Starting phenix.real_space_refine on Tue Aug 26 03:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv8_42611/08_2025/8uv8_42611_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv8_42611/08_2025/8uv8_42611.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/8uv8_42611/08_2025/8uv8_42611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv8_42611/08_2025/8uv8_42611.map" model { file = "/net/cci-nas-00/data/ceres_data/8uv8_42611/08_2025/8uv8_42611_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv8_42611/08_2025/8uv8_42611_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.286 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 10468 2.51 5 N 2932 2.21 5 O 3224 1.98 5 H 16360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33060 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 bond proxies already assigned to first conformer: 8208 Chain: "B" Number of atoms: 8206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 bond proxies already assigned to first conformer: 8208 Chain: "C" Number of atoms: 8206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 bond proxies already assigned to first conformer: 8208 Chain: "D" Number of atoms: 8206 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 535, 8164 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 bond proxies already assigned to first conformer: 8208 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'CTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'CTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'CTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'CTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.78, per 1000 atoms: 0.27 Number of scatterers: 33060 At special positions: 0 Unit cell: (98.6, 138.04, 131.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 24 15.00 Mg 4 11.99 O 3224 8.00 N 2932 7.00 C 10468 6.00 H 16360 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 20 sheets defined 47.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.928A pdb=" N THR A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.994A pdb=" N HIS A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 162 through 177 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.770A pdb=" N ILE A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.798A pdb=" N LYS A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.712A pdb=" N PHE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 297 removed outlier: 4.289A pdb=" N ASP A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.718A pdb=" N ALA A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.518A pdb=" N LYS A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.928A pdb=" N THR B 57 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.992A pdb=" N HIS B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.798A pdb=" N LYS B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.712A pdb=" N PHE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 4.292A pdb=" N ASP B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.706A pdb=" N ALA B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.513A pdb=" N LYS B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 535 through 552 Processing helix chain 'C' and resid 23 through 39 Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.919A pdb=" N THR C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.994A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 98 through 111 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 200 through 213 removed outlier: 3.769A pdb=" N ILE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.800A pdb=" N LYS C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.723A pdb=" N PHE C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 297 removed outlier: 4.289A pdb=" N ASP C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 3.698A pdb=" N ALA C 316 " --> pdb=" O LEU C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.514A pdb=" N LYS C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 372 through 386 Processing helix chain 'C' and resid 393 through 407 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 490 through 492 No H-bonds generated for 'chain 'C' and resid 490 through 492' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 535 through 552 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.920A pdb=" N THR D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.995A pdb=" N HIS D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 98 through 111 Processing helix chain 'D' and resid 123 through 135 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 162 through 177 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.795A pdb=" N LYS D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.712A pdb=" N PHE D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 297 removed outlier: 4.291A pdb=" N ASP D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 removed outlier: 3.697A pdb=" N ALA D 316 " --> pdb=" O LEU D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.510A pdb=" N LYS D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 524 through 529 Processing helix chain 'D' and resid 535 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 97 removed outlier: 6.758A pdb=" N LYS A 10 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR A 151 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 12 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE A 153 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 14 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY A 155 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 16 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 11 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 184 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 13 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 186 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 15 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU A 188 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE A 221 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A 185 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A 223 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 187 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 224 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.687A pdb=" N GLU A 197 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 341 removed outlier: 6.731A pdb=" N GLU A 300 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU A 336 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 302 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS A 338 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A 304 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 340 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU A 306 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU A 362 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 305 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL A 389 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR A 521 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY A 391 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY A 497 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 508 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE A 495 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 472 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 414 Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.755A pdb=" N LYS B 10 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR B 151 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 12 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE B 153 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 14 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY B 155 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY B 16 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B 11 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 184 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE B 13 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL B 186 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER B 15 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LEU B 188 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 221 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS B 185 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG B 223 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 187 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 224 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.690A pdb=" N GLU B 197 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 333 through 341 removed outlier: 6.741A pdb=" N GLU B 300 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU B 336 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 302 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS B 338 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B 304 " --> pdb=" O CYS B 338 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 340 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU B 306 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU B 362 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 305 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 389 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR B 521 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY B 391 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 497 " --> pdb=" O GLU B 506 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 508 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE B 495 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 472 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 412 through 414 Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.758A pdb=" N LYS C 10 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 151 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 12 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE C 153 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 14 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY C 155 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY C 16 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS C 11 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 184 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 13 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 186 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER C 15 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU C 188 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE C 221 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS C 185 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG C 223 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 187 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 224 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AB4, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.693A pdb=" N GLU C 197 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 333 through 341 removed outlier: 6.727A pdb=" N GLU C 300 " --> pdb=" O LYS C 334 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU C 336 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 302 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N CYS C 338 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 304 " --> pdb=" O CYS C 338 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 340 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU C 306 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LEU C 362 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 305 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 389 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR C 521 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY C 391 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY C 497 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 508 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE C 495 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 472 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.752A pdb=" N LYS D 10 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR D 151 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 12 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE D 153 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 14 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY D 155 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY D 16 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS D 11 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU D 184 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE D 13 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL D 186 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER D 15 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N LEU D 188 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE D 221 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS D 185 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ARG D 223 " --> pdb=" O HIS D 185 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER D 187 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 224 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 66 through 68 Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.694A pdb=" N GLU D 197 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 333 through 341 removed outlier: 6.716A pdb=" N GLU D 300 " --> pdb=" O LYS D 334 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU D 336 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 302 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N CYS D 338 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE D 304 " --> pdb=" O CYS D 338 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL D 340 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU D 306 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU D 362 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA D 305 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL D 389 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR D 521 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY D 391 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY D 497 " --> pdb=" O GLU D 506 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 508 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE D 495 " --> pdb=" O VAL D 508 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 472 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 412 through 414 716 hydrogen bonds defined for protein. 2088 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: 7.40 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16336 1.03 - 1.23: 29 1.23 - 1.42: 7003 1.42 - 1.61: 9960 1.61 - 1.81: 112 Bond restraints: 33440 Sorted by residual: bond pdb=" C2 CTP B 603 " pdb=" O2 CTP B 603 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C2 CTP A 601 " pdb=" O2 CTP A 601 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C2 CTP C 601 " pdb=" O2 CTP C 601 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C2 CTP D 603 " pdb=" O2 CTP D 603 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" C2 CTP C 603 " pdb=" O2 CTP C 603 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.82e+01 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 59411 1.77 - 3.54: 854 3.54 - 5.31: 181 5.31 - 7.09: 38 7.09 - 8.86: 28 Bond angle restraints: 60512 Sorted by residual: angle pdb=" CA PRO D 5 " pdb=" N PRO D 5 " pdb=" CD PRO D 5 " ideal model delta sigma weight residual 112.00 107.09 4.91 1.40e+00 5.10e-01 1.23e+01 angle pdb=" CA PRO B 5 " pdb=" N PRO B 5 " pdb=" CD PRO B 5 " ideal model delta sigma weight residual 112.00 107.12 4.88 1.40e+00 5.10e-01 1.22e+01 angle pdb=" C GLU D 161 " pdb=" N SER D 162 " pdb=" CA BSER D 162 " ideal model delta sigma weight residual 122.36 128.35 -5.99 1.72e+00 3.38e-01 1.21e+01 angle pdb=" C GLU B 161 " pdb=" N SER B 162 " pdb=" CA BSER B 162 " ideal model delta sigma weight residual 122.36 128.33 -5.97 1.72e+00 3.38e-01 1.20e+01 angle pdb=" C GLU C 161 " pdb=" N SER C 162 " pdb=" CA BSER C 162 " ideal model delta sigma weight residual 122.36 128.33 -5.97 1.72e+00 3.38e-01 1.20e+01 ... (remaining 60507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 15003 34.98 - 69.97: 747 69.97 - 104.95: 32 104.95 - 139.93: 4 139.93 - 174.92: 14 Dihedral angle restraints: 15800 sinusoidal: 8732 harmonic: 7068 Sorted by residual: dihedral pdb=" O3A CTP A 601 " pdb=" O3B CTP A 601 " pdb=" PB CTP A 601 " pdb=" PG CTP A 601 " ideal model delta sinusoidal sigma weight residual 204.50 29.58 174.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A CTP B 603 " pdb=" O3B CTP B 603 " pdb=" PB CTP B 603 " pdb=" PG CTP B 603 " ideal model delta sinusoidal sigma weight residual 204.50 29.78 174.72 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A CTP D 603 " pdb=" O3B CTP D 603 " pdb=" PB CTP D 603 " pdb=" PG CTP D 603 " ideal model delta sinusoidal sigma weight residual 204.50 30.21 174.29 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 15797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1443 0.031 - 0.062: 784 0.062 - 0.093: 248 0.093 - 0.124: 135 0.124 - 0.154: 26 Chirality restraints: 2636 Sorted by residual: chirality pdb=" CA ILE C 304 " pdb=" N ILE C 304 " pdb=" C ILE C 304 " pdb=" CB ILE C 304 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ILE D 304 " pdb=" N ILE D 304 " pdb=" C ILE D 304 " pdb=" CB ILE D 304 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 304 " pdb=" N ILE A 304 " pdb=" C ILE A 304 " pdb=" CB ILE A 304 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2633 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 110 " -0.138 9.50e-02 1.11e+02 5.21e-02 1.52e+01 pdb=" NE ARG A 110 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 110 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 110 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG A 110 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 110 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 110 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG A 110 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 110 " -0.138 9.50e-02 1.11e+02 5.19e-02 1.52e+01 pdb=" NE ARG C 110 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 110 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 110 " 0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG C 110 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG C 110 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 110 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG C 110 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.138 9.50e-02 1.11e+02 5.18e-02 1.50e+01 pdb=" NE ARG D 110 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG D 110 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG D 110 " 0.043 2.00e-02 2.50e+03 pdb="HH21 ARG D 110 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 110 " 0.009 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 961 2.13 - 2.75: 60646 2.75 - 3.36: 92944 3.36 - 3.98: 121275 3.98 - 4.60: 194254 Nonbonded interactions: 470080 Sorted by model distance: nonbonded pdb=" HG1 THR A 69 " pdb=" OD1 ASP A 71 " model vdw 1.511 2.450 nonbonded pdb=" HG1 THR B 69 " pdb=" OD1 ASP B 71 " model vdw 1.511 2.450 nonbonded pdb=" HG1 THR D 69 " pdb=" OD1 ASP D 71 " model vdw 1.512 2.450 nonbonded pdb=" HG1 THR C 69 " pdb=" OD1 ASP C 71 " model vdw 1.514 2.450 nonbonded pdb=" HG SER C 499 " pdb=" OD1 ASP C 501 " model vdw 1.554 2.450 ... (remaining 470075 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 161 or resid 163 through 256 or resid 258 throug \ h 361 or resid 363 through 552 or resid 603)) selection = (chain 'B' and (resid 5 through 161 or resid 163 through 256 or resid 258 throug \ h 361 or resid 363 through 552 or resid 603)) selection = (chain 'C' and (resid 5 through 161 or resid 163 through 256 or resid 258 throug \ h 361 or resid 363 through 552 or resid 603)) selection = (chain 'D' and (resid 5 through 161 or resid 163 through 256 or resid 258 throug \ h 361 or resid 363 through 552 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 30.300 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 0.008 0.166 17080 Z= 0.380 Angle : 0.827 8.857 23316 Z= 0.425 Chirality : 0.045 0.154 2636 Planarity : 0.010 0.091 3044 Dihedral : 15.246 174.919 6308 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.01 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.17), residues: 2136 helix: -0.70 (0.15), residues: 864 sheet: -0.03 (0.31), residues: 292 loop : -0.22 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG B 530 TYR 0.024 0.005 TYR B 82 PHE 0.014 0.003 PHE C 182 TRP 0.010 0.004 TRP B 288 HIS 0.011 0.002 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00794 (17080) covalent geometry : angle 0.82733 (23316) hydrogen bonds : bond 0.17156 ( 716) hydrogen bonds : angle 7.62781 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8878 (t) cc_final: 0.8566 (p) REVERT: A 84 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: A 211 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7776 (mtm180) REVERT: A 240 CYS cc_start: 0.8238 (m) cc_final: 0.7883 (m) REVERT: A 277 ASN cc_start: 0.8240 (t0) cc_final: 0.8033 (t0) REVERT: A 330 LYS cc_start: 0.8597 (tptt) cc_final: 0.8360 (tppp) REVERT: A 334 LYS cc_start: 0.8557 (tttt) cc_final: 0.8072 (tttp) REVERT: A 336 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6490 (mt-10) REVERT: A 526 GLU cc_start: 0.8289 (pm20) cc_final: 0.7981 (pm20) REVERT: A 528 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8146 (mttm) REVERT: B 43 THR cc_start: 0.8867 (t) cc_final: 0.8547 (p) REVERT: B 84 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: B 211 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7777 (mtm180) REVERT: B 240 CYS cc_start: 0.8234 (m) cc_final: 0.7903 (m) REVERT: B 330 LYS cc_start: 0.8606 (tptt) cc_final: 0.8358 (tppp) REVERT: B 334 LYS cc_start: 0.8604 (tttt) cc_final: 0.8139 (tttp) REVERT: B 526 GLU cc_start: 0.8290 (pm20) cc_final: 0.7973 (pm20) REVERT: B 528 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8150 (mttm) REVERT: C 43 THR cc_start: 0.8843 (t) cc_final: 0.8569 (p) REVERT: C 84 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.7566 (mtm-85) REVERT: C 211 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7775 (mtm180) REVERT: C 240 CYS cc_start: 0.8229 (m) cc_final: 0.7872 (m) REVERT: C 330 LYS cc_start: 0.8602 (tptt) cc_final: 0.8351 (tppp) REVERT: C 334 LYS cc_start: 0.8620 (tttt) cc_final: 0.8127 (tttp) REVERT: C 336 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6577 (mt-10) REVERT: C 526 GLU cc_start: 0.8279 (pm20) cc_final: 0.7971 (pm20) REVERT: C 528 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8217 (mttm) REVERT: D 43 THR cc_start: 0.8856 (t) cc_final: 0.8516 (p) REVERT: D 84 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: D 211 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7776 (mtm180) REVERT: D 240 CYS cc_start: 0.8237 (m) cc_final: 0.7909 (m) REVERT: D 330 LYS cc_start: 0.8593 (tptt) cc_final: 0.8371 (tppp) REVERT: D 334 LYS cc_start: 0.8553 (tttt) cc_final: 0.8076 (tttp) REVERT: D 336 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6516 (mt-10) REVERT: D 381 TYR cc_start: 0.8007 (t80) cc_final: 0.7661 (t80) REVERT: D 526 GLU cc_start: 0.8292 (pm20) cc_final: 0.7975 (pm20) REVERT: D 528 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8215 (mttm) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.3185 time to fit residues: 256.0512 Evaluate side-chains 468 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 95 ASN B 33 GLN B 95 ASN B 466 GLN C 33 GLN C 95 ASN C 277 ASN D 33 GLN D 95 ASN D 466 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.158940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122349 restraints weight = 113687.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134449 restraints weight = 38145.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139169 restraints weight = 13330.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139652 restraints weight = 8585.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141231 restraints weight = 8121.162| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17080 Z= 0.143 Angle : 0.649 6.439 23316 Z= 0.320 Chirality : 0.045 0.147 2636 Planarity : 0.005 0.048 3044 Dihedral : 13.059 174.119 2480 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.85 % Allowed : 7.16 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2136 helix: 0.77 (0.17), residues: 868 sheet: -0.32 (0.28), residues: 344 loop : 0.20 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.011 0.001 TYR A 114 PHE 0.008 0.001 PHE D 182 TRP 0.006 0.001 TRP C 285 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00327 (17080) covalent geometry : angle 0.64888 (23316) hydrogen bonds : bond 0.03961 ( 716) hydrogen bonds : angle 5.60120 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 490 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.9370 (m) cc_final: 0.9041 (p) REVERT: A 211 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7571 (mtm180) REVERT: A 230 GLU cc_start: 0.7349 (mp0) cc_final: 0.7025 (tp30) REVERT: A 330 LYS cc_start: 0.8636 (tptt) cc_final: 0.8349 (tppp) REVERT: A 334 LYS cc_start: 0.8502 (tttt) cc_final: 0.8164 (tttp) REVERT: A 336 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6587 (mt-10) REVERT: A 528 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7939 (mttm) REVERT: B 30 SER cc_start: 0.9376 (m) cc_final: 0.9063 (p) REVERT: B 211 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7594 (mtm180) REVERT: B 230 GLU cc_start: 0.7355 (mp0) cc_final: 0.7008 (tp30) REVERT: B 330 LYS cc_start: 0.8644 (tptt) cc_final: 0.8358 (tppp) REVERT: B 334 LYS cc_start: 0.8454 (tttt) cc_final: 0.8192 (tttp) REVERT: B 528 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7953 (mttm) REVERT: C 30 SER cc_start: 0.9382 (m) cc_final: 0.9065 (p) REVERT: C 211 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7553 (mtm180) REVERT: C 293 ARG cc_start: 0.6567 (ttm110) cc_final: 0.6300 (ttm110) REVERT: C 330 LYS cc_start: 0.8649 (tptt) cc_final: 0.8349 (tppp) REVERT: C 334 LYS cc_start: 0.8489 (tttt) cc_final: 0.8196 (tttp) REVERT: C 336 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6451 (mt-10) REVERT: C 528 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7950 (mttm) REVERT: D 30 SER cc_start: 0.9379 (m) cc_final: 0.9067 (p) REVERT: D 211 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7578 (mtm180) REVERT: D 230 GLU cc_start: 0.7271 (mp0) cc_final: 0.7053 (tp30) REVERT: D 293 ARG cc_start: 0.6591 (ttm110) cc_final: 0.6195 (ttm110) REVERT: D 330 LYS cc_start: 0.8646 (tptt) cc_final: 0.8393 (tppp) REVERT: D 334 LYS cc_start: 0.8529 (tttt) cc_final: 0.7983 (tttp) REVERT: D 336 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6600 (mt-10) REVERT: D 528 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7947 (mttm) outliers start: 15 outliers final: 14 residues processed: 497 average time/residue: 0.3018 time to fit residues: 216.5110 Evaluate side-chains 483 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 469 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 455 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116920 restraints weight = 93503.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125241 restraints weight = 32256.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130592 restraints weight = 16236.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133842 restraints weight = 10129.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135899 restraints weight = 7373.633| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17080 Z= 0.219 Angle : 0.652 7.647 23316 Z= 0.326 Chirality : 0.045 0.167 2636 Planarity : 0.005 0.048 3044 Dihedral : 11.516 163.919 2480 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.97 % Allowed : 11.25 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 2136 helix: 0.85 (0.18), residues: 876 sheet: -0.80 (0.28), residues: 344 loop : 0.05 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.016 0.002 TYR C 484 PHE 0.014 0.002 PHE A 182 TRP 0.009 0.002 TRP C 285 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00499 (17080) covalent geometry : angle 0.65219 (23316) hydrogen bonds : bond 0.04413 ( 716) hydrogen bonds : angle 5.31565 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 490 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 SER cc_start: 0.9333 (m) cc_final: 0.9068 (p) REVERT: A 43 THR cc_start: 0.8724 (t) cc_final: 0.8401 (p) REVERT: A 84 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: A 173 ARG cc_start: 0.8275 (tpt90) cc_final: 0.7664 (ttt90) REVERT: A 211 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7750 (mtm180) REVERT: A 281 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7512 (mtm110) REVERT: A 330 LYS cc_start: 0.8632 (tptt) cc_final: 0.8376 (tppp) REVERT: A 334 LYS cc_start: 0.8615 (tttt) cc_final: 0.8324 (tttp) REVERT: A 528 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8030 (mttm) REVERT: B 30 SER cc_start: 0.9354 (m) cc_final: 0.9063 (p) REVERT: B 43 THR cc_start: 0.8737 (t) cc_final: 0.8422 (p) REVERT: B 84 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: B 173 ARG cc_start: 0.8187 (tpt90) cc_final: 0.7692 (ttt90) REVERT: B 211 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7756 (mtm180) REVERT: B 330 LYS cc_start: 0.8650 (tptt) cc_final: 0.8406 (tppp) REVERT: B 334 LYS cc_start: 0.8584 (tttt) cc_final: 0.8332 (tttp) REVERT: B 528 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8027 (mttm) REVERT: C 84 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: C 173 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7704 (ttt90) REVERT: C 211 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7739 (mtm180) REVERT: C 293 ARG cc_start: 0.6332 (ttm110) cc_final: 0.6130 (ttm110) REVERT: C 330 LYS cc_start: 0.8663 (tptt) cc_final: 0.8408 (tppp) REVERT: C 334 LYS cc_start: 0.8591 (tttt) cc_final: 0.8282 (tttp) REVERT: C 336 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6655 (mt-10) REVERT: C 528 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8030 (mttm) REVERT: C 552 GLU cc_start: 0.6140 (pp20) cc_final: 0.5929 (pp20) REVERT: D 30 SER cc_start: 0.9353 (m) cc_final: 0.9061 (p) REVERT: D 43 THR cc_start: 0.8736 (t) cc_final: 0.8414 (p) REVERT: D 84 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: D 173 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7605 (ttt90) REVERT: D 211 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7742 (mtm180) REVERT: D 330 LYS cc_start: 0.8648 (tptt) cc_final: 0.8396 (tppp) REVERT: D 334 LYS cc_start: 0.8580 (tttt) cc_final: 0.8099 (tttp) REVERT: D 336 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6727 (mt-10) REVERT: D 528 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8030 (mttm) outliers start: 17 outliers final: 13 residues processed: 496 average time/residue: 0.3138 time to fit residues: 223.7949 Evaluate side-chains 485 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 472 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 110 optimal weight: 0.4980 chunk 170 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN C 174 HIS D 466 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119537 restraints weight = 103683.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129405 restraints weight = 36466.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135268 restraints weight = 14222.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135085 restraints weight = 9199.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135940 restraints weight = 8326.028| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17080 Z= 0.174 Angle : 0.616 6.968 23316 Z= 0.301 Chirality : 0.043 0.150 2636 Planarity : 0.005 0.042 3044 Dihedral : 9.451 153.189 2480 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.65 % Allowed : 12.05 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2136 helix: 1.12 (0.18), residues: 876 sheet: -0.97 (0.29), residues: 344 loop : 0.00 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 293 TYR 0.011 0.002 TYR C 484 PHE 0.010 0.002 PHE D 182 TRP 0.007 0.001 TRP B 285 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00397 (17080) covalent geometry : angle 0.61602 (23316) hydrogen bonds : bond 0.03713 ( 716) hydrogen bonds : angle 5.04860 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 483 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8243 (tpt90) cc_final: 0.7702 (ttt90) REVERT: A 211 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7799 (mtm180) REVERT: A 281 ARG cc_start: 0.7762 (mtm180) cc_final: 0.7541 (mtm110) REVERT: A 330 LYS cc_start: 0.8622 (tptt) cc_final: 0.8367 (tppp) REVERT: A 334 LYS cc_start: 0.8607 (tttt) cc_final: 0.8269 (tttp) REVERT: A 499 SER cc_start: 0.7490 (OUTLIER) cc_final: 0.7269 (t) REVERT: A 528 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7980 (mttm) REVERT: B 30 SER cc_start: 0.9335 (m) cc_final: 0.9122 (p) REVERT: B 43 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 173 ARG cc_start: 0.8259 (tpt90) cc_final: 0.7675 (ttt90) REVERT: B 211 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7752 (mtm180) REVERT: B 330 LYS cc_start: 0.8642 (tptt) cc_final: 0.8382 (tppp) REVERT: B 334 LYS cc_start: 0.8582 (tttt) cc_final: 0.8289 (tttp) REVERT: B 429 MET cc_start: 0.7723 (tpp) cc_final: 0.7466 (mmp) REVERT: B 528 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7985 (mttm) REVERT: C 173 ARG cc_start: 0.8253 (tpt90) cc_final: 0.7678 (ttt90) REVERT: C 211 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7779 (mtm180) REVERT: C 330 LYS cc_start: 0.8638 (tptt) cc_final: 0.8378 (tppp) REVERT: C 334 LYS cc_start: 0.8548 (tttt) cc_final: 0.8244 (tttp) REVERT: C 336 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6631 (mt-10) REVERT: C 528 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7976 (mttm) REVERT: D 30 SER cc_start: 0.9328 (m) cc_final: 0.9119 (p) REVERT: D 173 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7736 (ttt90) REVERT: D 211 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7735 (mtm180) REVERT: D 330 LYS cc_start: 0.8646 (tptt) cc_final: 0.8389 (tppp) REVERT: D 334 LYS cc_start: 0.8549 (tttt) cc_final: 0.8283 (tttp) REVERT: D 528 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7978 (mttm) outliers start: 29 outliers final: 19 residues processed: 490 average time/residue: 0.2995 time to fit residues: 213.3171 Evaluate side-chains 493 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 472 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 161 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS A 95 ASN A 466 GLN B 11 HIS B 95 ASN C 11 HIS C 95 ASN D 11 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118728 restraints weight = 99165.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128766 restraints weight = 36518.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134689 restraints weight = 14227.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134877 restraints weight = 8501.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135030 restraints weight = 8190.328| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17080 Z= 0.224 Angle : 0.638 7.951 23316 Z= 0.318 Chirality : 0.044 0.168 2636 Planarity : 0.005 0.072 3044 Dihedral : 8.440 118.712 2480 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 12.61 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.19), residues: 2136 helix: 1.03 (0.18), residues: 876 sheet: -1.26 (0.29), residues: 344 loop : -0.19 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 293 TYR 0.016 0.002 TYR C 484 PHE 0.013 0.002 PHE A 182 TRP 0.009 0.001 TRP C 285 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00512 (17080) covalent geometry : angle 0.63846 (23316) hydrogen bonds : bond 0.04011 ( 716) hydrogen bonds : angle 5.07729 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 473 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8218 (tpt90) cc_final: 0.7733 (ttt90) REVERT: A 211 ARG cc_start: 0.8278 (mtt-85) cc_final: 0.7827 (mtm180) REVERT: A 330 LYS cc_start: 0.8645 (tptt) cc_final: 0.8378 (tppp) REVERT: A 334 LYS cc_start: 0.8622 (tttt) cc_final: 0.8289 (tttp) REVERT: A 528 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8069 (mttm) REVERT: B 30 SER cc_start: 0.9339 (m) cc_final: 0.9138 (p) REVERT: B 43 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 173 ARG cc_start: 0.8233 (tpt90) cc_final: 0.7608 (ttt90) REVERT: B 211 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7813 (mtm180) REVERT: B 330 LYS cc_start: 0.8657 (tptt) cc_final: 0.8385 (tppp) REVERT: B 334 LYS cc_start: 0.8628 (tttt) cc_final: 0.8338 (tttp) REVERT: B 429 MET cc_start: 0.7678 (tpp) cc_final: 0.7420 (mmp) REVERT: B 528 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8089 (mttm) REVERT: C 173 ARG cc_start: 0.8232 (tpt90) cc_final: 0.7618 (ttt90) REVERT: C 211 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7820 (mtm180) REVERT: C 330 LYS cc_start: 0.8656 (tptt) cc_final: 0.8394 (tppp) REVERT: C 334 LYS cc_start: 0.8580 (tttt) cc_final: 0.8301 (tttp) REVERT: C 528 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8077 (mttm) REVERT: D 173 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7664 (ttt90) REVERT: D 211 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7804 (mtm180) REVERT: D 330 LYS cc_start: 0.8659 (tptt) cc_final: 0.8400 (tppp) REVERT: D 334 LYS cc_start: 0.8653 (tttt) cc_final: 0.8128 (tttp) REVERT: D 336 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6826 (mt-10) REVERT: D 528 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8069 (mttm) outliers start: 38 outliers final: 25 residues processed: 488 average time/residue: 0.3070 time to fit residues: 217.6198 Evaluate side-chains 479 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 453 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 171 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120222 restraints weight = 99835.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129798 restraints weight = 36094.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136419 restraints weight = 14191.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136026 restraints weight = 8392.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136664 restraints weight = 8127.863| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17080 Z= 0.114 Angle : 0.559 6.841 23316 Z= 0.272 Chirality : 0.043 0.152 2636 Planarity : 0.004 0.051 3044 Dihedral : 7.504 104.795 2480 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.14 % Allowed : 13.47 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 2136 helix: 1.44 (0.18), residues: 872 sheet: -1.38 (0.32), residues: 288 loop : -0.23 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 293 TYR 0.009 0.001 TYR D 381 PHE 0.006 0.001 PHE B 61 TRP 0.004 0.001 TRP C 339 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00265 (17080) covalent geometry : angle 0.55925 (23316) hydrogen bonds : bond 0.03161 ( 716) hydrogen bonds : angle 4.71065 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 468 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8217 (tpt90) cc_final: 0.7700 (ttt90) REVERT: A 211 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7725 (mtm180) REVERT: A 330 LYS cc_start: 0.8583 (tptt) cc_final: 0.8312 (tppp) REVERT: A 334 LYS cc_start: 0.8603 (tttt) cc_final: 0.8076 (tttp) REVERT: A 528 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8062 (mttm) REVERT: B 30 SER cc_start: 0.9327 (m) cc_final: 0.9108 (p) REVERT: B 211 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7664 (mtm180) REVERT: B 330 LYS cc_start: 0.8592 (tptt) cc_final: 0.8321 (tppp) REVERT: B 334 LYS cc_start: 0.8610 (tttt) cc_final: 0.8313 (tttp) REVERT: B 448 LEU cc_start: 0.8436 (mp) cc_final: 0.7977 (mp) REVERT: B 528 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8065 (mttm) REVERT: C 30 SER cc_start: 0.9302 (m) cc_final: 0.9090 (p) REVERT: C 173 ARG cc_start: 0.8232 (tpt90) cc_final: 0.8029 (ttp80) REVERT: C 197 GLU cc_start: 0.6843 (pt0) cc_final: 0.6332 (pt0) REVERT: C 211 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7708 (mtm180) REVERT: C 330 LYS cc_start: 0.8569 (tptt) cc_final: 0.8297 (tppp) REVERT: C 334 LYS cc_start: 0.8576 (tttt) cc_final: 0.8080 (tttp) REVERT: C 336 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6786 (mt-10) REVERT: C 429 MET cc_start: 0.7700 (tpp) cc_final: 0.7483 (mmp) REVERT: C 528 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8063 (mttm) REVERT: D 30 SER cc_start: 0.9323 (m) cc_final: 0.9098 (p) REVERT: D 173 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7725 (ttt90) REVERT: D 211 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7671 (mtm180) REVERT: D 330 LYS cc_start: 0.8597 (tptt) cc_final: 0.8330 (tppp) REVERT: D 334 LYS cc_start: 0.8610 (tttt) cc_final: 0.8282 (tttp) REVERT: D 528 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8066 (mttm) outliers start: 20 outliers final: 12 residues processed: 473 average time/residue: 0.3113 time to fit residues: 216.5858 Evaluate side-chains 465 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 453 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 141 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 GLN C 466 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122052 restraints weight = 99551.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130834 restraints weight = 32328.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136458 restraints weight = 15815.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139927 restraints weight = 9684.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141982 restraints weight = 6931.093| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17080 Z= 0.201 Angle : 0.610 7.816 23316 Z= 0.303 Chirality : 0.044 0.157 2636 Planarity : 0.005 0.062 3044 Dihedral : 7.688 124.506 2480 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.88 % Allowed : 13.75 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 2136 helix: 1.22 (0.18), residues: 880 sheet: -1.48 (0.32), residues: 288 loop : -0.30 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 293 TYR 0.013 0.002 TYR C 484 PHE 0.015 0.002 PHE A 67 TRP 0.009 0.001 TRP B 285 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00461 (17080) covalent geometry : angle 0.60969 (23316) hydrogen bonds : bond 0.03717 ( 716) hydrogen bonds : angle 4.84487 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 457 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8202 (tpt90) cc_final: 0.7598 (ttt90) REVERT: A 211 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7758 (mtm180) REVERT: A 330 LYS cc_start: 0.8655 (tptt) cc_final: 0.8389 (tppp) REVERT: A 334 LYS cc_start: 0.8583 (tttt) cc_final: 0.8236 (tttp) REVERT: A 429 MET cc_start: 0.7696 (tpp) cc_final: 0.7339 (mmp) REVERT: A 528 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8009 (mttm) REVERT: B 211 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7710 (mtm180) REVERT: B 330 LYS cc_start: 0.8656 (tptt) cc_final: 0.8385 (tppp) REVERT: B 334 LYS cc_start: 0.8595 (tttt) cc_final: 0.8291 (tttp) REVERT: B 429 MET cc_start: 0.7521 (mmp) cc_final: 0.7162 (mmp) REVERT: B 448 LEU cc_start: 0.8352 (mp) cc_final: 0.7884 (mp) REVERT: B 528 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7985 (mttm) REVERT: C 173 ARG cc_start: 0.8194 (tpt90) cc_final: 0.7608 (ttt90) REVERT: C 197 GLU cc_start: 0.6742 (pt0) cc_final: 0.6478 (pt0) REVERT: C 211 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7755 (mtm180) REVERT: C 330 LYS cc_start: 0.8614 (tptt) cc_final: 0.8338 (tppp) REVERT: C 334 LYS cc_start: 0.8569 (tttt) cc_final: 0.8075 (tttp) REVERT: C 385 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7229 (mmm-85) REVERT: C 528 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7988 (mttm) REVERT: D 30 SER cc_start: 0.9323 (m) cc_final: 0.9120 (p) REVERT: D 173 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7829 (ttt90) REVERT: D 211 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7720 (mtm180) REVERT: D 330 LYS cc_start: 0.8611 (tptt) cc_final: 0.8337 (tppp) REVERT: D 334 LYS cc_start: 0.8598 (tttt) cc_final: 0.8257 (tttp) REVERT: D 429 MET cc_start: 0.7516 (tpp) cc_final: 0.7305 (mmp) REVERT: D 528 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7992 (mttm) outliers start: 33 outliers final: 31 residues processed: 466 average time/residue: 0.3139 time to fit residues: 212.1166 Evaluate side-chains 483 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 452 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 205 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 446 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 174 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 187 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117771 restraints weight = 97968.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126300 restraints weight = 32713.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131830 restraints weight = 16224.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135190 restraints weight = 10025.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137297 restraints weight = 7226.820| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17080 Z= 0.117 Angle : 0.563 7.010 23316 Z= 0.275 Chirality : 0.042 0.150 2636 Planarity : 0.005 0.062 3044 Dihedral : 7.390 125.311 2480 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.85 % Allowed : 15.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 2136 helix: 1.42 (0.18), residues: 880 sheet: -1.36 (0.32), residues: 288 loop : -0.22 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 293 TYR 0.011 0.001 TYR D 175 PHE 0.012 0.001 PHE B 67 TRP 0.004 0.001 TRP D 285 HIS 0.003 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00271 (17080) covalent geometry : angle 0.56344 (23316) hydrogen bonds : bond 0.03171 ( 716) hydrogen bonds : angle 4.61204 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 457 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7918 (pp20) cc_final: 0.7596 (pp20) REVERT: A 173 ARG cc_start: 0.8152 (tpt90) cc_final: 0.7693 (ttt90) REVERT: A 211 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7776 (mtm180) REVERT: A 330 LYS cc_start: 0.8573 (tptt) cc_final: 0.8319 (tppp) REVERT: A 334 LYS cc_start: 0.8618 (tttt) cc_final: 0.8096 (tttp) REVERT: A 429 MET cc_start: 0.7670 (tpp) cc_final: 0.7289 (mmp) REVERT: A 528 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8037 (mttm) REVERT: B 173 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7624 (ttt90) REVERT: B 211 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7690 (mtm180) REVERT: B 330 LYS cc_start: 0.8576 (tptt) cc_final: 0.8316 (tppp) REVERT: B 334 LYS cc_start: 0.8629 (tttt) cc_final: 0.8285 (tttp) REVERT: B 429 MET cc_start: 0.7524 (mmp) cc_final: 0.7201 (mmp) REVERT: B 528 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8044 (mttm) REVERT: C 30 SER cc_start: 0.9319 (m) cc_final: 0.9090 (p) REVERT: C 197 GLU cc_start: 0.6613 (pt0) cc_final: 0.6387 (pt0) REVERT: C 211 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7759 (mtm180) REVERT: C 218 ASP cc_start: 0.8520 (m-30) cc_final: 0.8211 (m-30) REVERT: C 330 LYS cc_start: 0.8559 (tptt) cc_final: 0.8299 (tppp) REVERT: C 334 LYS cc_start: 0.8594 (tttt) cc_final: 0.8108 (tttp) REVERT: C 336 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6820 (mt-10) REVERT: C 429 MET cc_start: 0.7455 (mmp) cc_final: 0.7095 (mmp) REVERT: C 528 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8033 (mttm) REVERT: D 30 SER cc_start: 0.9331 (m) cc_final: 0.9098 (p) REVERT: D 173 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7785 (ttt90) REVERT: D 211 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7685 (mtm180) REVERT: D 330 LYS cc_start: 0.8585 (tptt) cc_final: 0.8330 (tppp) REVERT: D 334 LYS cc_start: 0.8617 (tttt) cc_final: 0.8115 (tttp) REVERT: D 528 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8039 (mttm) outliers start: 15 outliers final: 14 residues processed: 457 average time/residue: 0.3189 time to fit residues: 210.5694 Evaluate side-chains 462 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 448 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119228 restraints weight = 107348.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128408 restraints weight = 40890.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133562 restraints weight = 16155.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134560 restraints weight = 10714.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135705 restraints weight = 9153.189| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17080 Z= 0.175 Angle : 0.594 7.591 23316 Z= 0.293 Chirality : 0.043 0.152 2636 Planarity : 0.006 0.094 3044 Dihedral : 7.514 130.128 2480 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.25 % Allowed : 14.89 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 2136 helix: 1.29 (0.18), residues: 880 sheet: -1.42 (0.32), residues: 288 loop : -0.33 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 293 TYR 0.013 0.002 TYR C 50 PHE 0.013 0.002 PHE D 67 TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00404 (17080) covalent geometry : angle 0.59438 (23316) hydrogen bonds : bond 0.03473 ( 716) hydrogen bonds : angle 4.68402 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 461 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7957 (pp20) cc_final: 0.7635 (pp20) REVERT: A 173 ARG cc_start: 0.8197 (tpt90) cc_final: 0.7575 (ttt90) REVERT: A 211 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7931 (mtm180) REVERT: A 330 LYS cc_start: 0.8578 (tptt) cc_final: 0.8325 (tppp) REVERT: A 334 LYS cc_start: 0.8640 (tttt) cc_final: 0.8127 (tttp) REVERT: A 429 MET cc_start: 0.7716 (tpp) cc_final: 0.7358 (mmp) REVERT: A 528 LYS cc_start: 0.8433 (mtpt) cc_final: 0.8071 (mttm) REVERT: B 173 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7709 (ttt90) REVERT: B 211 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7835 (mtm180) REVERT: B 330 LYS cc_start: 0.8595 (tptt) cc_final: 0.8333 (tppp) REVERT: B 334 LYS cc_start: 0.8659 (tttt) cc_final: 0.8317 (tttp) REVERT: B 429 MET cc_start: 0.7628 (mmp) cc_final: 0.7295 (mmp) REVERT: B 528 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8078 (mttm) REVERT: C 173 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7712 (ttt90) REVERT: C 197 GLU cc_start: 0.6678 (pt0) cc_final: 0.6459 (pt0) REVERT: C 211 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7929 (mtm180) REVERT: C 330 LYS cc_start: 0.8602 (tptt) cc_final: 0.8317 (tppp) REVERT: C 334 LYS cc_start: 0.8623 (tttt) cc_final: 0.8162 (tttp) REVERT: C 429 MET cc_start: 0.7552 (mmp) cc_final: 0.7227 (mmp) REVERT: C 528 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8069 (mttm) REVERT: D 30 SER cc_start: 0.9344 (m) cc_final: 0.9085 (p) REVERT: D 173 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7831 (ttt90) REVERT: D 211 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7830 (mtm180) REVERT: D 330 LYS cc_start: 0.8586 (tptt) cc_final: 0.8331 (tppp) REVERT: D 334 LYS cc_start: 0.8612 (tttt) cc_final: 0.8129 (tttp) REVERT: D 528 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8065 (mttm) outliers start: 22 outliers final: 20 residues processed: 464 average time/residue: 0.3257 time to fit residues: 219.0897 Evaluate side-chains 474 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 454 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 HIS Chi-restraints excluded: chain D residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 210 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 201 optimal weight: 0.0770 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.161040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123531 restraints weight = 108004.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134726 restraints weight = 34923.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139608 restraints weight = 14744.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.141706 restraints weight = 9441.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144453 restraints weight = 7339.752| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17080 Z= 0.107 Angle : 0.558 6.964 23316 Z= 0.272 Chirality : 0.042 0.150 2636 Planarity : 0.005 0.085 3044 Dihedral : 7.219 126.764 2480 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.85 % Allowed : 15.51 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 2136 helix: 1.52 (0.18), residues: 880 sheet: -1.33 (0.33), residues: 288 loop : -0.22 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 293 TYR 0.015 0.001 TYR C 50 PHE 0.014 0.001 PHE D 67 TRP 0.004 0.001 TRP B 285 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00251 (17080) covalent geometry : angle 0.55827 (23316) hydrogen bonds : bond 0.03021 ( 716) hydrogen bonds : angle 4.50067 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 447 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7946 (pp20) cc_final: 0.7592 (pp20) REVERT: A 173 ARG cc_start: 0.8140 (tpt90) cc_final: 0.7554 (ttt90) REVERT: A 211 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7637 (mtm180) REVERT: A 330 LYS cc_start: 0.8504 (tptt) cc_final: 0.8248 (tppp) REVERT: A 334 LYS cc_start: 0.8589 (tttt) cc_final: 0.8028 (tttp) REVERT: A 429 MET cc_start: 0.7774 (tpp) cc_final: 0.7290 (mmp) REVERT: A 528 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7925 (mttm) REVERT: B 173 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7771 (ttt90) REVERT: B 211 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7620 (mtm180) REVERT: B 330 LYS cc_start: 0.8590 (tptt) cc_final: 0.8305 (tppp) REVERT: B 334 LYS cc_start: 0.8537 (tttt) cc_final: 0.8190 (tttp) REVERT: B 429 MET cc_start: 0.7615 (mmp) cc_final: 0.7268 (mmp) REVERT: B 528 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7926 (mttm) REVERT: C 173 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7744 (ttt90) REVERT: C 197 GLU cc_start: 0.6606 (pt0) cc_final: 0.6361 (pt0) REVERT: C 211 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7637 (mtm180) REVERT: C 330 LYS cc_start: 0.8520 (tptt) cc_final: 0.8234 (tppp) REVERT: C 334 LYS cc_start: 0.8503 (tttt) cc_final: 0.7989 (tttp) REVERT: C 336 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6759 (mt-10) REVERT: C 429 MET cc_start: 0.7546 (mmp) cc_final: 0.7205 (mmp) REVERT: C 528 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7926 (mttm) REVERT: D 30 SER cc_start: 0.9340 (m) cc_final: 0.9095 (p) REVERT: D 173 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7808 (ttt90) REVERT: D 211 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7608 (mtm180) REVERT: D 330 LYS cc_start: 0.8582 (tptt) cc_final: 0.8309 (tppp) REVERT: D 334 LYS cc_start: 0.8510 (tttt) cc_final: 0.7990 (tttp) REVERT: D 385 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7141 (mmm-85) REVERT: D 528 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7926 (mttm) outliers start: 15 outliers final: 14 residues processed: 451 average time/residue: 0.3164 time to fit residues: 208.9963 Evaluate side-chains 445 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 431 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 471 SER Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 172 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 154 optimal weight: 0.0040 chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 164 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.157880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121833 restraints weight = 104202.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132325 restraints weight = 36186.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138772 restraints weight = 13910.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139059 restraints weight = 7942.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139242 restraints weight = 7448.659| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17080 Z= 0.108 Angle : 0.553 7.143 23316 Z= 0.269 Chirality : 0.042 0.150 2636 Planarity : 0.006 0.089 3044 Dihedral : 6.984 122.269 2480 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 15.74 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 2136 helix: 1.64 (0.18), residues: 880 sheet: -1.23 (0.33), residues: 288 loop : -0.19 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 293 TYR 0.010 0.001 TYR B 381 PHE 0.014 0.001 PHE D 67 TRP 0.004 0.001 TRP A 285 HIS 0.003 0.000 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00258 (17080) covalent geometry : angle 0.55255 (23316) hydrogen bonds : bond 0.02927 ( 716) hydrogen bonds : angle 4.42622 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6000.06 seconds wall clock time: 102 minutes 34.14 seconds (6154.14 seconds total)