Starting phenix.real_space_refine on Fri Sep 11 03:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.map" model { file = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i2i_0331/09_2026/6i2i_0331.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 4303 2.51 5 N 1157 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6830 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.45, per 1000 atoms: 0.21 Number of scatterers: 6830 At special positions: 0 Unit cell: (75.35, 71.24, 115.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1316 8.00 N 1157 7.00 C 4303 6.00 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: 0.52 Conformation dependent library (CDL) restraints added in 383.5 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 47.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.648A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 29 " --> pdb=" O CYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.888A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.140A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.890A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 127 removed outlier: 4.222A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 4.280A pdb=" N GLY A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 149' Processing helix chain 'A' and resid 149 through 161 removed outlier: 4.048A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.595A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.812A pdb=" N TYR A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 211' Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 239 removed outlier: 3.693A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.848A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.595A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 297' Processing helix chain 'A' and resid 324 through 338 removed outlier: 4.229A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.605A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.900A pdb=" N TRP A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.658A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 29 removed outlier: 3.771A pdb=" N ALA B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 4.423A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.551A pdb=" N VAL B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.405A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 126 removed outlier: 4.309A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.967A pdb=" N SER B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 4.050A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 196 removed outlier: 4.107A pdb=" N THR B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.887A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 4.111A pdb=" N HIS B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.797A pdb=" N ASN B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.779A pdb=" N GLN B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.776A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.776A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.619A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.795A pdb=" N GLY B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 433 removed outlier: 3.514A pdb=" N GLU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 9.087A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 168 " --> pdb=" O CYS A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 9.087A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 8.693A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 165 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 135 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 139 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 171 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 202 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 356 removed outlier: 3.748A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1172 1.32 - 1.44: 1885 1.44 - 1.56: 3844 1.56 - 1.69: 15 1.69 - 1.81: 74 Bond restraints: 6990 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.585 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" O5' G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.656 1.574 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.463 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C01 TA1 B 503 " pdb=" C45 TA1 B 503 " ideal model delta sigma weight residual 1.553 1.615 -0.062 2.00e-02 2.50e+03 9.71e+00 bond pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.850 1.796 0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 6985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 9353 3.46 - 6.92: 129 6.92 - 10.38: 20 10.38 - 13.84: 8 13.84 - 17.30: 2 Bond angle restraints: 9512 Sorted by residual: angle pdb=" C14 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" O04 TA1 B 503 " ideal model delta sigma weight residual 119.42 102.12 17.30 3.00e+00 1.11e-01 3.33e+01 angle pdb=" C10 TA1 B 503 " pdb=" C18 TA1 B 503 " pdb=" C20 TA1 B 503 " ideal model delta sigma weight residual 104.78 120.74 -15.96 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O2A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O5' G2P B 501 " ideal model delta sigma weight residual 107.71 121.30 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" O2' G2P B 501 " ideal model delta sigma weight residual 116.29 103.49 12.80 3.00e+00 1.11e-01 1.82e+01 angle pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " pdb=" O2A G2P B 501 " ideal model delta sigma weight residual 117.48 105.46 12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 9507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.48: 4059 33.48 - 66.97: 38 66.97 - 100.45: 6 100.45 - 133.93: 1 133.93 - 167.41: 3 Dihedral angle restraints: 4107 sinusoidal: 1636 harmonic: 2471 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.32 -167.41 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -53.53 158.12 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 131.59 142.53 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 790 0.072 - 0.145: 226 0.145 - 0.217: 21 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1042 Sorted by residual: chirality pdb=" C10 TA1 B 503 " pdb=" C02 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" C18 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.54 2.18 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C26 TA1 B 503 " pdb=" C25 TA1 B 503 " pdb=" C43 TA1 B 503 " pdb=" O11 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1039 not shown) Planarity restraints: 1231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 TA1 B 503 " 0.004 2.00e-02 2.50e+03 3.19e-02 1.79e+01 pdb=" C04 TA1 B 503 " 0.046 2.00e-02 2.50e+03 pdb=" C05 TA1 B 503 " -0.057 2.00e-02 2.50e+03 pdb=" C06 TA1 B 503 " 0.021 2.00e-02 2.50e+03 pdb=" C07 TA1 B 503 " 0.023 2.00e-02 2.50e+03 pdb=" C08 TA1 B 503 " -0.026 2.00e-02 2.50e+03 pdb=" C09 TA1 B 503 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 TA1 B 503 " 0.053 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C04 TA1 B 503 " -0.015 2.00e-02 2.50e+03 pdb=" O02 TA1 B 503 " -0.017 2.00e-02 2.50e+03 pdb=" O03 TA1 B 503 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 32 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.038 5.00e-02 4.00e+02 ... (remaining 1228 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 96 2.59 - 3.17: 5570 3.17 - 3.75: 10399 3.75 - 4.32: 14846 4.32 - 4.90: 23677 Nonbonded interactions: 54588 Sorted by model distance: nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 2.019 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.064 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN B 101 " pdb=" O3G G2P B 501 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B 27 " pdb=" OG SER B 236 " model vdw 2.275 3.040 ... (remaining 54583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.009 0.131 6990 Z= 0.402 Angle : 1.175 17.302 9512 Z= 0.583 Chirality : 0.065 0.361 1042 Planarity : 0.008 0.069 1231 Dihedral : 12.379 167.414 2523 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.28 % Allowed : 2.21 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -5.22 (0.21), residues: 850 helix: -4.20 (0.14), residues: 330 sheet: -3.16 (0.39), residues: 132 loop : -2.73 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.036 0.004 TYR B 312 PHE 0.028 0.004 PHE A 351 TRP 0.026 0.004 TRP A 346 HIS 0.014 0.003 HIS B 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.40 ( 6990) covalent geometry : angle 1.17452 / 0.58 ( 9512) hydrogen bonds : bond 0.30038 / 20.89 ( 176) hydrogen bonds : angle 10.20210 / 7.37 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7601 (tt0) REVERT: A 176 GLN cc_start: 0.8097 (mm110) cc_final: 0.7790 (mm110) REVERT: A 302 MET cc_start: 0.8358 (mmp) cc_final: 0.7880 (mmm) REVERT: A 313 MET cc_start: 0.7282 (mtt) cc_final: 0.7030 (mtp) REVERT: A 388 TRP cc_start: 0.5549 (m-10) cc_final: 0.5184 (m-10) REVERT: A 397 LEU cc_start: 0.8594 (mt) cc_final: 0.8384 (mt) REVERT: B 1 MET cc_start: 0.6986 (mmt) cc_final: 0.6196 (tmm) REVERT: B 6 HIS cc_start: 0.7620 (t70) cc_final: 0.7091 (t-170) REVERT: B 37 HIS cc_start: 0.7721 (m90) cc_final: 0.7375 (m170) REVERT: B 110 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7779 (tt0) REVERT: B 247 GLN cc_start: 0.8092 (mt0) cc_final: 0.7853 (tt0) REVERT: B 282 GLN cc_start: 0.8400 (mm110) cc_final: 0.7598 (mp10) REVERT: B 300 ASN cc_start: 0.8709 (t160) cc_final: 0.8207 (m-40) REVERT: B 325 MET cc_start: 0.8388 (mmm) cc_final: 0.8093 (tpt) REVERT: B 330 GLU cc_start: 0.8808 (tt0) cc_final: 0.8487 (tp30) REVERT: B 333 LEU cc_start: 0.9134 (tp) cc_final: 0.8767 (tp) REVERT: B 417 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7580 (tp30) outliers start: 2 outliers final: 1 residues processed: 220 average time/residue: 0.0794 time to fit residues: 22.9439 Evaluate side-chains 145 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 88 HIS A 256 GLN A 258 ASN A 372 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 192 HIS B 249 ASN B 258 ASN ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.127138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106210 restraints weight = 12170.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110059 restraints weight = 6443.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.112751 restraints weight = 4191.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.114630 restraints weight = 3082.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116050 restraints weight = 2451.752| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6990 Z= 0.190 Angle : 0.714 7.838 9512 Z= 0.357 Chirality : 0.047 0.213 1042 Planarity : 0.006 0.063 1231 Dihedral : 12.118 176.583 955 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.76 % Allowed : 10.76 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -4.04 (0.25), residues: 850 helix: -2.97 (0.21), residues: 352 sheet: -2.59 (0.41), residues: 136 loop : -2.19 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 284 TYR 0.021 0.002 TYR B 312 PHE 0.020 0.002 PHE A 395 TRP 0.013 0.002 TRP A 346 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 6990) covalent geometry : angle 0.71396 / 0.36 ( 9512) hydrogen bonds : bond 0.05438 / 3.67 ( 176) hydrogen bonds : angle 6.17537 / 4.52 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6961 (mt) REVERT: A 176 GLN cc_start: 0.8220 (mm110) cc_final: 0.7900 (mm110) REVERT: A 267 PHE cc_start: 0.8603 (m-80) cc_final: 0.8167 (m-80) REVERT: A 280 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7432 (mtpp) REVERT: A 313 MET cc_start: 0.7409 (mtt) cc_final: 0.7176 (mtp) REVERT: A 413 MET cc_start: 0.6496 (tpt) cc_final: 0.5898 (mtp) REVERT: B 26 ASP cc_start: 0.8106 (m-30) cc_final: 0.7608 (m-30) REVERT: B 48 ARG cc_start: 0.7506 (mpt180) cc_final: 0.7046 (tpp80) REVERT: B 110 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7060 (tt0) REVERT: B 113 GLU cc_start: 0.7706 (mp0) cc_final: 0.7278 (mp0) REVERT: B 124 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8240 (tttt) REVERT: B 136 GLN cc_start: 0.8076 (mt0) cc_final: 0.7707 (mt0) REVERT: B 163 ASP cc_start: 0.7818 (p0) cc_final: 0.7529 (p0) REVERT: B 166 MET cc_start: 0.7671 (mpp) cc_final: 0.7243 (mpt) REVERT: B 167 ASN cc_start: 0.7057 (m-40) cc_final: 0.6536 (m110) REVERT: B 243 ARG cc_start: 0.8984 (mtm110) cc_final: 0.7613 (mtm180) REVERT: B 293 GLN cc_start: 0.8161 (tp40) cc_final: 0.7923 (tp40) REVERT: B 300 ASN cc_start: 0.8670 (t160) cc_final: 0.8256 (m-40) REVERT: B 372 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8104 (ttpp) REVERT: B 417 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7531 (tp30) outliers start: 20 outliers final: 15 residues processed: 181 average time/residue: 0.0872 time to fit residues: 20.9211 Evaluate side-chains 150 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 406 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 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 = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106376 restraints weight = 12021.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110345 restraints weight = 6224.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.113080 restraints weight = 3991.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.114991 restraints weight = 2905.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.116296 restraints weight = 2288.345| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6990 Z= 0.151 Angle : 0.640 9.242 9512 Z= 0.315 Chirality : 0.046 0.185 1042 Planarity : 0.005 0.062 1231 Dihedral : 11.619 178.461 955 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.76 % Allowed : 13.52 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.49 (0.26), residues: 850 helix: -2.39 (0.23), residues: 369 sheet: -2.28 (0.43), residues: 134 loop : -1.99 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.019 0.001 TYR B 312 PHE 0.022 0.002 PHE B 395 TRP 0.013 0.002 TRP A 21 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6990) covalent geometry : angle 0.64019 / 0.31 ( 9512) hydrogen bonds : bond 0.04234 / 2.88 ( 176) hydrogen bonds : angle 5.45153 / 4.00 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7416 (mtpp) REVERT: A 302 MET cc_start: 0.8253 (mmp) cc_final: 0.7937 (mmm) REVERT: A 313 MET cc_start: 0.7366 (mtt) cc_final: 0.7052 (mtp) REVERT: A 413 MET cc_start: 0.6698 (tpt) cc_final: 0.6036 (mtp) REVERT: B 26 ASP cc_start: 0.7942 (m-30) cc_final: 0.7578 (m-30) REVERT: B 110 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7245 (tt0) REVERT: B 124 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8252 (tttt) REVERT: B 163 ASP cc_start: 0.7802 (p0) cc_final: 0.7487 (p0) REVERT: B 167 ASN cc_start: 0.7240 (m-40) cc_final: 0.6712 (m110) REVERT: B 243 ARG cc_start: 0.8906 (mtm110) cc_final: 0.7686 (mtm180) REVERT: B 372 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8137 (ttpp) REVERT: B 417 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7436 (tp30) outliers start: 20 outliers final: 13 residues processed: 161 average time/residue: 0.0877 time to fit residues: 18.8361 Evaluate side-chains 149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.103494 restraints weight = 12345.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.107424 restraints weight = 6364.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110167 restraints weight = 4101.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.111995 restraints weight = 2989.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.113389 restraints weight = 2375.052| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6990 Z= 0.202 Angle : 0.666 8.698 9512 Z= 0.333 Chirality : 0.048 0.176 1042 Planarity : 0.005 0.063 1231 Dihedral : 11.572 176.809 955 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.59 % Allowed : 14.76 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.13 (0.27), residues: 850 helix: -2.08 (0.24), residues: 361 sheet: -2.35 (0.41), residues: 143 loop : -1.69 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 156 TYR 0.021 0.002 TYR B 312 PHE 0.022 0.002 PHE A 395 TRP 0.016 0.002 TRP A 388 HIS 0.009 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 6990) covalent geometry : angle 0.66621 / 0.33 ( 9512) hydrogen bonds : bond 0.04218 / 2.82 ( 176) hydrogen bonds : angle 5.41255 / 3.96 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6831 (tptt) REVERT: A 313 MET cc_start: 0.7335 (mtt) cc_final: 0.7051 (mtp) REVERT: A 413 MET cc_start: 0.6620 (tpt) cc_final: 0.6023 (mtp) REVERT: B 26 ASP cc_start: 0.7944 (m-30) cc_final: 0.7502 (m-30) REVERT: B 110 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7290 (tt0) REVERT: B 124 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8207 (tttt) REVERT: B 163 ASP cc_start: 0.7813 (p0) cc_final: 0.7509 (p0) REVERT: B 167 ASN cc_start: 0.7468 (m-40) cc_final: 0.6706 (m-40) REVERT: B 330 GLU cc_start: 0.7822 (tp30) cc_final: 0.7578 (tp30) REVERT: B 372 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8157 (ttpp) REVERT: B 417 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7459 (tp30) outliers start: 26 outliers final: 21 residues processed: 151 average time/residue: 0.0784 time to fit residues: 16.1181 Evaluate side-chains 153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 197 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.129723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108922 restraints weight = 12128.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113210 restraints weight = 6122.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.116096 restraints weight = 3870.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118026 restraints weight = 2795.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.119488 restraints weight = 2212.655| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6990 Z= 0.097 Angle : 0.580 9.291 9512 Z= 0.277 Chirality : 0.044 0.177 1042 Planarity : 0.004 0.061 1231 Dihedral : 11.126 179.043 955 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 15.17 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.43 (0.27), residues: 850 helix: -1.44 (0.26), residues: 354 sheet: -1.92 (0.42), residues: 139 loop : -1.46 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 390 TYR 0.010 0.001 TYR B 312 PHE 0.025 0.001 PHE A 395 TRP 0.016 0.001 TRP A 388 HIS 0.007 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6990) covalent geometry : angle 0.58034 / 0.28 ( 9512) hydrogen bonds : bond 0.03184 / 2.11 ( 176) hydrogen bonds : angle 4.66191 / 3.38 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.270 Fit side-chains REVERT: A 217 LEU cc_start: 0.8505 (tp) cc_final: 0.8277 (tp) REVERT: A 271 THR cc_start: 0.8026 (t) cc_final: 0.7527 (m) REVERT: A 280 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7285 (mtpp) REVERT: A 302 MET cc_start: 0.8350 (mmp) cc_final: 0.8136 (mmt) REVERT: A 313 MET cc_start: 0.7326 (mtt) cc_final: 0.6998 (mtp) REVERT: A 413 MET cc_start: 0.6650 (tpt) cc_final: 0.5922 (mtp) REVERT: B 26 ASP cc_start: 0.7907 (m-30) cc_final: 0.7465 (m-30) REVERT: B 110 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7361 (tt0) REVERT: B 124 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8122 (tttt) REVERT: B 163 ASP cc_start: 0.7862 (p0) cc_final: 0.7463 (p0) REVERT: B 166 MET cc_start: 0.7862 (mpp) cc_final: 0.7608 (mpt) REVERT: B 167 ASN cc_start: 0.7385 (m-40) cc_final: 0.6630 (m-40) REVERT: B 243 ARG cc_start: 0.8806 (mtm110) cc_final: 0.7708 (mtm180) REVERT: B 302 MET cc_start: 0.7647 (mtt) cc_final: 0.7367 (mmm) REVERT: B 372 LYS cc_start: 0.8557 (ttpp) cc_final: 0.7992 (ttpp) REVERT: B 390 ARG cc_start: 0.8245 (mtm180) cc_final: 0.7953 (ptp-170) REVERT: B 391 ILE cc_start: 0.7578 (mm) cc_final: 0.7266 (mt) REVERT: B 417 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7329 (tp30) outliers start: 16 outliers final: 11 residues processed: 156 average time/residue: 0.0805 time to fit residues: 17.0767 Evaluate side-chains 142 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 chunk 44 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.126543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106103 restraints weight = 12177.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110139 restraints weight = 6135.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112938 restraints weight = 3905.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114839 restraints weight = 2834.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.116152 restraints weight = 2233.346| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6990 Z= 0.143 Angle : 0.606 9.018 9512 Z= 0.294 Chirality : 0.046 0.211 1042 Planarity : 0.004 0.062 1231 Dihedral : 11.222 179.479 955 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.59 % Allowed : 15.17 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.27 (0.28), residues: 850 helix: -1.29 (0.26), residues: 369 sheet: -1.83 (0.43), residues: 140 loop : -1.36 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 322 TYR 0.015 0.001 TYR B 312 PHE 0.027 0.002 PHE A 255 TRP 0.016 0.002 TRP A 388 HIS 0.008 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6990) covalent geometry : angle 0.60587 / 0.29 ( 9512) hydrogen bonds : bond 0.03542 / 2.40 ( 176) hydrogen bonds : angle 4.74716 / 3.47 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 210 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 280 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7248 (mtpp) REVERT: A 313 MET cc_start: 0.7289 (mtt) cc_final: 0.7049 (mtp) REVERT: A 413 MET cc_start: 0.6788 (tpt) cc_final: 0.6028 (mtp) REVERT: B 26 ASP cc_start: 0.7940 (m-30) cc_final: 0.7490 (m-30) REVERT: B 110 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7542 (tt0) REVERT: B 124 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8153 (tttt) REVERT: B 163 ASP cc_start: 0.7778 (p0) cc_final: 0.7447 (p0) REVERT: B 167 ASN cc_start: 0.7349 (m-40) cc_final: 0.6629 (m-40) REVERT: B 372 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8037 (ttpp) REVERT: B 391 ILE cc_start: 0.7579 (mm) cc_final: 0.7188 (mt) REVERT: B 395 PHE cc_start: 0.7243 (t80) cc_final: 0.6890 (t80) REVERT: B 417 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7376 (tp30) outliers start: 26 outliers final: 24 residues processed: 145 average time/residue: 0.0802 time to fit residues: 15.9553 Evaluate side-chains 153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 34 optimal weight: 0.0000 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 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 = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107342 restraints weight = 11893.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111561 restraints weight = 6156.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.114394 restraints weight = 3959.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.116405 restraints weight = 2912.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117811 restraints weight = 2305.406| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6990 Z= 0.141 Angle : 0.607 8.892 9512 Z= 0.293 Chirality : 0.046 0.188 1042 Planarity : 0.004 0.060 1231 Dihedral : 11.190 179.803 955 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.86 % Allowed : 14.48 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.08 (0.29), residues: 850 helix: -1.09 (0.27), residues: 366 sheet: -1.68 (0.44), residues: 142 loop : -1.35 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.014 0.001 TYR B 312 PHE 0.025 0.002 PHE A 395 TRP 0.018 0.002 TRP A 388 HIS 0.006 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6990) covalent geometry : angle 0.60660 / 0.29 ( 9512) hydrogen bonds : bond 0.03505 / 2.37 ( 176) hydrogen bonds : angle 4.69398 / 3.43 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 210 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: A 280 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7214 (mtpp) REVERT: A 302 MET cc_start: 0.8401 (mmp) cc_final: 0.7629 (mmm) REVERT: A 313 MET cc_start: 0.7226 (mtt) cc_final: 0.6961 (mtp) REVERT: A 413 MET cc_start: 0.6653 (tpt) cc_final: 0.6018 (mtp) REVERT: B 19 LYS cc_start: 0.8327 (tptt) cc_final: 0.7977 (tppt) REVERT: B 26 ASP cc_start: 0.7918 (m-30) cc_final: 0.7459 (m-30) REVERT: B 124 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8152 (tttt) REVERT: B 163 ASP cc_start: 0.7816 (p0) cc_final: 0.7476 (p0) REVERT: B 167 ASN cc_start: 0.7624 (m-40) cc_final: 0.6814 (m-40) REVERT: B 372 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8036 (ttpp) REVERT: B 391 ILE cc_start: 0.7555 (mm) cc_final: 0.7164 (mt) REVERT: B 395 PHE cc_start: 0.7243 (t80) cc_final: 0.6867 (t80) REVERT: B 417 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7422 (tp30) outliers start: 28 outliers final: 23 residues processed: 149 average time/residue: 0.0781 time to fit residues: 15.9503 Evaluate side-chains 148 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 79 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108609 restraints weight = 11931.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112964 restraints weight = 6056.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.115945 restraints weight = 3840.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.118006 restraints weight = 2779.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.119285 restraints weight = 2186.389| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6990 Z= 0.112 Angle : 0.595 8.814 9512 Z= 0.286 Chirality : 0.045 0.194 1042 Planarity : 0.004 0.062 1231 Dihedral : 11.027 178.734 955 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.72 % Allowed : 15.45 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.29), residues: 850 helix: -0.90 (0.27), residues: 367 sheet: -1.44 (0.45), residues: 140 loop : -1.25 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 322 TYR 0.013 0.001 TYR A 172 PHE 0.026 0.001 PHE A 395 TRP 0.015 0.002 TRP A 388 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6990) covalent geometry : angle 0.59486 / 0.29 ( 9512) hydrogen bonds : bond 0.03212 / 2.15 ( 176) hydrogen bonds : angle 4.55523 / 3.30 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8437 (tt0) cc_final: 0.7802 (pt0) REVERT: A 155 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 210 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: A 217 LEU cc_start: 0.8612 (tp) cc_final: 0.8361 (tp) REVERT: A 280 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7142 (mtpp) REVERT: A 313 MET cc_start: 0.7179 (mtt) cc_final: 0.6926 (mtp) REVERT: A 377 MET cc_start: 0.8163 (ttp) cc_final: 0.7827 (tmm) REVERT: A 393 HIS cc_start: 0.7340 (t-90) cc_final: 0.6751 (t-90) REVERT: A 413 MET cc_start: 0.6761 (tpt) cc_final: 0.5991 (mtp) REVERT: B 19 LYS cc_start: 0.8240 (tptt) cc_final: 0.7910 (tppt) REVERT: B 26 ASP cc_start: 0.7894 (m-30) cc_final: 0.7458 (m-30) REVERT: B 124 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8123 (tttm) REVERT: B 163 ASP cc_start: 0.7959 (p0) cc_final: 0.7534 (p0) REVERT: B 167 ASN cc_start: 0.7593 (m-40) cc_final: 0.6827 (m-40) REVERT: B 269 MET cc_start: 0.7929 (ptp) cc_final: 0.7534 (ptp) REVERT: B 372 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8290 (ttmm) REVERT: B 391 ILE cc_start: 0.7516 (mm) cc_final: 0.7102 (mt) REVERT: B 395 PHE cc_start: 0.7237 (t80) cc_final: 0.6862 (t80) REVERT: B 417 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7456 (tp30) outliers start: 27 outliers final: 24 residues processed: 148 average time/residue: 0.0786 time to fit residues: 15.9654 Evaluate side-chains 150 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 228 ASN B 28 HIS B 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.132969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112038 restraints weight = 11964.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.116302 restraints weight = 6054.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.119233 restraints weight = 3812.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.121238 restraints weight = 2737.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.122670 restraints weight = 2133.832| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6990 Z= 0.092 Angle : 0.586 8.265 9512 Z= 0.279 Chirality : 0.043 0.204 1042 Planarity : 0.004 0.064 1231 Dihedral : 10.592 171.581 955 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.62 % Allowed : 17.10 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.29), residues: 850 helix: -0.52 (0.28), residues: 357 sheet: -1.16 (0.45), residues: 136 loop : -1.16 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 322 TYR 0.008 0.001 TYR A 172 PHE 0.026 0.001 PHE A 395 TRP 0.014 0.001 TRP A 388 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 6990) covalent geometry : angle 0.58577 / 0.28 ( 9512) hydrogen bonds : bond 0.02860 / 1.94 ( 176) hydrogen bonds : angle 4.26910 / 3.04 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 302 MET cc_start: 0.8013 (mmp) cc_final: 0.7786 (mmt) REVERT: A 372 GLN cc_start: 0.7290 (mt0) cc_final: 0.6765 (mm-40) REVERT: A 393 HIS cc_start: 0.7287 (t-90) cc_final: 0.6731 (t-90) REVERT: A 413 MET cc_start: 0.6657 (tpt) cc_final: 0.5792 (mtp) REVERT: B 19 LYS cc_start: 0.8137 (tptt) cc_final: 0.7804 (tppt) REVERT: B 26 ASP cc_start: 0.7857 (m-30) cc_final: 0.7402 (m-30) REVERT: B 124 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8231 (tmmt) REVERT: B 163 ASP cc_start: 0.8002 (p0) cc_final: 0.7536 (p0) REVERT: B 167 ASN cc_start: 0.7570 (m-40) cc_final: 0.6828 (m-40) REVERT: B 243 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8567 (mtm180) REVERT: B 325 MET cc_start: 0.7806 (mmm) cc_final: 0.7509 (mmm) REVERT: B 372 LYS cc_start: 0.8557 (ttpp) cc_final: 0.7920 (ttpp) REVERT: B 391 ILE cc_start: 0.7386 (mm) cc_final: 0.6922 (mt) REVERT: B 395 PHE cc_start: 0.7379 (t80) cc_final: 0.7123 (t80) REVERT: B 417 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7318 (tp30) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.0826 time to fit residues: 16.6660 Evaluate side-chains 144 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 0.0020 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.127065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.106305 restraints weight = 11997.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110480 restraints weight = 6098.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.113313 restraints weight = 3880.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.115220 restraints weight = 2814.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.116499 restraints weight = 2226.412| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6990 Z= 0.159 Angle : 0.642 8.099 9512 Z= 0.312 Chirality : 0.046 0.203 1042 Planarity : 0.005 0.071 1231 Dihedral : 10.998 178.733 955 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.62 % Allowed : 17.66 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.29), residues: 850 helix: -0.64 (0.28), residues: 361 sheet: -1.28 (0.45), residues: 145 loop : -1.15 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 322 TYR 0.018 0.002 TYR A 172 PHE 0.025 0.002 PHE A 395 TRP 0.012 0.002 TRP A 346 HIS 0.005 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6990) covalent geometry : angle 0.64152 / 0.31 ( 9512) hydrogen bonds : bond 0.03477 / 2.33 ( 176) hydrogen bonds : angle 4.67655 / 3.39 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8153 (tmtt) REVERT: A 155 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 210 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: A 302 MET cc_start: 0.8395 (mmp) cc_final: 0.7652 (mmm) REVERT: A 372 GLN cc_start: 0.7392 (mt0) cc_final: 0.6894 (mm-40) REVERT: A 393 HIS cc_start: 0.7307 (t-90) cc_final: 0.6743 (t-90) REVERT: A 413 MET cc_start: 0.6709 (tpt) cc_final: 0.5902 (mtp) REVERT: B 19 LYS cc_start: 0.8285 (tptt) cc_final: 0.7952 (tppt) REVERT: B 26 ASP cc_start: 0.7930 (m-30) cc_final: 0.7451 (m-30) REVERT: B 163 ASP cc_start: 0.7864 (p0) cc_final: 0.7524 (p0) REVERT: B 167 ASN cc_start: 0.7728 (m-40) cc_final: 0.7009 (m-40) REVERT: B 227 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 372 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8283 (ttmm) REVERT: B 395 PHE cc_start: 0.7079 (t80) cc_final: 0.6767 (t80) REVERT: B 417 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7391 (tp30) outliers start: 19 outliers final: 17 residues processed: 139 average time/residue: 0.0779 time to fit residues: 14.8238 Evaluate side-chains 140 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 56 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105803 restraints weight = 11849.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.110015 restraints weight = 6133.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.112817 restraints weight = 3929.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114815 restraints weight = 2881.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116244 restraints weight = 2286.225| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6990 Z= 0.183 Angle : 0.664 8.277 9512 Z= 0.327 Chirality : 0.048 0.202 1042 Planarity : 0.005 0.068 1231 Dihedral : 11.181 179.185 955 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.90 % Allowed : 17.66 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.29), residues: 850 helix: -0.90 (0.27), residues: 368 sheet: -1.44 (0.45), residues: 145 loop : -1.16 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 84 TYR 0.016 0.002 TYR A 172 PHE 0.030 0.002 PHE A 395 TRP 0.014 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 6990) covalent geometry : angle 0.66354 / 0.33 ( 9512) hydrogen bonds : bond 0.03660 / 2.45 ( 176) hydrogen bonds : angle 4.94839 / 3.62 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.38 seconds wall clock time: 21 minutes 21.96 seconds (1281.96 seconds total)