.054 2476 Dihedral : 10.165 176.062 1991 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.76 % Allowed : 12.96 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.20), residues: 1748 helix: 2.67 (0.16), residues: 1068 sheet: -0.24 (0.41), residues: 151 loop : 0.09 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 73 TYR 0.011 0.001 TYR D 286 PHE 0.013 0.001 PHE E 305 TRP 0.006 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00434 (14488) covalent geometry : angle 0.55572 (19588) hydrogen bonds : bond 0.03877 ( 825) hydrogen bonds : angle 3.91318 ( 2397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 LEU cc_start: 0.8856 (tp) cc_final: 0.8654 (tp) REVERT: B 77 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8200 (mp0) REVERT: B 186 TYR cc_start: 0.8742 (p90) cc_final: 0.8520 (p90) REVERT: B 301 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8682 (mt-10) REVERT: C 81 GLU cc_start: 0.8580 (mp0) cc_final: 0.8337 (mp0) REVERT: C 94 ARG cc_start: 0.9074 (ttp80) cc_final: 0.8665 (tmm-80) REVERT: E 74 GLN cc_start: 0.8298 (mp10) cc_final: 0.8024 (mp-120) REVERT: E 114 LYS cc_start: 0.9175 (mtpm) cc_final: 0.8965 (tmtt) REVERT: A 285 MET cc_start: 0.2207 (mmm) cc_final: 0.1885 (mmm) REVERT: A 351 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7920 (m90) REVERT: A 500 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8080 (tmmt) outliers start: 12 outliers final: 7 residues processed: 133 average time/residue: 1.2758 time to fit residues: 187.8069 Evaluate side-chains 132 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 170 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 HIS A 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.080446 restraints weight = 68957.839| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.86 r_work: 0.2918 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14488 Z= 0.106 Angle : 0.534 7.485 19588 Z= 0.258 Chirality : 0.037 0.149 2252 Planarity : 0.003 0.050 2476 Dihedral : 9.962 179.633 1991 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.51 % Allowed : 13.15 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.21), residues: 1748 helix: 2.77 (0.16), residues: 1074 sheet: -0.02 (0.43), residues: 143 loop : 0.11 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 73 TYR 0.009 0.001 TYR D 286 PHE 0.016 0.001 PHE D 203 TRP 0.009 0.001 TRP E 259 HIS 0.004 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00244 (14488) covalent geometry : angle 0.53381 (19588) hydrogen bonds : bond 0.03336 ( 825) hydrogen bonds : angle 3.77444 ( 2397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3496 Ramachandran restraints generated. 1748 Oldfield, 0 Emsley, 1748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 119 is missing expected H atoms. Skipping. Residue LEU 503 is missing expected H atoms. Skipping. Residue LEU 555 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 MET cc_start: 0.8154 (ttp) cc_final: 0.7706 (pp-130) REVERT: B 76 LEU cc_start: 0.8900 (tp) cc_final: 0.8682 (tp) REVERT: B 77 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8228 (mp0) REVERT: B 119 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.5407 (mmm) REVERT: B 301 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: C 81 GLU cc_start: 0.8577 (mp0) cc_final: 0.8339 (mp0) REVERT: E 74 GLN cc_start: 0.8286 (mp10) cc_final: 0.7999 (mp-120) REVERT: E 114 LYS cc_start: 0.9164 (mtpm) cc_final: 0.8964 (tmtt) REVERT: A 285 MET cc_start: 0.2365 (mmm) cc_final: 0.2151 (mmm) REVERT: A 351 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7859 (m90) REVERT: A 500 LYS cc_start: 0.8337 (mmtm) cc_final: 0.8064 (tmmt) outliers start: 8 outliers final: 6 residues processed: 132 average time/residue: 1.2904 time to fit residues: 188.8359 Evaluate side-chains 133 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.139890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078520 restraints weight = 69448.362| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.89 r_work: 0.2906 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14488 Z= 0.143 Angle : 0.538 7.425 19588 Z= 0.262 Chirality : 0.037 0.147 2252 Planarity : 0.003 0.051 2476 Dihedral : 9.909 174.789 1991 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.70 % Allowed : 13.02 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.21), residues: 1748 helix: 2.76 (0.16), residues: 1075 sheet: -0.08 (0.42), residues: 144 loop : 0.12 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 73 TYR 0.013 0.001 TYR B 186 PHE 0.013 0.001 PHE D 203 TRP 0.006 0.001 TRP E 259 HIS 0.005 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00332 (14488) covalent geometry : angle 0.53801 (19588) hydrogen bonds : bond 0.03552 ( 825) hydrogen bonds : angle 3.80399 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13304.90 seconds wall clock time: 224 minutes 43.35 seconds (13483.35 seconds total)