Starting phenix.real_space_refine on Mon Apr 28 07:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_0331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_0331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_0331.map" model { file = "/net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_0331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i2i_0331/04_2025/6i2i_0331.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.20, per 1000 atoms: 0.61 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: 2.13 Conformation dependent library (CDL) restraints added in 931.1 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: 0.65 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: 1.78 Time building geometry restraints manager: 2.28 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: 4147 33.48 - 66.97: 57 66.97 - 100.45: 12 100.45 - 133.93: 13 133.93 - 167.41: 7 Dihedral angle restraints: 4236 sinusoidal: 1765 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 4233 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.310 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 16.637 167.414 2652 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.004 TRP A 346 HIS 0.014 0.003 HIS B 229 PHE 0.028 0.004 PHE A 351 TYR 0.036 0.004 TYR B 312 ARG 0.009 0.001 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.30038 ( 176) hydrogen bonds : angle 10.20210 ( 495) covalent geometry : bond 0.00899 ( 6990) covalent geometry : angle 1.17452 ( 9512) *********************** 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 : 0.713 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: 0.8098 (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: 0.7031 (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: 0.8389 (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: 0.2162 time to fit residues: 61.1171 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 : 0.762 ------------------------------------------------------------------------------- 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 71 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 88 HIS A 256 GLN A 258 ASN A 372 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 300 ASN B 337 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.128177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.107131 restraints weight = 11880.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.111062 restraints weight = 6303.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.113770 restraints weight = 4104.537| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2924 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= 0.174 Angle : 0.707 9.579 9512 Z= 0.350 Chirality : 0.049 0.455 1042 Planarity : 0.006 0.062 1231 Dihedral : 14.296 177.522 1084 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.76 % Allowed : 10.34 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.25), residues: 850 helix: -2.97 (0.21), residues: 358 sheet: -2.59 (0.41), residues: 139 loop : -2.11 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.005 0.001 HIS A 8 PHE 0.021 0.002 PHE A 395 TYR 0.021 0.002 TYR B 312 ARG 0.005 0.001 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 176) hydrogen bonds : angle 5.97554 ( 495) covalent geometry : bond 0.00388 ( 6990) covalent geometry : angle 0.70714 ( 9512) *********************** 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 196 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6979 (mt) REVERT: A 176 GLN cc_start: 0.8228 (mm110) cc_final: 0.7901 (mm110) REVERT: A 280 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7417 (mtpp) REVERT: A 313 MET cc_start: 0.7386 (mtt) cc_final: 0.7139 (mtp) REVERT: A 378 LEU cc_start: 0.9101 (mp) cc_final: 0.8880 (mp) REVERT: A 413 MET cc_start: 0.6758 (tpt) cc_final: 0.5906 (mtp) REVERT: B 6 HIS cc_start: 0.7156 (t70) cc_final: 0.6862 (t-170) REVERT: B 26 ASP cc_start: 0.8123 (m-30) cc_final: 0.7622 (m-30) REVERT: B 48 ARG cc_start: 0.7484 (mpt180) cc_final: 0.7081 (tpp80) REVERT: B 110 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7043 (tt0) REVERT: B 113 GLU cc_start: 0.7742 (mp0) cc_final: 0.7306 (mp0) REVERT: B 124 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8168 (tttt) REVERT: B 136 GLN cc_start: 0.8158 (mt0) cc_final: 0.7779 (mt0) REVERT: B 163 ASP cc_start: 0.7967 (p0) cc_final: 0.7669 (p0) REVERT: B 166 MET cc_start: 0.7634 (mpp) cc_final: 0.7207 (mpt) REVERT: B 167 ASN cc_start: 0.6947 (m-40) cc_final: 0.6395 (m110) REVERT: B 243 ARG cc_start: 0.8977 (mtm110) cc_final: 0.7790 (mtm180) REVERT: B 293 GLN cc_start: 0.8199 (tp40) cc_final: 0.7949 (tp40) REVERT: B 372 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8110 (ttpp) REVERT: B 417 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7499 (tp30) outliers start: 20 outliers final: 15 residues processed: 185 average time/residue: 0.2042 time to fit residues: 49.0670 Evaluate side-chains 154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 39 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 197 HIS ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN B 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105907 restraints weight = 12218.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.109931 restraints weight = 6487.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112728 restraints weight = 4191.535| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3600 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= 0.140 Angle : 0.614 9.230 9512 Z= 0.304 Chirality : 0.046 0.271 1042 Planarity : 0.005 0.062 1231 Dihedral : 12.805 178.582 1084 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 12.83 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.26), residues: 850 helix: -2.35 (0.23), residues: 369 sheet: -2.23 (0.43), residues: 136 loop : -1.93 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS A 8 PHE 0.023 0.002 PHE B 395 TYR 0.018 0.001 TYR B 312 ARG 0.003 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 176) hydrogen bonds : angle 5.33585 ( 495) covalent geometry : bond 0.00319 ( 6990) covalent geometry : angle 0.61415 ( 9512) *********************** 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: 23 poor density : 147 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6913 (mt) REVERT: A 280 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7425 (mtpp) REVERT: A 313 MET cc_start: 0.7378 (mtt) cc_final: 0.7077 (mtp) REVERT: A 378 LEU cc_start: 0.9039 (mp) cc_final: 0.8838 (mp) REVERT: A 413 MET cc_start: 0.6779 (tpt) cc_final: 0.5996 (mtp) REVERT: B 26 ASP cc_start: 0.7937 (m-30) cc_final: 0.7469 (m-30) REVERT: B 110 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7244 (tt0) REVERT: B 124 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8198 (tttt) REVERT: B 136 GLN cc_start: 0.7833 (mt0) cc_final: 0.7502 (mt0) REVERT: B 163 ASP cc_start: 0.7814 (p0) cc_final: 0.7514 (p0) REVERT: B 167 ASN cc_start: 0.7173 (m-40) cc_final: 0.6572 (m-40) REVERT: B 243 ARG cc_start: 0.8879 (mtm110) cc_final: 0.7743 (mtm180) REVERT: B 372 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8154 (ttpp) REVERT: B 417 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7411 (tp30) outliers start: 23 outliers final: 15 residues processed: 160 average time/residue: 0.1937 time to fit residues: 40.6462 Evaluate side-chains 148 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 77 GLU Chi-restraints excluded: chain A residue 93 ILE 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 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 85 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3985 r_free = 0.3985 target = 0.124164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103879 restraints weight = 12384.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107701 restraints weight = 6515.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110354 restraints weight = 4199.866| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6990 Z= 0.190 Angle : 0.639 9.203 9512 Z= 0.320 Chirality : 0.047 0.256 1042 Planarity : 0.005 0.064 1231 Dihedral : 12.884 177.190 1084 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.86 % Allowed : 14.21 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.27), residues: 850 helix: -2.00 (0.24), residues: 367 sheet: -2.17 (0.43), residues: 140 loop : -1.72 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.022 0.002 PHE A 395 TYR 0.020 0.002 TYR B 312 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 176) hydrogen bonds : angle 5.30611 ( 495) covalent geometry : bond 0.00438 ( 6990) covalent geometry : angle 0.63940 ( 9512) *********************** 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 167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.7017 (mt) REVERT: A 280 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6787 (tptt) REVERT: A 313 MET cc_start: 0.7481 (mtt) cc_final: 0.7198 (mtp) REVERT: A 413 MET cc_start: 0.6670 (tpt) cc_final: 0.5968 (mtp) REVERT: B 26 ASP cc_start: 0.7906 (m-30) cc_final: 0.7469 (m-30) REVERT: B 110 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7293 (tt0) REVERT: B 124 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8217 (tttt) REVERT: B 136 GLN cc_start: 0.7304 (mt0) cc_final: 0.7096 (mt0) REVERT: B 163 ASP cc_start: 0.7914 (p0) cc_final: 0.7636 (p0) REVERT: B 167 ASN cc_start: 0.7388 (m-40) cc_final: 0.6639 (m-40) REVERT: B 417 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7408 (tp30) outliers start: 28 outliers final: 23 residues processed: 156 average time/residue: 0.1923 time to fit residues: 39.5955 Evaluate side-chains 157 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain A residue 125 LEU 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 209 ILE 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 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 23 VAL 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 Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 327 GLU 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 26 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 336 GLN B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105103 restraints weight = 12111.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108964 restraints weight = 6362.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.111582 restraints weight = 4084.116| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6990 Z= 0.152 Angle : 0.611 9.272 9512 Z= 0.301 Chirality : 0.046 0.232 1042 Planarity : 0.005 0.061 1231 Dihedral : 12.675 178.375 1084 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 13.66 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.28), residues: 850 helix: -1.60 (0.25), residues: 367 sheet: -1.97 (0.43), residues: 140 loop : -1.51 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 388 HIS 0.010 0.001 HIS B 6 PHE 0.023 0.002 PHE A 395 TYR 0.017 0.001 TYR B 312 ARG 0.004 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 176) hydrogen bonds : angle 5.00187 ( 495) covalent geometry : bond 0.00351 ( 6990) covalent geometry : angle 0.61068 ( 9512) *********************** 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 167 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6937 (mt) REVERT: A 97 GLU cc_start: 0.5861 (tm-30) cc_final: 0.5256 (tm-30) REVERT: A 280 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6756 (tptt) REVERT: A 302 MET cc_start: 0.8347 (mmp) cc_final: 0.8139 (mmm) REVERT: A 313 MET cc_start: 0.7317 (mtt) cc_final: 0.7087 (mtp) REVERT: A 413 MET cc_start: 0.6720 (tpt) cc_final: 0.5966 (mtp) REVERT: B 26 ASP cc_start: 0.7842 (m-30) cc_final: 0.7428 (m-30) REVERT: B 110 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7356 (tt0) REVERT: B 124 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8195 (tttt) REVERT: B 163 ASP cc_start: 0.7926 (p0) cc_final: 0.7646 (p0) REVERT: B 166 MET cc_start: 0.7900 (mpp) cc_final: 0.7677 (mpt) REVERT: B 167 ASN cc_start: 0.7424 (m-40) cc_final: 0.6682 (m-40) REVERT: B 372 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7998 (ttpp) REVERT: B 395 PHE cc_start: 0.7282 (t80) cc_final: 0.6893 (t80) REVERT: B 417 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7395 (tp30) outliers start: 30 outliers final: 26 residues processed: 155 average time/residue: 0.1854 time to fit residues: 38.4402 Evaluate side-chains 158 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 93 ILE 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 182 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER 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 23 VAL 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 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 60 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 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 = 0.4018 r_free = 0.4018 target = 0.127077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106678 restraints weight = 12037.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110665 restraints weight = 6231.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.113400 restraints weight = 3965.262| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6990 Z= 0.117 Angle : 0.573 9.173 9512 Z= 0.278 Chirality : 0.045 0.224 1042 Planarity : 0.004 0.062 1231 Dihedral : 12.361 179.785 1084 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.00 % Allowed : 14.90 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.28), residues: 850 helix: -1.23 (0.26), residues: 370 sheet: -1.74 (0.45), residues: 138 loop : -1.36 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.008 0.001 HIS B 6 PHE 0.025 0.001 PHE A 395 TYR 0.012 0.001 TYR B 312 ARG 0.004 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 176) hydrogen bonds : angle 4.68172 ( 495) covalent geometry : bond 0.00271 ( 6990) covalent geometry : angle 0.57275 ( 9512) *********************** 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 163 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.825 Fit side-chains REVERT: A 154 MET cc_start: 0.7149 (mmt) cc_final: 0.6267 (tpp) REVERT: A 271 THR cc_start: 0.8146 (t) cc_final: 0.7586 (m) REVERT: A 280 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6687 (tptt) REVERT: A 302 MET cc_start: 0.8241 (mmp) cc_final: 0.8023 (mmt) REVERT: A 313 MET cc_start: 0.7290 (mtt) cc_final: 0.7081 (mtp) REVERT: A 413 MET cc_start: 0.6731 (tpt) cc_final: 0.5907 (mtp) REVERT: B 26 ASP cc_start: 0.7926 (m-30) cc_final: 0.7481 (m-30) REVERT: B 110 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7326 (tt0) REVERT: B 124 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8138 (tttt) REVERT: B 163 ASP cc_start: 0.7987 (p0) cc_final: 0.7676 (p0) REVERT: B 167 ASN cc_start: 0.7489 (m-40) cc_final: 0.6695 (m-40) REVERT: B 372 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8005 (ttpp) REVERT: B 395 PHE cc_start: 0.7262 (t80) cc_final: 0.6901 (t80) REVERT: B 417 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7357 (tp30) outliers start: 29 outliers final: 25 residues processed: 152 average time/residue: 0.1890 time to fit residues: 39.0837 Evaluate side-chains 152 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER 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 180 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 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 = 0.4007 r_free = 0.4007 target = 0.126444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.106024 restraints weight = 11935.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110029 restraints weight = 6218.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.112731 restraints weight = 3970.446| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6990 Z= 0.130 Angle : 0.577 8.671 9512 Z= 0.283 Chirality : 0.046 0.217 1042 Planarity : 0.004 0.061 1231 Dihedral : 12.158 179.867 1084 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.59 % Allowed : 15.31 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.29), residues: 850 helix: -0.97 (0.27), residues: 371 sheet: -1.59 (0.45), residues: 138 loop : -1.29 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.008 0.001 HIS B 6 PHE 0.026 0.001 PHE A 395 TYR 0.014 0.001 TYR A 357 ARG 0.004 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 176) hydrogen bonds : angle 4.71647 ( 495) covalent geometry : bond 0.00302 ( 6990) covalent geometry : angle 0.57738 ( 9512) *********************** 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 155 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.717 Fit side-chains REVERT: A 154 MET cc_start: 0.7193 (mmt) cc_final: 0.6295 (tpp) REVERT: A 280 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6703 (tptt) REVERT: A 313 MET cc_start: 0.7323 (mtt) cc_final: 0.7065 (mtp) REVERT: A 393 HIS cc_start: 0.7361 (t-90) cc_final: 0.6789 (t-90) REVERT: A 413 MET cc_start: 0.6751 (tpt) cc_final: 0.6168 (mtp) REVERT: B 26 ASP cc_start: 0.7939 (m-30) cc_final: 0.7512 (m-30) REVERT: B 110 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7324 (tt0) REVERT: B 124 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8138 (tttt) REVERT: B 163 ASP cc_start: 0.7949 (p0) cc_final: 0.7662 (p0) REVERT: B 167 ASN cc_start: 0.7557 (m-40) cc_final: 0.6804 (m-40) REVERT: B 269 MET cc_start: 0.8050 (ptp) cc_final: 0.7699 (ptp) REVERT: B 372 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7996 (ttpp) REVERT: B 395 PHE cc_start: 0.7154 (t80) cc_final: 0.6861 (t80) REVERT: B 417 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7397 (tp30) outliers start: 26 outliers final: 24 residues processed: 143 average time/residue: 0.1864 time to fit residues: 36.1327 Evaluate side-chains 147 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER 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 180 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU 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 58 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 B 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.124063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103506 restraints weight = 12115.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107506 restraints weight = 6222.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110073 restraints weight = 3989.757| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6990 Z= 0.199 Angle : 0.651 8.424 9512 Z= 0.323 Chirality : 0.048 0.245 1042 Planarity : 0.005 0.063 1231 Dihedral : 12.187 176.850 1084 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.41 % Allowed : 15.17 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.29), residues: 850 helix: -1.05 (0.27), residues: 370 sheet: -1.63 (0.45), residues: 140 loop : -1.38 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.006 0.001 HIS B 6 PHE 0.026 0.002 PHE A 395 TYR 0.017 0.002 TYR A 172 ARG 0.005 0.001 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 176) hydrogen bonds : angle 5.05195 ( 495) covalent geometry : bond 0.00458 ( 6990) covalent geometry : angle 0.65126 ( 9512) *********************** 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 154 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 302 MET cc_start: 0.7923 (mmt) cc_final: 0.7613 (mmt) REVERT: A 313 MET cc_start: 0.7354 (mtt) cc_final: 0.7084 (mtp) REVERT: A 357 TYR cc_start: 0.7702 (m-10) cc_final: 0.7499 (m-10) REVERT: A 413 MET cc_start: 0.6841 (tpt) cc_final: 0.6301 (mtp) REVERT: B 26 ASP cc_start: 0.8045 (m-30) cc_final: 0.7637 (m-30) REVERT: B 110 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7369 (tt0) REVERT: B 124 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8156 (tttt) REVERT: B 163 ASP cc_start: 0.7925 (p0) cc_final: 0.7647 (p0) REVERT: B 167 ASN cc_start: 0.7851 (m-40) cc_final: 0.7143 (m-40) REVERT: B 372 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8002 (ttpp) REVERT: B 395 PHE cc_start: 0.7179 (t80) cc_final: 0.6842 (t80) REVERT: B 417 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7445 (tp30) outliers start: 32 outliers final: 28 residues processed: 142 average time/residue: 0.1788 time to fit residues: 34.6909 Evaluate side-chains 149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU 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 A residue 349 THR 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 191 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU 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 46 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** 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 = 0.3993 r_free = 0.3993 target = 0.125362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104821 restraints weight = 12079.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.108763 restraints weight = 6273.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.111463 restraints weight = 4006.905| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6990 Z= 0.141 Angle : 0.608 8.380 9512 Z= 0.296 Chirality : 0.046 0.231 1042 Planarity : 0.005 0.064 1231 Dihedral : 11.927 179.670 1084 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.00 % Allowed : 15.31 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.29), residues: 850 helix: -0.74 (0.28), residues: 366 sheet: -1.57 (0.45), residues: 140 loop : -1.18 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.024 0.001 PHE A 395 TYR 0.014 0.001 TYR B 312 ARG 0.005 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 176) hydrogen bonds : angle 4.76248 ( 495) covalent geometry : bond 0.00329 ( 6990) covalent geometry : angle 0.60758 ( 9512) *********************** 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 153 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.720 Fit side-chains REVERT: A 35 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: A 154 MET cc_start: 0.7233 (mmt) cc_final: 0.6322 (tpp) REVERT: A 313 MET cc_start: 0.7293 (mtt) cc_final: 0.7014 (mtp) REVERT: A 377 MET cc_start: 0.8139 (ttp) cc_final: 0.7929 (tmm) REVERT: A 413 MET cc_start: 0.6815 (tpt) cc_final: 0.6186 (mtp) REVERT: B 26 ASP cc_start: 0.7907 (m-30) cc_final: 0.7523 (m-30) REVERT: B 110 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7279 (tt0) REVERT: B 124 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8159 (tttt) REVERT: B 163 ASP cc_start: 0.8041 (p0) cc_final: 0.7751 (p0) REVERT: B 167 ASN cc_start: 0.7629 (m-40) cc_final: 0.6853 (m-40) REVERT: B 372 LYS cc_start: 0.8544 (ttpp) cc_final: 0.7996 (ttpp) REVERT: B 395 PHE cc_start: 0.7162 (t80) cc_final: 0.6857 (t80) REVERT: B 417 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7428 (tp30) outliers start: 29 outliers final: 26 residues processed: 142 average time/residue: 0.1665 time to fit residues: 32.4353 Evaluate side-chains 145 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 74 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 182 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU 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 180 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU 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 40 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102793 restraints weight = 12320.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.106761 restraints weight = 6284.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109407 restraints weight = 4012.462| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6990 Z= 0.211 Angle : 0.670 8.104 9512 Z= 0.333 Chirality : 0.049 0.240 1042 Planarity : 0.005 0.067 1231 Dihedral : 12.159 177.375 1084 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.86 % Allowed : 16.00 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.29), residues: 850 helix: -1.02 (0.26), residues: 371 sheet: -1.74 (0.45), residues: 140 loop : -1.32 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 388 HIS 0.005 0.001 HIS A 88 PHE 0.030 0.002 PHE A 395 TYR 0.021 0.002 TYR A 172 ARG 0.005 0.001 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 176) hydrogen bonds : angle 5.13985 ( 495) covalent geometry : bond 0.00484 ( 6990) covalent geometry : angle 0.67028 ( 9512) ********************** 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 149 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: A 69 ASP cc_start: 0.5356 (t0) cc_final: 0.5142 (t0) REVERT: A 313 MET cc_start: 0.7360 (mtt) cc_final: 0.7082 (mtp) REVERT: A 357 TYR cc_start: 0.7757 (m-10) cc_final: 0.7554 (m-10) REVERT: A 377 MET cc_start: 0.8200 (ttp) cc_final: 0.7980 (tmm) REVERT: A 413 MET cc_start: 0.6803 (tpt) cc_final: 0.6323 (mtp) REVERT: B 26 ASP cc_start: 0.8035 (m-30) cc_final: 0.7639 (m-30) REVERT: B 110 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7405 (tt0) REVERT: B 124 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8175 (tttt) REVERT: B 163 ASP cc_start: 0.7978 (p0) cc_final: 0.7703 (p0) REVERT: B 167 ASN cc_start: 0.7434 (m-40) cc_final: 0.6627 (m-40) REVERT: B 395 PHE cc_start: 0.7226 (t80) cc_final: 0.6884 (t80) REVERT: B 417 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7424 (tp30) outliers start: 28 outliers final: 27 residues processed: 139 average time/residue: 0.1766 time to fit residues: 33.5106 Evaluate side-chains 146 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 74 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 182 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU 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 A residue 384 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 205 ASP Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 327 GLU 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 21 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 67 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** 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 = 0.4022 r_free = 0.4022 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106820 restraints weight = 11946.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.110821 restraints weight = 6122.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.113534 restraints weight = 3892.414| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4997 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= 0.110 Angle : 0.599 8.710 9512 Z= 0.289 Chirality : 0.045 0.216 1042 Planarity : 0.004 0.066 1231 Dihedral : 11.679 178.227 1084 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.31 % Allowed : 16.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.30), residues: 850 helix: -0.61 (0.28), residues: 368 sheet: -1.53 (0.45), residues: 140 loop : -1.04 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.005 0.001 HIS A 88 PHE 0.028 0.001 PHE A 395 TYR 0.013 0.001 TYR A 172 ARG 0.006 0.000 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 176) hydrogen bonds : angle 4.61726 ( 495) covalent geometry : bond 0.00260 ( 6990) covalent geometry : angle 0.59878 ( 9512) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.36 seconds wall clock time: 41 minutes 9.52 seconds (2469.52 seconds total)