Starting phenix.real_space_refine on Mon Jul 6 05:38:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_42611_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_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 { model { file = "/net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_42611_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_42611_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_42611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv8_42611/07_2026/8uv8_42611.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 9.47, per 1000 atoms: 0.29 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: 2.50 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.64 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: 7.95 Time building geometry restraints manager: 3.61 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 1.224 1.396 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C2 CTP A 601 " pdb=" O2 CTP A 601 " ideal model delta sigma weight residual 1.224 1.396 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C2 CTP C 601 " pdb=" O2 CTP C 601 " ideal model delta sigma weight residual 1.224 1.396 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C2 CTP D 603 " pdb=" O2 CTP D 603 " ideal model delta sigma weight residual 1.224 1.396 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C2 CTP C 603 " pdb=" O2 CTP C 603 " ideal model delta sigma weight residual 1.224 1.395 -0.171 2.00e-02 2.50e+03 7.33e+01 ... (remaining 33435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 60315 3.91 - 7.81: 103 7.81 - 11.72: 63 11.72 - 15.62: 15 15.62 - 19.53: 16 Bond angle restraints: 60512 Sorted by residual: angle pdb=" O1A CTP C 601 " pdb=" PA CTP C 601 " pdb=" O2A CTP C 601 " ideal model delta sigma weight residual 120.17 100.64 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" O1A CTP A 601 " pdb=" PA CTP A 601 " pdb=" O2A CTP A 601 " ideal model delta sigma weight residual 120.17 100.74 19.43 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O1A CTP B 603 " pdb=" PA CTP B 603 " pdb=" O2A CTP B 603 " ideal model delta sigma weight residual 120.17 100.76 19.41 3.00e+00 1.11e-01 4.19e+01 angle pdb=" O1A CTP D 603 " pdb=" PA CTP D 603 " pdb=" O2A CTP D 603 " ideal model delta sigma weight residual 120.17 100.80 19.37 3.00e+00 1.11e-01 4.17e+01 angle pdb=" O1A CTP C 603 " pdb=" PA CTP C 603 " pdb=" O2A CTP C 603 " ideal model delta sigma weight residual 120.17 101.39 18.78 3.00e+00 1.11e-01 3.92e+01 ... (remaining 60507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 14017 15.31 - 30.62: 1022 30.62 - 45.93: 359 45.93 - 61.23: 418 61.23 - 76.54: 176 Dihedral angle restraints: 15992 sinusoidal: 8924 harmonic: 7068 Sorted by residual: dihedral pdb=" CA BSER D 162 " pdb=" C SER D 162 " pdb=" N GLN D 163 " pdb=" CA GLN D 163 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA BSER A 162 " pdb=" C SER A 162 " pdb=" N GLN A 163 " pdb=" CA GLN A 163 " ideal model delta harmonic sigma weight residual 180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA BSER C 162 " pdb=" C SER C 162 " pdb=" N GLN C 163 " pdb=" CA GLN C 163 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 15989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1864 0.044 - 0.087: 566 0.087 - 0.131: 183 0.131 - 0.174: 15 0.174 - 0.218: 8 Chirality restraints: 2636 Sorted by residual: chirality pdb=" C3' CTP D 603 " pdb=" C2' CTP D 603 " pdb=" C4' CTP D 603 " pdb=" O3' CTP D 603 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3' CTP A 601 " pdb=" C2' CTP A 601 " pdb=" C4' CTP A 601 " pdb=" O3' CTP A 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' CTP B 603 " pdb=" C2' CTP B 603 " pdb=" C4' CTP B 603 " pdb=" O3' CTP B 603 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2633 not shown) Planarity restraints: 5048 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 5045 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: 0.02 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: 1.810 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: 0.230 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.580 Find NCS groups from input model: 0.690 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 0.172 17080 Z= 0.408 Angle : 1.089 19.527 23316 Z= 0.486 Chirality : 0.047 0.218 2636 Planarity : 0.010 0.091 3036 Dihedral : 13.690 76.542 6500 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 are 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/Z covalent geometry : bond 0.00847 / 0.41 (17080) covalent geometry : angle 1.08855 / 0.49 (23316) hydrogen bonds : bond 0.17156 / 11.22 ( 716) hydrogen bonds : angle 7.62781 / 5.49 ( 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 : 0.729 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: 0.8567 (p) REVERT: A 84 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.7718 (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: 0.8239 (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: 0.7776 (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: 0.8291 (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: 0.7873 (m) REVERT: C 330 LYS cc_start: 0.8602 (tptt) cc_final: 0.8351 (tppp) REVERT: C 334 LYS cc_start: 0.8621 (tttt) cc_final: 0.8127 (tttp) REVERT: C 336 GLU cc_start: 0.6824 (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: 0.6815 (mt-10) cc_final: 0.6515 (mt-10) REVERT: D 381 TYR cc_start: 0.8008 (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: 0.3413 time to fit residues: 276.3301 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 : 0.737 ------------------------------------------------------------------------------- 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... 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 = 0.3754 r_free = 0.3754 target = 0.158533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120860 restraints weight = 106224.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130052 restraints weight = 34164.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135872 restraints weight = 16430.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139361 restraints weight = 9936.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141564 restraints weight = 7080.762| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2245 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= 0.142 Angle : 0.604 4.833 23316 Z= 0.310 Chirality : 0.044 0.146 2636 Planarity : 0.005 0.043 3036 Dihedral : 8.759 56.475 2672 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.85 % Allowed : 7.56 % Favored : 91.59 % 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 are not related in a simple way. whole: 0.39 (0.18), residues: 2136 helix: 0.73 (0.17), residues: 868 sheet: -0.24 (0.29), residues: 344 loop : 0.19 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 293 TYR 0.009 0.001 TYR C 102 PHE 0.008 0.001 PHE C 182 TRP 0.006 0.001 TRP C 285 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17080) covalent geometry : angle 0.60350 / 0.31 (23316) hydrogen bonds : bond 0.04360 / 2.94 ( 716) hydrogen bonds : angle 5.71397 / 4.15 ( 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 498 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 483 time to evaluate : 0.906 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: A 30 SER cc_start: 0.9371 (m) cc_final: 0.9050 (p) REVERT: A 211 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7591 (mtm180) REVERT: A 218 ASP cc_start: 0.8310 (m-30) cc_final: 0.8098 (m-30) REVERT: A 230 GLU cc_start: 0.7375 (mp0) cc_final: 0.7047 (tp30) REVERT: A 330 LYS cc_start: 0.8627 (tptt) cc_final: 0.8355 (tppp) REVERT: A 334 LYS cc_start: 0.8522 (tttt) cc_final: 0.7969 (tttp) REVERT: A 336 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 528 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7984 (mttm) REVERT: B 30 SER cc_start: 0.9370 (m) cc_final: 0.9064 (p) REVERT: B 211 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7591 (mtm180) REVERT: B 218 ASP cc_start: 0.8328 (m-30) cc_final: 0.8106 (m-30) REVERT: B 230 GLU cc_start: 0.7384 (mp0) cc_final: 0.7043 (tp30) REVERT: B 330 LYS cc_start: 0.8655 (tptt) cc_final: 0.8381 (tppp) REVERT: B 334 LYS cc_start: 0.8519 (tttt) cc_final: 0.8224 (tttp) REVERT: B 528 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8004 (mttm) REVERT: C 30 SER cc_start: 0.9372 (m) cc_final: 0.9052 (p) REVERT: C 211 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7581 (mtm180) REVERT: C 293 ARG cc_start: 0.6484 (ttm110) cc_final: 0.6197 (ttm110) REVERT: C 330 LYS cc_start: 0.8641 (tptt) cc_final: 0.8349 (tppp) REVERT: C 334 LYS cc_start: 0.8508 (tttt) cc_final: 0.8015 (tttp) REVERT: C 336 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6465 (mt-10) REVERT: C 528 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8017 (mttm) REVERT: D 30 SER cc_start: 0.9371 (m) cc_final: 0.9065 (p) REVERT: D 211 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7577 (mtm180) REVERT: D 230 GLU cc_start: 0.7263 (mp0) cc_final: 0.7048 (tp30) REVERT: D 293 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6150 (ttm110) REVERT: D 330 LYS cc_start: 0.8641 (tptt) cc_final: 0.8365 (tppp) REVERT: D 334 LYS cc_start: 0.8547 (tttt) cc_final: 0.8027 (tttp) REVERT: D 336 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6641 (mt-10) REVERT: D 528 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8001 (mttm) outliers start: 15 outliers final: 14 residues processed: 489 average time/residue: 0.3334 time to fit residues: 239.2723 Evaluate side-chains 477 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 463 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3719 r_free = 0.3719 target = 0.154539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118183 restraints weight = 92196.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126530 restraints weight = 31951.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131935 restraints weight = 16138.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135182 restraints weight = 10056.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137121 restraints weight = 7326.619| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17080 Z= 0.276 Angle : 0.660 5.614 23316 Z= 0.344 Chirality : 0.045 0.149 2636 Planarity : 0.005 0.049 3036 Dihedral : 8.454 53.420 2672 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.82 % Allowed : 10.68 % Favored : 87.50 % 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 are not related in a simple way. whole: 0.01 (0.18), residues: 2136 helix: 0.63 (0.17), residues: 872 sheet: -0.91 (0.28), residues: 352 loop : -0.03 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 293 TYR 0.019 0.002 TYR C 484 PHE 0.017 0.002 PHE B 182 TRP 0.012 0.002 TRP C 285 HIS 0.006 0.001 HIS C 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.28 (17080) covalent geometry : angle 0.66018 / 0.34 (23316) hydrogen bonds : bond 0.04787 / 3.24 ( 716) hydrogen bonds : angle 5.52567 / 4.01 ( 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 496 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 464 time to evaluate : 0.517 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: A 43 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 173 ARG cc_start: 0.8295 (tpt90) cc_final: 0.7662 (ttt90) REVERT: A 211 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7822 (mtt90) REVERT: A 258 ASP cc_start: 0.6138 (m-30) cc_final: 0.5690 (t0) REVERT: A 293 ARG cc_start: 0.6317 (ttm110) cc_final: 0.6096 (ttm110) REVERT: A 330 LYS cc_start: 0.8634 (tptt) cc_final: 0.8366 (tppp) REVERT: A 334 LYS cc_start: 0.8641 (tttt) cc_final: 0.8346 (tttp) REVERT: A 528 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8015 (mttm) REVERT: B 43 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 173 ARG cc_start: 0.8237 (tpt90) cc_final: 0.8034 (ttp80) REVERT: B 211 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7775 (mtt90) REVERT: B 218 ASP cc_start: 0.8422 (m-30) cc_final: 0.8111 (m-30) REVERT: B 330 LYS cc_start: 0.8656 (tptt) cc_final: 0.8409 (tppp) REVERT: B 334 LYS cc_start: 0.8609 (tttt) cc_final: 0.8360 (tttp) REVERT: B 528 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8039 (mttm) REVERT: C 43 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8416 (p) REVERT: C 173 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7701 (ttt90) REVERT: C 211 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7820 (mtt90) REVERT: C 218 ASP cc_start: 0.8416 (m-30) cc_final: 0.8121 (m-30) REVERT: C 330 LYS cc_start: 0.8677 (tptt) cc_final: 0.8421 (tppp) REVERT: C 334 LYS cc_start: 0.8600 (tttt) cc_final: 0.8317 (tttp) REVERT: C 336 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6702 (mt-10) REVERT: C 528 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8044 (mttm) REVERT: D 43 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8399 (p) REVERT: D 84 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: D 173 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7644 (ttt90) REVERT: D 211 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7786 (mtt90) REVERT: D 330 LYS cc_start: 0.8655 (tptt) cc_final: 0.8399 (tppp) REVERT: D 334 LYS cc_start: 0.8602 (tttt) cc_final: 0.8329 (tttp) REVERT: D 336 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6790 (mt-10) REVERT: D 528 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8040 (mttm) outliers start: 32 outliers final: 24 residues processed: 473 average time/residue: 0.3323 time to fit residues: 228.3089 Evaluate side-chains 472 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 444 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 43 THR 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 B residue 29 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 43 THR 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 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=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: 0.1980 chunk 170 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 144 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 163 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN B 466 GLN C 95 ASN D 95 ASN D 466 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121183 restraints weight = 104535.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130522 restraints weight = 40981.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134975 restraints weight = 15890.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137145 restraints weight = 11154.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138753 restraints weight = 8902.731| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17080 Z= 0.098 Angle : 0.525 5.362 23316 Z= 0.266 Chirality : 0.042 0.154 2636 Planarity : 0.004 0.040 3036 Dihedral : 7.592 57.259 2672 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.80 % Allowed : 12.22 % Favored : 86.99 % 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 are not related in a simple way. whole: 0.67 (0.19), residues: 2136 helix: 1.34 (0.18), residues: 872 sheet: -0.67 (0.29), residues: 340 loop : 0.16 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 293 TYR 0.011 0.001 TYR D 381 PHE 0.006 0.001 PHE C 417 TRP 0.004 0.001 TRP C 339 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17080) covalent geometry : angle 0.52460 / 0.27 (23316) hydrogen bonds : bond 0.03136 / 2.15 ( 716) hydrogen bonds : angle 4.85838 / 3.54 ( 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 497 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 483 time to evaluate : 0.875 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: A 30 SER cc_start: 0.9305 (m) cc_final: 0.9071 (p) REVERT: A 173 ARG cc_start: 0.8154 (tpt90) cc_final: 0.7597 (ttt90) REVERT: A 211 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7631 (mtm180) REVERT: A 330 LYS cc_start: 0.8542 (tptt) cc_final: 0.8282 (tppp) REVERT: A 334 LYS cc_start: 0.8541 (tttt) cc_final: 0.8199 (tttp) REVERT: A 528 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7944 (mttm) REVERT: B 30 SER cc_start: 0.9295 (m) cc_final: 0.9063 (p) REVERT: B 211 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7602 (mtm180) REVERT: B 330 LYS cc_start: 0.8555 (tptt) cc_final: 0.8281 (tppp) REVERT: B 334 LYS cc_start: 0.8551 (tttt) cc_final: 0.8248 (tttp) REVERT: B 528 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7965 (mttm) REVERT: C 30 SER cc_start: 0.9287 (m) cc_final: 0.9041 (p) REVERT: C 211 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7615 (mtm180) REVERT: C 330 LYS cc_start: 0.8606 (tptt) cc_final: 0.8342 (tppp) REVERT: C 334 LYS cc_start: 0.8545 (tttt) cc_final: 0.8023 (tttp) REVERT: C 336 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6499 (mt-10) REVERT: C 528 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7967 (mttm) REVERT: C 552 GLU cc_start: 0.6117 (pp20) cc_final: 0.5906 (pp20) REVERT: D 30 SER cc_start: 0.9291 (m) cc_final: 0.9062 (p) REVERT: D 173 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7630 (ttt90) REVERT: D 211 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7601 (mtm180) REVERT: D 330 LYS cc_start: 0.8569 (tptt) cc_final: 0.8315 (tppp) REVERT: D 334 LYS cc_start: 0.8535 (tttt) cc_final: 0.8240 (tttp) REVERT: D 528 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7953 (mttm) outliers start: 14 outliers final: 10 residues processed: 485 average time/residue: 0.3440 time to fit residues: 244.4616 Evaluate side-chains 469 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 459 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 B residue 455 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 115 LEU 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: 2.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 466 GLN B 95 ASN B 466 GLN C 174 HIS D 466 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118483 restraints weight = 99174.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129283 restraints weight = 36366.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133602 restraints weight = 14260.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134410 restraints weight = 9349.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134799 restraints weight = 8702.652| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17080 Z= 0.198 Angle : 0.571 4.681 23316 Z= 0.293 Chirality : 0.043 0.154 2636 Planarity : 0.005 0.052 3036 Dihedral : 7.579 56.459 2672 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.65 % Allowed : 12.73 % Favored : 85.62 % 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 are not related in a simple way. whole: 0.54 (0.19), residues: 2136 helix: 1.32 (0.18), residues: 880 sheet: -0.86 (0.29), residues: 340 loop : 0.04 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 293 TYR 0.015 0.002 TYR C 484 PHE 0.013 0.002 PHE D 67 TRP 0.008 0.001 TRP D 285 HIS 0.005 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (17080) covalent geometry : angle 0.57052 / 0.29 (23316) hydrogen bonds : bond 0.03764 / 2.57 ( 716) hydrogen bonds : angle 4.92311 / 3.58 ( 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 514 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 485 time to evaluate : 0.863 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: A 173 ARG cc_start: 0.8228 (tpt90) cc_final: 0.7749 (ttt90) REVERT: A 211 ARG cc_start: 0.8229 (mtt-85) cc_final: 0.7829 (mtm180) REVERT: A 330 LYS cc_start: 0.8622 (tptt) cc_final: 0.8368 (tppp) REVERT: A 334 LYS cc_start: 0.8621 (tttt) cc_final: 0.8279 (tttp) REVERT: A 528 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7958 (mttm) REVERT: B 30 SER cc_start: 0.9336 (m) cc_final: 0.9061 (p) REVERT: B 173 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7651 (ttt90) REVERT: B 211 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7797 (mtm180) REVERT: B 330 LYS cc_start: 0.8641 (tptt) cc_final: 0.8380 (tppp) REVERT: B 334 LYS cc_start: 0.8609 (tttt) cc_final: 0.8300 (tttp) REVERT: B 528 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7996 (mttm) REVERT: C 84 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: C 173 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7650 (ttt90) REVERT: C 211 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7819 (mtm180) REVERT: C 330 LYS cc_start: 0.8641 (tptt) cc_final: 0.8361 (tppp) REVERT: C 334 LYS cc_start: 0.8564 (tttt) cc_final: 0.8064 (tttp) REVERT: C 336 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6605 (mt-10) REVERT: C 528 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7978 (mttm) REVERT: D 30 SER cc_start: 0.9374 (m) cc_final: 0.9064 (p) REVERT: D 84 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8119 (mtm-85) REVERT: D 173 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7669 (ttt90) REVERT: D 211 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7792 (mtm180) REVERT: D 330 LYS cc_start: 0.8641 (tptt) cc_final: 0.8393 (tppp) REVERT: D 334 LYS cc_start: 0.8586 (tttt) cc_final: 0.8274 (tttp) REVERT: D 336 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6786 (mt-10) REVERT: D 528 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7969 (mttm) outliers start: 29 outliers final: 23 residues processed: 489 average time/residue: 0.3462 time to fit residues: 247.1435 Evaluate side-chains 497 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 474 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ASP 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 D residue 66 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 125 ILE 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 446 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN B 466 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.155521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119713 restraints weight = 100208.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129712 restraints weight = 36131.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135762 restraints weight = 14255.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136187 restraints weight = 8320.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136454 restraints weight = 7852.120| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 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 = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17080 Z= 0.124 Angle : 0.518 5.088 23316 Z= 0.263 Chirality : 0.042 0.153 2636 Planarity : 0.005 0.061 3036 Dihedral : 7.155 57.634 2672 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.19 % Allowed : 13.81 % Favored : 85.00 % 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 are not related in a simple way. whole: 0.55 (0.19), residues: 2136 helix: 1.49 (0.18), residues: 880 sheet: -1.14 (0.32), residues: 284 loop : -0.10 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 293 TYR 0.010 0.001 TYR B 381 PHE 0.011 0.001 PHE D 67 TRP 0.005 0.001 TRP B 285 HIS 0.004 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17080) covalent geometry : angle 0.51782 / 0.26 (23316) hydrogen bonds : bond 0.03176 / 2.17 ( 716) hydrogen bonds : angle 4.66667 / 3.39 ( 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 494 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 473 time to evaluate : 0.876 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: A 173 ARG cc_start: 0.8166 (tpt90) cc_final: 0.7692 (ttt90) REVERT: A 211 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7712 (mtm180) REVERT: A 330 LYS cc_start: 0.8574 (tptt) cc_final: 0.8313 (tppp) REVERT: A 334 LYS cc_start: 0.8577 (tttt) cc_final: 0.8225 (tttp) REVERT: A 429 MET cc_start: 0.7697 (tpp) cc_final: 0.7310 (mmp) REVERT: A 528 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7942 (mttm) REVERT: B 30 SER cc_start: 0.9325 (m) cc_final: 0.9076 (p) REVERT: B 173 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8042 (ttp80) REVERT: B 211 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7650 (mtm180) REVERT: B 330 LYS cc_start: 0.8575 (tptt) cc_final: 0.8311 (tppp) REVERT: B 334 LYS cc_start: 0.8596 (tttt) cc_final: 0.8290 (tttp) REVERT: B 528 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8001 (mttm) REVERT: C 30 SER cc_start: 0.9319 (m) cc_final: 0.9061 (p) REVERT: C 173 ARG cc_start: 0.8255 (tpt90) cc_final: 0.8047 (ttp80) REVERT: C 211 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7684 (mtm180) REVERT: C 330 LYS cc_start: 0.8588 (tptt) cc_final: 0.8286 (tppp) REVERT: C 334 LYS cc_start: 0.8565 (tttt) cc_final: 0.8045 (tttp) REVERT: C 336 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6743 (mt-10) REVERT: C 528 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7950 (mttm) REVERT: D 30 SER cc_start: 0.9332 (m) cc_final: 0.9080 (p) REVERT: D 173 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7728 (ttt90) REVERT: D 211 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7659 (mtm180) REVERT: D 330 LYS cc_start: 0.8593 (tptt) cc_final: 0.8331 (tppp) REVERT: D 334 LYS cc_start: 0.8579 (tttt) cc_final: 0.8238 (tttp) REVERT: D 528 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7941 (mttm) outliers start: 21 outliers final: 18 residues processed: 482 average time/residue: 0.3392 time to fit residues: 240.6371 Evaluate side-chains 481 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 463 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 446 MET Chi-restraints excluded: chain B residue 205 HIS 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 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 324 LEU 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: 3.9990 chunk 177 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 HIS A 41 HIS A 466 GLN B 11 HIS C 11 HIS C 466 GLN D 11 HIS D 466 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118097 restraints weight = 100808.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128351 restraints weight = 36415.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133228 restraints weight = 14335.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134518 restraints weight = 8997.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135008 restraints weight = 8344.297| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 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 = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3826 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= 0.184 Angle : 0.558 4.545 23316 Z= 0.286 Chirality : 0.042 0.153 2636 Planarity : 0.006 0.091 3036 Dihedral : 7.294 56.564 2672 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.76 % Allowed : 14.09 % Favored : 84.15 % 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 are not related in a simple way. whole: 0.32 (0.19), residues: 2136 helix: 1.32 (0.18), residues: 880 sheet: -1.25 (0.32), residues: 288 loop : -0.25 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 293 TYR 0.014 0.002 TYR C 50 PHE 0.011 0.002 PHE C 182 TRP 0.008 0.001 TRP D 285 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (17080) covalent geometry : angle 0.55831 / 0.29 (23316) hydrogen bonds : bond 0.03596 / 2.46 ( 716) hydrogen bonds : angle 4.76302 / 3.45 ( 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 496 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 465 time to evaluate : 0.845 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 70 GLU cc_start: 0.8017 (pp20) cc_final: 0.7678 (pp20) REVERT: A 173 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7603 (ttt90) REVERT: A 211 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7752 (mtm180) REVERT: A 330 LYS cc_start: 0.8594 (tptt) cc_final: 0.8315 (tppp) REVERT: A 334 LYS cc_start: 0.8563 (tttt) cc_final: 0.8016 (tttp) REVERT: A 429 MET cc_start: 0.7777 (tpp) cc_final: 0.7353 (mmp) REVERT: A 528 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7923 (mttm) REVERT: B 30 SER cc_start: 0.9343 (m) cc_final: 0.9059 (p) REVERT: B 173 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7613 (ttt90) REVERT: B 211 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7754 (mtm180) REVERT: B 330 LYS cc_start: 0.8604 (tptt) cc_final: 0.8324 (tppp) REVERT: B 334 LYS cc_start: 0.8584 (tttt) cc_final: 0.8266 (tttp) REVERT: B 528 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7985 (mttm) REVERT: C 30 SER cc_start: 0.9335 (m) cc_final: 0.9053 (p) REVERT: C 173 ARG cc_start: 0.8257 (tpt90) cc_final: 0.7622 (ttt90) REVERT: C 211 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7749 (mtm180) REVERT: C 330 LYS cc_start: 0.8677 (tptt) cc_final: 0.8376 (tppp) REVERT: C 334 LYS cc_start: 0.8545 (tttt) cc_final: 0.8021 (tttp) REVERT: C 336 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6607 (mt-10) REVERT: C 385 ARG cc_start: 0.7517 (mmm160) cc_final: 0.7286 (mmm-85) REVERT: C 528 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7965 (mttm) REVERT: D 30 SER cc_start: 0.9347 (m) cc_final: 0.9065 (p) REVERT: D 173 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7802 (ttt90) REVERT: D 211 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7744 (mtm180) REVERT: D 330 LYS cc_start: 0.8603 (tptt) cc_final: 0.8324 (tppp) REVERT: D 334 LYS cc_start: 0.8563 (tttt) cc_final: 0.8190 (tttp) REVERT: D 336 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6841 (mt-10) REVERT: D 429 MET cc_start: 0.7718 (tpp) cc_final: 0.7403 (mmp) REVERT: D 528 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7959 (mttm) outliers start: 31 outliers final: 25 residues processed: 476 average time/residue: 0.3361 time to fit residues: 236.6552 Evaluate side-chains 474 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 449 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 446 MET 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 337 ILE Chi-restraints excluded: chain B residue 446 MET 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 205 HIS Chi-restraints excluded: chain C residue 324 LEU 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 238 LEU 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: 1.9990 chunk 80 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118649 restraints weight = 97802.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127055 restraints weight = 32513.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132506 restraints weight = 16113.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135828 restraints weight = 9974.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137903 restraints weight = 7166.906| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 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 = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17080 Z= 0.136 Angle : 0.528 5.985 23316 Z= 0.269 Chirality : 0.042 0.152 2636 Planarity : 0.005 0.082 3036 Dihedral : 7.076 57.216 2672 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.42 % Allowed : 14.20 % 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 are not related in a simple way. whole: 0.41 (0.19), residues: 2136 helix: 1.41 (0.18), residues: 880 sheet: -1.23 (0.32), residues: 288 loop : -0.21 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 293 TYR 0.014 0.001 TYR C 50 PHE 0.008 0.001 PHE D 67 TRP 0.006 0.001 TRP B 285 HIS 0.004 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17080) covalent geometry : angle 0.52790 / 0.27 (23316) hydrogen bonds : bond 0.03262 / 2.23 ( 716) hydrogen bonds : angle 4.62145 / 3.35 ( 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 477 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 452 time to evaluate : 0.875 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 70 GLU cc_start: 0.8010 (pp20) cc_final: 0.7645 (pp20) REVERT: A 173 ARG cc_start: 0.8225 (tpt90) cc_final: 0.7600 (ttt90) REVERT: A 211 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7800 (mtm180) REVERT: A 330 LYS cc_start: 0.8590 (tptt) cc_final: 0.8330 (tppp) REVERT: A 334 LYS cc_start: 0.8600 (tttt) cc_final: 0.8071 (tttp) REVERT: A 429 MET cc_start: 0.7639 (tpp) cc_final: 0.7346 (mmp) REVERT: A 528 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8014 (mttm) REVERT: B 30 SER cc_start: 0.9329 (m) cc_final: 0.9096 (p) REVERT: B 173 ARG cc_start: 0.8231 (tpt90) cc_final: 0.8013 (ttp80) REVERT: B 211 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7688 (mtm180) REVERT: B 330 LYS cc_start: 0.8581 (tptt) cc_final: 0.8320 (tppp) REVERT: B 334 LYS cc_start: 0.8625 (tttt) cc_final: 0.8279 (tttp) REVERT: B 528 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8033 (mttm) REVERT: C 30 SER cc_start: 0.9328 (m) cc_final: 0.9090 (p) REVERT: C 173 ARG cc_start: 0.8230 (tpt90) cc_final: 0.8017 (ttp80) REVERT: C 211 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7771 (mtm180) REVERT: C 330 LYS cc_start: 0.8605 (tptt) cc_final: 0.8305 (tppp) REVERT: C 334 LYS cc_start: 0.8583 (tttt) cc_final: 0.8084 (tttp) REVERT: C 336 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6622 (mt-10) REVERT: C 528 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8027 (mttm) REVERT: D 30 SER cc_start: 0.9327 (m) cc_final: 0.9100 (p) REVERT: D 173 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7806 (ttt90) REVERT: D 211 ARG cc_start: 0.8121 (mtt-85) cc_final: 0.7702 (mtm180) REVERT: D 330 LYS cc_start: 0.8586 (tptt) cc_final: 0.8332 (tppp) REVERT: D 334 LYS cc_start: 0.8603 (tttt) cc_final: 0.8094 (tttp) REVERT: D 429 MET cc_start: 0.7608 (tpp) cc_final: 0.7364 (mmp) REVERT: D 528 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8004 (mttm) outliers start: 25 outliers final: 22 residues processed: 461 average time/residue: 0.3279 time to fit residues: 224.1041 Evaluate side-chains 467 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 445 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 446 MET 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 455 LEU 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 446 MET Chi-restraints excluded: chain D residue 68 VAL 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 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 193 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119240 restraints weight = 107795.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129532 restraints weight = 37116.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136346 restraints weight = 14563.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136449 restraints weight = 8504.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136678 restraints weight = 7723.167| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 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 = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4075 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= 0.138 Angle : 0.523 4.966 23316 Z= 0.266 Chirality : 0.041 0.153 2636 Planarity : 0.005 0.079 3036 Dihedral : 6.955 58.059 2672 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.25 % Allowed : 14.49 % Favored : 84.26 % 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 are not related in a simple way. whole: 0.44 (0.19), residues: 2136 helix: 1.47 (0.18), residues: 880 sheet: -1.25 (0.32), residues: 288 loop : -0.22 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 293 TYR 0.009 0.001 TYR C 381 PHE 0.007 0.001 PHE D 182 TRP 0.005 0.001 TRP B 285 HIS 0.004 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17080) covalent geometry : angle 0.52332 / 0.27 (23316) hydrogen bonds : bond 0.03168 / 2.17 ( 716) hydrogen bonds : angle 4.54785 / 3.30 ( 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 471 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 449 time to evaluate : 0.849 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: A 70 GLU cc_start: 0.8029 (pp20) cc_final: 0.7640 (pp20) REVERT: A 173 ARG cc_start: 0.8219 (tpt90) cc_final: 0.7587 (ttt90) REVERT: A 211 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7789 (mtm180) REVERT: A 330 LYS cc_start: 0.8597 (tptt) cc_final: 0.8322 (tppp) REVERT: A 334 LYS cc_start: 0.8567 (tttt) cc_final: 0.8027 (tttp) REVERT: A 429 MET cc_start: 0.7710 (tpp) cc_final: 0.7304 (mmp) REVERT: A 528 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7942 (mttm) REVERT: B 30 SER cc_start: 0.9328 (m) cc_final: 0.9053 (p) REVERT: B 173 ARG cc_start: 0.8226 (tpt90) cc_final: 0.8000 (ttp80) REVERT: B 211 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7684 (mtm180) REVERT: B 330 LYS cc_start: 0.8593 (tptt) cc_final: 0.8313 (tppp) REVERT: B 334 LYS cc_start: 0.8595 (tttt) cc_final: 0.8067 (tttp) REVERT: B 528 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7980 (mttm) REVERT: C 30 SER cc_start: 0.9329 (m) cc_final: 0.9051 (p) REVERT: C 211 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7773 (mtm180) REVERT: C 330 LYS cc_start: 0.8616 (tptt) cc_final: 0.8297 (tppp) REVERT: C 334 LYS cc_start: 0.8559 (tttt) cc_final: 0.8043 (tttp) REVERT: C 336 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6783 (mt-10) REVERT: C 429 MET cc_start: 0.7608 (mmp) cc_final: 0.7267 (mmp) REVERT: C 528 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7952 (mttm) REVERT: D 30 SER cc_start: 0.9335 (m) cc_final: 0.9060 (p) REVERT: D 173 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7832 (ttt90) REVERT: D 211 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7702 (mtm180) REVERT: D 289 ASP cc_start: 0.7324 (p0) cc_final: 0.6975 (p0) REVERT: D 330 LYS cc_start: 0.8602 (tptt) cc_final: 0.8324 (tppp) REVERT: D 334 LYS cc_start: 0.8556 (tttt) cc_final: 0.8048 (tttp) REVERT: D 429 MET cc_start: 0.7701 (tpp) cc_final: 0.7334 (mmp) REVERT: D 528 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7947 (mttm) outliers start: 22 outliers final: 21 residues processed: 455 average time/residue: 0.3355 time to fit residues: 226.7145 Evaluate side-chains 471 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 450 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 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 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 C residue 68 VAL 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 446 MET Chi-restraints excluded: chain D residue 68 VAL 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 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 210 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 131 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120162 restraints weight = 108405.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130650 restraints weight = 36820.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137488 restraints weight = 14177.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137374 restraints weight = 8133.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137477 restraints weight = 7717.679| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17080 Z= 0.097 Angle : 0.508 7.900 23316 Z= 0.256 Chirality : 0.041 0.151 2636 Planarity : 0.005 0.074 3036 Dihedral : 6.729 59.494 2672 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.91 % Allowed : 14.94 % Favored : 84.15 % 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 are not related in a simple way. whole: 0.65 (0.19), residues: 2136 helix: 1.67 (0.18), residues: 880 sheet: -1.13 (0.33), residues: 288 loop : -0.13 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 293 TYR 0.010 0.001 TYR B 381 PHE 0.007 0.001 PHE D 67 TRP 0.004 0.001 TRP D 339 HIS 0.004 0.000 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (17080) covalent geometry : angle 0.50765 / 0.26 (23316) hydrogen bonds : bond 0.02864 / 1.96 ( 716) hydrogen bonds : angle 4.41649 / 3.21 ( 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 457 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 441 time to evaluate : 0.846 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 30 SER cc_start: 0.9319 (m) cc_final: 0.9082 (p) REVERT: A 70 GLU cc_start: 0.8005 (pp20) cc_final: 0.7622 (pp20) REVERT: A 173 ARG cc_start: 0.8179 (tpt90) cc_final: 0.7551 (ttt90) REVERT: A 211 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7650 (mtm180) REVERT: A 330 LYS cc_start: 0.8511 (tptt) cc_final: 0.8259 (tppp) REVERT: A 334 LYS cc_start: 0.8524 (tttt) cc_final: 0.7999 (tttp) REVERT: A 429 MET cc_start: 0.7685 (tpp) cc_final: 0.7283 (mmp) REVERT: A 528 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7929 (mttm) REVERT: B 30 SER cc_start: 0.9310 (m) cc_final: 0.9071 (p) REVERT: B 211 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7618 (mtm180) REVERT: B 330 LYS cc_start: 0.8568 (tptt) cc_final: 0.8291 (tppp) REVERT: B 334 LYS cc_start: 0.8550 (tttt) cc_final: 0.8212 (tttp) REVERT: B 528 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7953 (mttm) REVERT: C 30 SER cc_start: 0.9309 (m) cc_final: 0.9067 (p) REVERT: C 211 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7627 (mtm180) REVERT: C 330 LYS cc_start: 0.8595 (tptt) cc_final: 0.8288 (tppp) REVERT: C 334 LYS cc_start: 0.8534 (tttt) cc_final: 0.8025 (tttp) REVERT: C 336 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6803 (mt-10) REVERT: C 429 MET cc_start: 0.7588 (mmp) cc_final: 0.7246 (mmp) REVERT: C 528 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7942 (mttm) REVERT: D 30 SER cc_start: 0.9319 (m) cc_final: 0.9076 (p) REVERT: D 173 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7803 (ttt90) REVERT: D 211 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7610 (mtm180) REVERT: D 330 LYS cc_start: 0.8507 (tptt) cc_final: 0.8264 (tppp) REVERT: D 334 LYS cc_start: 0.8526 (tttt) cc_final: 0.7961 (tttp) REVERT: D 336 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6883 (mt-10) REVERT: D 385 ARG cc_start: 0.7512 (mmm160) cc_final: 0.7043 (mmm-85) REVERT: D 429 MET cc_start: 0.7675 (tpp) cc_final: 0.7320 (mmp) REVERT: D 528 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7936 (mttm) outliers start: 16 outliers final: 15 residues processed: 444 average time/residue: 0.3203 time to fit residues: 210.3594 Evaluate side-chains 451 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 436 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 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 205 HIS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 324 LEU 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 446 MET 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: 0.6980 chunk 49 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 164 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120333 restraints weight = 104089.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130803 restraints weight = 35057.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136063 restraints weight = 14530.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137656 restraints weight = 9699.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139152 restraints weight = 7645.342| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4191 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= 0.115 Angle : 0.513 6.696 23316 Z= 0.260 Chirality : 0.041 0.151 2636 Planarity : 0.005 0.075 3036 Dihedral : 6.665 59.888 2672 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.02 % Allowed : 15.11 % 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 are not related in a simple way. whole: 0.66 (0.19), residues: 2136 helix: 1.69 (0.18), residues: 880 sheet: -1.13 (0.33), residues: 288 loop : -0.14 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 293 TYR 0.010 0.001 TYR B 381 PHE 0.017 0.001 PHE B 67 TRP 0.005 0.001 TRP B 285 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (17080) covalent geometry : angle 0.51337 / 0.26 (23316) hydrogen bonds : bond 0.02914 / 1.99 ( 716) hydrogen bonds : angle 4.40710 / 3.20 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6526.53 seconds wall clock time: 111 minutes 36.97 seconds (6696.97 seconds total)