Starting phenix.real_space_refine on Mon Jul 6 04:59:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612.map" model { file = "/net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uv9_42612/07_2026/8uv9_42612_trim.cif" } resolution = 2.8 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= 0.062 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: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 52 5.16 5 C 10456 2.51 5 N 2936 2.21 5 O 3180 1.98 5 F 4 1.80 5 H 16292 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 32936 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "B" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "D" Number of atoms: 8162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8162 Classifications: {'peptide': 535} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 501} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 2, 'Q2N': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 2, 'Q2N': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'Q2N': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'Q2N': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.93, per 1000 atoms: 0.18 Number of scatterers: 32936 At special positions: 0 Unit cell: (132.351, 137.409, 96.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 52 16.00 P 12 15.00 Mg 4 11.99 F 4 9.00 O 3180 8.00 N 2936 7.00 C 10456 6.00 H 16292 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: 3.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 20 sheets defined 47.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 23 through 38 Processing helix chain 'A' and resid 54 through 58 removed outlier: 3.848A 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 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 120 through 136 removed outlier: 7.209A pdb=" N THR A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.587A pdb=" N ILE A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 241 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 276 Processing helix chain 'A' and resid 285 through 297 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 371 through 386 removed outlier: 3.854A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.658A pdb=" N GLU A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.848A 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 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 120 through 136 removed outlier: 7.209A pdb=" N THR B 126 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 213 removed outlier: 3.587A pdb=" N ILE B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 241 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 276 Processing helix chain 'B' and resid 285 through 297 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 371 through 386 removed outlier: 3.862A pdb=" N LYS B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 484 through 490 removed outlier: 3.655A pdb=" N GLU B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 535 through 552 Processing helix chain 'C' and resid 23 through 38 Processing helix chain 'C' and resid 54 through 58 removed outlier: 3.847A 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 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 120 through 136 removed outlier: 7.211A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 177 Processing helix chain 'C' and resid 200 through 213 removed outlier: 3.581A pdb=" N ILE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 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 276 Processing helix chain 'C' and resid 285 through 297 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 343 through 346 Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 371 through 386 removed outlier: 3.858A pdb=" N LYS C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 484 through 490 removed outlier: 3.651A pdb=" N GLU C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 535 through 552 Processing helix chain 'D' and resid 23 through 38 Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.845A 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 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 120 through 136 removed outlier: 7.210A pdb=" N THR D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET D 136 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 177 Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.587A pdb=" N ILE D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 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 276 Processing helix chain 'D' and resid 285 through 297 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.864A pdb=" N LYS D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 484 through 490 removed outlier: 3.655A pdb=" N GLU D 490 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 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: 6.965A pdb=" N THR A 43 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU A 152 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN A 45 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY A 16 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N ALA A 219 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 183 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE A 221 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 185 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG A 223 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER A 187 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 220 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A 250 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 222 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 341 removed outlier: 6.588A pdb=" N GLU A 300 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU A 336 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 302 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N CYS A 338 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 304 " --> pdb=" O CYS A 338 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 340 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A 306 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N GLY A 360 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ARG A 303 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 362 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 305 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 361 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 392 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 363 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 505 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 498 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE A 507 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 413 through 414 removed outlier: 6.827A pdb=" N ASN A 413 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.965A pdb=" N THR B 43 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLU B 152 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN B 45 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY B 16 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N ALA B 219 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE B 183 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE B 221 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS B 185 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG B 223 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 187 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 220 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 250 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU B 222 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA9, first strand: chain 'B' and resid 333 through 341 removed outlier: 6.592A pdb=" N GLU B 300 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU B 336 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 302 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS B 338 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 304 " --> pdb=" O CYS B 338 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 340 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 306 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N GLY B 360 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG B 303 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU B 362 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 305 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 361 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU B 392 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 363 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 505 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 498 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE B 507 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 414 removed outlier: 6.831A pdb=" N ASN B 413 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.965A pdb=" N THR C 43 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU C 152 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN C 45 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY C 16 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N ALA C 219 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE C 183 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE C 221 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 185 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ARG C 223 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER C 187 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 220 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C 250 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU C 222 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'C' and resid 191 through 192 Processing sheet with id=AB5, first strand: chain 'C' and resid 333 through 341 removed outlier: 6.597A pdb=" N GLU C 300 " --> pdb=" O LYS C 334 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLU C 336 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 302 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYS C 338 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE C 304 " --> pdb=" O CYS C 338 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 340 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU C 306 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N GLY C 360 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG C 303 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU C 362 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA C 305 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 361 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU C 392 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 363 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 505 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR C 498 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE C 507 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 413 through 414 removed outlier: 6.830A pdb=" N ASN C 413 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.964A pdb=" N THR D 43 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU D 152 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN D 45 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY D 16 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N ALA D 219 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE D 183 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE D 221 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS D 185 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG D 223 " --> pdb=" O HIS D 185 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 187 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 220 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 250 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU D 222 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 192 Processing sheet with id=AC1, first strand: chain 'D' and resid 333 through 341 removed outlier: 6.597A pdb=" N GLU D 300 " --> pdb=" O LYS D 334 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLU D 336 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 302 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYS D 338 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE D 304 " --> pdb=" O CYS D 338 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 340 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU D 306 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLY D 360 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG D 303 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU D 362 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA D 305 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL D 361 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU D 392 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 363 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL D 505 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 498 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE D 507 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 413 through 414 removed outlier: 6.823A pdb=" N ASN D 413 " --> pdb=" O ILE D 426 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2172 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: 8.72 Time building geometry restraints manager: 4.60 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: 16268 1.03 - 1.22: 60 1.22 - 1.42: 6984 1.42 - 1.61: 9896 1.61 - 1.81: 92 Bond restraints: 33300 Sorted by residual: bond pdb=" C07 Q2N A 602 " pdb=" N11 Q2N A 602 " ideal model delta sigma weight residual 1.370 1.588 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C07 Q2N C 603 " pdb=" N11 Q2N C 603 " ideal model delta sigma weight residual 1.370 1.588 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C07 Q2N D 603 " pdb=" N11 Q2N D 603 " ideal model delta sigma weight residual 1.370 1.588 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C07 Q2N B 602 " pdb=" N11 Q2N B 602 " ideal model delta sigma weight residual 1.370 1.587 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C6 UTP B 604 " pdb=" N1 UTP B 604 " ideal model delta sigma weight residual 1.369 1.579 -0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 33295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 60018 4.01 - 8.01: 136 8.01 - 12.02: 40 12.02 - 16.02: 6 16.02 - 20.03: 12 Bond angle restraints: 60212 Sorted by residual: angle pdb=" O1A UTP A 604 " pdb=" PA UTP A 604 " pdb=" O2A UTP A 604 " ideal model delta sigma weight residual 121.55 101.52 20.03 3.00e+00 1.11e-01 4.46e+01 angle pdb=" O1A UTP B 604 " pdb=" PA UTP B 604 " pdb=" O2A UTP B 604 " ideal model delta sigma weight residual 121.55 101.56 19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" O1A UTP D 602 " pdb=" PA UTP D 602 " pdb=" O2A UTP D 602 " ideal model delta sigma weight residual 121.55 101.62 19.93 3.00e+00 1.11e-01 4.41e+01 angle pdb=" O1A UTP C 602 " pdb=" PA UTP C 602 " pdb=" O2A UTP C 602 " ideal model delta sigma weight residual 121.55 101.62 19.93 3.00e+00 1.11e-01 4.41e+01 angle pdb=" O1B UTP B 604 " pdb=" PB UTP B 604 " pdb=" O2B UTP B 604 " ideal model delta sigma weight residual 119.49 101.10 18.39 3.00e+00 1.11e-01 3.76e+01 ... (remaining 60207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13980 17.78 - 35.55: 890 35.55 - 53.32: 410 53.32 - 71.10: 440 71.10 - 88.87: 32 Dihedral angle restraints: 15752 sinusoidal: 8752 harmonic: 7000 Sorted by residual: dihedral pdb=" CA ALA D 333 " pdb=" C ALA D 333 " pdb=" N LYS D 334 " pdb=" CA LYS D 334 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ALA A 333 " pdb=" C ALA A 333 " pdb=" N LYS A 334 " pdb=" CA LYS A 334 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ALA B 333 " pdb=" C ALA B 333 " pdb=" N LYS B 334 " pdb=" CA LYS B 334 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 15749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1617 0.043 - 0.086: 708 0.086 - 0.129: 245 0.129 - 0.172: 27 0.172 - 0.215: 11 Chirality restraints: 2608 Sorted by residual: chirality pdb=" C3' UTP C 602 " pdb=" C2' UTP C 602 " pdb=" C4' UTP C 602 " pdb=" O3' UTP C 602 " both_signs ideal model delta sigma weight residual False -2.69 -2.47 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' UTP D 602 " pdb=" C2' UTP D 602 " pdb=" C4' UTP D 602 " pdb=" O3' UTP D 602 " both_signs ideal model delta sigma weight residual False -2.69 -2.48 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO A 536 " pdb=" N PRO A 536 " pdb=" C PRO A 536 " pdb=" CB PRO A 536 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2605 not shown) Planarity restraints: 5044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 132 " 0.105 9.50e-02 1.11e+02 6.16e-02 5.91e+01 pdb=" NE ARG D 132 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG D 132 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG D 132 " -0.096 2.00e-02 2.50e+03 pdb=" NH2 ARG D 132 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG D 132 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG D 132 " 0.097 2.00e-02 2.50e+03 pdb="HH21 ARG D 132 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 132 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 132 " -0.107 9.50e-02 1.11e+02 6.19e-02 5.89e+01 pdb=" NE ARG A 132 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 132 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 132 " 0.096 2.00e-02 2.50e+03 pdb=" NH2 ARG A 132 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 132 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 132 " -0.097 2.00e-02 2.50e+03 pdb="HH21 ARG A 132 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 132 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 132 " 0.106 9.50e-02 1.11e+02 6.17e-02 5.87e+01 pdb=" NE ARG C 132 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 132 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG C 132 " -0.096 2.00e-02 2.50e+03 pdb=" NH2 ARG C 132 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG C 132 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 132 " 0.097 2.00e-02 2.50e+03 pdb="HH21 ARG C 132 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 132 " -0.028 2.00e-02 2.50e+03 ... (remaining 5041 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1278 2.15 - 2.76: 61820 2.76 - 3.38: 94279 3.38 - 3.99: 125539 3.99 - 4.60: 194868 Nonbonded interactions: 477784 Sorted by model distance: nonbonded pdb=" HG1 THR D 69 " pdb=" OD1 ASP D 71 " model vdw 1.539 2.450 nonbonded pdb=" HG1 THR A 69 " pdb=" OD1 ASP A 71 " model vdw 1.540 2.450 nonbonded pdb=" HG1 THR B 69 " pdb=" OD1 ASP B 71 " model vdw 1.540 2.450 nonbonded pdb=" HG1 THR C 69 " pdb=" OD1 ASP C 71 " model vdw 1.540 2.450 nonbonded pdb="HH22 ARG D 385 " pdb=" OE2 GLU D 552 " model vdw 1.614 2.450 ... (remaining 477779 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 0.220 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 0.010 0.218 17008 Z= 0.452 Angle : 1.103 20.028 23164 Z= 0.545 Chirality : 0.052 0.215 2608 Planarity : 0.010 0.076 3044 Dihedral : 13.702 88.874 6324 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.59 % Favored : 97.03 % Rotamer: Outliers : 0.68 % Allowed : 4.11 % Favored : 95.21 % 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: -0.45 (0.17), residues: 2124 helix: -0.65 (0.15), residues: 876 sheet: 0.46 (0.29), residues: 344 loop : -0.01 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG C 132 TYR 0.028 0.006 TYR B 102 PHE 0.024 0.003 PHE C 182 TRP 0.021 0.004 TRP C 339 HIS 0.009 0.002 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00957 / 0.45 (17008) covalent geometry : angle 1.10348 / 0.54 (23164) hydrogen bonds : bond 0.15090 / 10.47 ( 760) hydrogen bonds : angle 7.03576 / 5.02 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 386 time to evaluate : 0.938 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: A 402 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 468 THR cc_start: 0.7732 (p) cc_final: 0.7397 (t) REVERT: B 274 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6975 (mtp180) REVERT: B 402 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 468 THR cc_start: 0.7722 (p) cc_final: 0.7418 (t) REVERT: C 402 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7100 (tm-30) REVERT: C 468 THR cc_start: 0.7736 (p) cc_final: 0.7368 (t) REVERT: C 469 GLN cc_start: 0.7827 (mt0) cc_final: 0.7482 (mm-40) REVERT: D 402 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7115 (tm-30) REVERT: D 468 THR cc_start: 0.7718 (p) cc_final: 0.7382 (t) REVERT: D 469 GLN cc_start: 0.7818 (mt0) cc_final: 0.7475 (mm-40) outliers start: 12 outliers final: 4 residues processed: 394 average time/residue: 1.2387 time to fit residues: 545.7338 Evaluate side-chains 279 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 275 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain D residue 376 ILE 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: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 204 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.137611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.104001 restraints weight = 52009.998| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.54 r_work: 0.2892 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17008 Z= 0.137 Angle : 0.590 6.871 23164 Z= 0.304 Chirality : 0.044 0.142 2608 Planarity : 0.005 0.050 3044 Dihedral : 8.021 55.685 2512 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.74 % Allowed : 9.19 % Favored : 90.07 % 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: 1.00 (0.18), residues: 2124 helix: 1.32 (0.18), residues: 884 sheet: 0.62 (0.28), residues: 344 loop : 0.15 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 145 TYR 0.012 0.002 TYR C 381 PHE 0.014 0.001 PHE B 417 TRP 0.008 0.002 TRP D 288 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17008) covalent geometry : angle 0.59003 / 0.30 (23164) hydrogen bonds : bond 0.04266 / 2.91 ( 760) hydrogen bonds : angle 5.25595 / 3.75 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 299 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: A 274 ARG cc_start: 0.7620 (mtm110) cc_final: 0.7276 (mtp180) REVERT: A 402 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 468 THR cc_start: 0.7808 (p) cc_final: 0.7405 (t) REVERT: B 266 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 274 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7098 (mtp180) REVERT: B 332 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7482 (mtt90) REVERT: B 468 THR cc_start: 0.7851 (p) cc_final: 0.7457 (t) REVERT: C 274 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7288 (mtp180) REVERT: C 402 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7352 (tm-30) REVERT: C 468 THR cc_start: 0.7860 (p) cc_final: 0.7428 (t) REVERT: C 469 GLN cc_start: 0.8072 (mt0) cc_final: 0.7588 (mm-40) REVERT: D 274 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7287 (mtp180) REVERT: D 402 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 468 THR cc_start: 0.7824 (p) cc_final: 0.7382 (t) REVERT: D 469 GLN cc_start: 0.8056 (mt0) cc_final: 0.7579 (mm-40) outliers start: 13 outliers final: 4 residues processed: 307 average time/residue: 1.2116 time to fit residues: 421.0924 Evaluate side-chains 277 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 14 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 503 HIS B 503 HIS C 204 GLN C 503 HIS D 503 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.135799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.101980 restraints weight = 51803.422| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.53 r_work: 0.2856 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17008 Z= 0.148 Angle : 0.545 6.462 23164 Z= 0.280 Chirality : 0.044 0.147 2608 Planarity : 0.005 0.046 3044 Dihedral : 6.610 53.504 2504 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.03 % Allowed : 10.33 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2124 helix: 1.88 (0.18), residues: 884 sheet: 0.76 (0.28), residues: 360 loop : 0.17 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.008 0.001 TYR A 50 PHE 0.013 0.001 PHE D 417 TRP 0.007 0.002 TRP C 288 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (17008) covalent geometry : angle 0.54526 / 0.28 (23164) hydrogen bonds : bond 0.04302 / 2.94 ( 760) hydrogen bonds : angle 4.82387 / 3.45 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 288 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7301 (mtp180) REVERT: A 402 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7464 (tm-30) REVERT: A 468 THR cc_start: 0.7945 (p) cc_final: 0.7533 (t) REVERT: B 274 ARG cc_start: 0.7474 (ttp80) cc_final: 0.6937 (mtp180) REVERT: B 385 ARG cc_start: 0.7456 (mmm-85) cc_final: 0.7206 (mmm-85) REVERT: B 468 THR cc_start: 0.7949 (p) cc_final: 0.7539 (t) REVERT: C 274 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7293 (mtp180) REVERT: C 402 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 468 THR cc_start: 0.7939 (p) cc_final: 0.7507 (t) REVERT: C 469 GLN cc_start: 0.8076 (mt0) cc_final: 0.7662 (mm-40) REVERT: D 145 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7586 (ttp-170) REVERT: D 274 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7284 (mtp180) REVERT: D 402 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 468 THR cc_start: 0.7940 (p) cc_final: 0.7499 (t) REVERT: D 469 GLN cc_start: 0.8060 (mt0) cc_final: 0.7589 (mm110) outliers start: 18 outliers final: 5 residues processed: 297 average time/residue: 1.3017 time to fit residues: 430.4145 Evaluate side-chains 272 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain D residue 238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 139 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 522 GLN B 95 ASN B 163 GLN B 522 GLN C 59 ASN C 95 ASN C 522 GLN D 95 ASN D 163 GLN D 522 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.099863 restraints weight = 51526.337| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.51 r_work: 0.2846 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17008 Z= 0.190 Angle : 0.577 7.028 23164 Z= 0.297 Chirality : 0.045 0.147 2608 Planarity : 0.006 0.046 3044 Dihedral : 6.803 57.338 2504 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 9.87 % Favored : 87.96 % 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: 1.29 (0.18), residues: 2124 helix: 2.01 (0.18), residues: 856 sheet: 0.80 (0.28), residues: 344 loop : -0.18 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.013 0.002 TYR D 478 PHE 0.017 0.002 PHE D 61 TRP 0.007 0.002 TRP C 288 HIS 0.007 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (17008) covalent geometry : angle 0.57697 / 0.30 (23164) hydrogen bonds : bond 0.04516 / 3.08 ( 760) hydrogen bonds : angle 4.82550 / 3.46 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.792 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: A 275 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8162 (tpt-90) REVERT: A 402 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 468 THR cc_start: 0.7993 (p) cc_final: 0.7589 (t) REVERT: B 274 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7063 (mtp180) REVERT: B 275 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8053 (tpt170) REVERT: B 468 THR cc_start: 0.8007 (p) cc_final: 0.7568 (t) REVERT: B 469 GLN cc_start: 0.8154 (mt0) cc_final: 0.7544 (mm-40) REVERT: C 275 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8107 (tpt-90) REVERT: C 468 THR cc_start: 0.8017 (p) cc_final: 0.7605 (t) REVERT: C 469 GLN cc_start: 0.8100 (mt0) cc_final: 0.7657 (mm-40) REVERT: D 275 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8068 (tpt-90) REVERT: D 334 LYS cc_start: 0.8245 (tttp) cc_final: 0.7936 (tttp) REVERT: D 468 THR cc_start: 0.7996 (p) cc_final: 0.7567 (t) REVERT: D 469 GLN cc_start: 0.8092 (mt0) cc_final: 0.7616 (mm110) outliers start: 38 outliers final: 14 residues processed: 296 average time/residue: 1.3797 time to fit residues: 453.2445 Evaluate side-chains 282 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 496 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN C 163 GLN D 59 ASN D 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.133076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.099501 restraints weight = 51649.860| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.49 r_work: 0.2842 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17008 Z= 0.175 Angle : 0.555 6.971 23164 Z= 0.283 Chirality : 0.045 0.144 2608 Planarity : 0.005 0.035 3044 Dihedral : 6.713 58.757 2504 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.40 % Allowed : 10.10 % 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: 1.34 (0.18), residues: 2124 helix: 2.10 (0.18), residues: 856 sheet: 0.86 (0.28), residues: 344 loop : -0.23 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.016 0.002 TYR B 484 PHE 0.016 0.002 PHE C 61 TRP 0.007 0.002 TRP D 339 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.17 (17008) covalent geometry : angle 0.55502 / 0.28 (23164) hydrogen bonds : bond 0.04303 / 2.93 ( 760) hydrogen bonds : angle 4.77344 / 3.42 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.918 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: A 275 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8157 (tpt-90) REVERT: A 468 THR cc_start: 0.8009 (p) cc_final: 0.7611 (t) REVERT: B 173 ARG cc_start: 0.8399 (tpt90) cc_final: 0.7760 (tpt-90) REVERT: B 274 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7081 (mtp180) REVERT: B 275 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8072 (tpt-90) REVERT: B 468 THR cc_start: 0.8010 (p) cc_final: 0.7593 (t) REVERT: B 469 GLN cc_start: 0.8187 (mt0) cc_final: 0.7631 (mm-40) REVERT: C 275 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8142 (tpt-90) REVERT: C 468 THR cc_start: 0.8034 (p) cc_final: 0.7641 (t) REVERT: C 469 GLN cc_start: 0.8126 (mt0) cc_final: 0.7697 (mm-40) REVERT: D 275 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8149 (tpt-90) REVERT: D 334 LYS cc_start: 0.8265 (tttp) cc_final: 0.7814 (tptp) REVERT: D 468 THR cc_start: 0.8012 (p) cc_final: 0.7611 (t) REVERT: D 469 GLN cc_start: 0.8105 (mt0) cc_final: 0.7650 (mm110) outliers start: 42 outliers final: 17 residues processed: 295 average time/residue: 1.5086 time to fit residues: 492.1638 Evaluate side-chains 286 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 496 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS B 59 ASN B 62 GLN D 41 HIS D 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099155 restraints weight = 51593.951| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.49 r_work: 0.2839 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17008 Z= 0.181 Angle : 0.560 6.977 23164 Z= 0.285 Chirality : 0.045 0.146 2608 Planarity : 0.005 0.038 3044 Dihedral : 6.734 59.505 2504 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 9.87 % Favored : 87.73 % 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: 1.30 (0.18), residues: 2124 helix: 2.09 (0.18), residues: 856 sheet: 0.91 (0.28), residues: 344 loop : -0.30 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.018 0.002 TYR B 478 PHE 0.016 0.002 PHE A 61 TRP 0.007 0.002 TRP C 339 HIS 0.006 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (17008) covalent geometry : angle 0.56016 / 0.29 (23164) hydrogen bonds : bond 0.04327 / 2.94 ( 760) hydrogen bonds : angle 4.76874 / 3.42 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.939 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: A 275 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8156 (tpt-90) REVERT: A 468 THR cc_start: 0.8029 (p) cc_final: 0.7663 (t) REVERT: B 173 ARG cc_start: 0.8406 (tpt90) cc_final: 0.7758 (tpt-90) REVERT: B 274 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7063 (mtp180) REVERT: B 275 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (tpt-90) REVERT: B 468 THR cc_start: 0.8027 (p) cc_final: 0.7702 (m) REVERT: B 469 GLN cc_start: 0.8179 (mt0) cc_final: 0.7632 (mm-40) REVERT: C 275 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8142 (tpt-90) REVERT: C 468 THR cc_start: 0.8054 (p) cc_final: 0.7663 (t) REVERT: C 469 GLN cc_start: 0.8140 (mt0) cc_final: 0.7734 (mm-40) REVERT: D 275 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8141 (tpt-90) REVERT: D 334 LYS cc_start: 0.8281 (tttp) cc_final: 0.7905 (tttp) REVERT: D 468 THR cc_start: 0.8043 (p) cc_final: 0.7692 (m) REVERT: D 469 GLN cc_start: 0.8106 (mt0) cc_final: 0.7655 (mm110) outliers start: 42 outliers final: 16 residues processed: 287 average time/residue: 1.3508 time to fit residues: 431.0942 Evaluate side-chains 290 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 170 optimal weight: 0.0370 chunk 69 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS B 59 ASN C 59 ASN D 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.134768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.101481 restraints weight = 51560.053| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.49 r_work: 0.2875 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17008 Z= 0.100 Angle : 0.488 6.330 23164 Z= 0.245 Chirality : 0.043 0.143 2608 Planarity : 0.004 0.034 3044 Dihedral : 6.270 57.168 2504 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.37 % Allowed : 11.13 % 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: 1.69 (0.18), residues: 2124 helix: 2.51 (0.18), residues: 856 sheet: 1.00 (0.27), residues: 340 loop : -0.14 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.016 0.001 TYR D 478 PHE 0.010 0.001 PHE C 61 TRP 0.006 0.001 TRP A 339 HIS 0.003 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (17008) covalent geometry : angle 0.48846 / 0.25 (23164) hydrogen bonds : bond 0.03382 / 2.29 ( 760) hydrogen bonds : angle 4.48541 / 3.22 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 THR cc_start: 0.8012 (p) cc_final: 0.7654 (t) REVERT: B 274 ARG cc_start: 0.7423 (ttp80) cc_final: 0.6891 (mtp180) REVERT: B 385 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.7223 (mmm-85) REVERT: B 413 ASN cc_start: 0.8169 (t0) cc_final: 0.7841 (t0) REVERT: B 468 THR cc_start: 0.8012 (p) cc_final: 0.7652 (t) REVERT: B 469 GLN cc_start: 0.8145 (mt0) cc_final: 0.7518 (mm110) REVERT: C 466 GLN cc_start: 0.7826 (mm110) cc_final: 0.7540 (mm110) REVERT: C 468 THR cc_start: 0.8038 (p) cc_final: 0.7659 (t) REVERT: C 469 GLN cc_start: 0.8102 (mt0) cc_final: 0.7714 (mm-40) REVERT: D 334 LYS cc_start: 0.8241 (tttp) cc_final: 0.7951 (tttp) REVERT: D 413 ASN cc_start: 0.8088 (t0) cc_final: 0.7779 (t0) REVERT: D 468 THR cc_start: 0.8023 (p) cc_final: 0.7677 (m) REVERT: D 469 GLN cc_start: 0.8076 (mt0) cc_final: 0.7635 (mm110) outliers start: 24 outliers final: 11 residues processed: 300 average time/residue: 1.4587 time to fit residues: 486.8768 Evaluate side-chains 291 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 280 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 238 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 103 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 208 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS D 41 HIS D 59 ASN D 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100337 restraints weight = 51452.873| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.48 r_work: 0.2854 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17008 Z= 0.141 Angle : 0.521 6.555 23164 Z= 0.262 Chirality : 0.044 0.144 2608 Planarity : 0.005 0.034 3044 Dihedral : 6.469 58.536 2504 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.20 % Allowed : 11.36 % Favored : 87.44 % 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: 1.64 (0.18), residues: 2124 helix: 2.44 (0.18), residues: 856 sheet: 1.10 (0.27), residues: 340 loop : -0.19 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 88 TYR 0.016 0.001 TYR D 478 PHE 0.014 0.001 PHE B 61 TRP 0.006 0.002 TRP B 339 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (17008) covalent geometry : angle 0.52100 / 0.26 (23164) hydrogen bonds : bond 0.03820 / 2.59 ( 760) hydrogen bonds : angle 4.56772 / 3.27 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.966 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: A 468 THR cc_start: 0.8022 (p) cc_final: 0.7659 (t) REVERT: B 274 ARG cc_start: 0.7486 (ttp80) cc_final: 0.6938 (mtp180) REVERT: B 275 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8147 (tpt-90) REVERT: B 385 ARG cc_start: 0.7472 (mmm-85) cc_final: 0.7219 (mmm-85) REVERT: B 413 ASN cc_start: 0.8205 (t0) cc_final: 0.7883 (t0) REVERT: B 468 THR cc_start: 0.8028 (p) cc_final: 0.7712 (m) REVERT: B 469 GLN cc_start: 0.8144 (mt0) cc_final: 0.7627 (mm-40) REVERT: C 468 THR cc_start: 0.8042 (p) cc_final: 0.7680 (t) REVERT: C 469 GLN cc_start: 0.8125 (mt0) cc_final: 0.7737 (mm-40) REVERT: D 334 LYS cc_start: 0.8273 (tttp) cc_final: 0.7908 (tttp) REVERT: D 413 ASN cc_start: 0.8117 (t0) cc_final: 0.7804 (t0) REVERT: D 468 THR cc_start: 0.8030 (p) cc_final: 0.7710 (m) REVERT: D 469 GLN cc_start: 0.8078 (mt0) cc_final: 0.7650 (mm110) outliers start: 21 outliers final: 12 residues processed: 291 average time/residue: 1.4775 time to fit residues: 478.0091 Evaluate side-chains 292 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 162 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS B 59 ASN B 62 GLN D 41 HIS D 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.101719 restraints weight = 51352.727| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.49 r_work: 0.2876 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17008 Z= 0.098 Angle : 0.484 6.255 23164 Z= 0.242 Chirality : 0.042 0.144 2608 Planarity : 0.004 0.035 3044 Dihedral : 6.180 57.091 2504 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.20 % Allowed : 11.82 % 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: 1.86 (0.18), residues: 2124 helix: 2.69 (0.19), residues: 856 sheet: 1.00 (0.27), residues: 340 loop : -0.04 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 145 TYR 0.016 0.001 TYR C 478 PHE 0.009 0.001 PHE A 61 TRP 0.006 0.001 TRP A 339 HIS 0.004 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (17008) covalent geometry : angle 0.48440 / 0.24 (23164) hydrogen bonds : bond 0.03283 / 2.22 ( 760) hydrogen bonds : angle 4.40458 / 3.16 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 0.816 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: A 309 LYS cc_start: 0.7721 (tttp) cc_final: 0.7212 (ttmt) REVERT: A 468 THR cc_start: 0.8023 (p) cc_final: 0.7664 (t) REVERT: B 274 ARG cc_start: 0.7427 (ttp80) cc_final: 0.6897 (mtp180) REVERT: B 385 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7159 (mmm-85) REVERT: B 413 ASN cc_start: 0.8123 (t0) cc_final: 0.7823 (t0) REVERT: B 468 THR cc_start: 0.8022 (p) cc_final: 0.7707 (m) REVERT: B 469 GLN cc_start: 0.8109 (mt0) cc_final: 0.7517 (mm110) REVERT: C 413 ASN cc_start: 0.8083 (t0) cc_final: 0.7787 (t0) REVERT: C 466 GLN cc_start: 0.7833 (mm110) cc_final: 0.7543 (mm110) REVERT: C 468 THR cc_start: 0.8041 (p) cc_final: 0.7659 (t) REVERT: C 469 GLN cc_start: 0.8088 (mt0) cc_final: 0.7705 (mm-40) REVERT: D 334 LYS cc_start: 0.8266 (tttp) cc_final: 0.7906 (tttp) REVERT: D 413 ASN cc_start: 0.8048 (t0) cc_final: 0.7752 (t0) REVERT: D 468 THR cc_start: 0.8035 (p) cc_final: 0.7696 (m) REVERT: D 469 GLN cc_start: 0.8061 (mt0) cc_final: 0.7626 (mm110) outliers start: 21 outliers final: 12 residues processed: 290 average time/residue: 1.3750 time to fit residues: 443.9590 Evaluate side-chains 290 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS B 59 ASN D 41 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.133585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.100109 restraints weight = 51934.762| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.50 r_work: 0.2853 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17008 Z= 0.158 Angle : 0.534 6.640 23164 Z= 0.269 Chirality : 0.044 0.144 2608 Planarity : 0.005 0.038 3044 Dihedral : 6.476 58.636 2504 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.08 % Allowed : 12.16 % Favored : 86.76 % 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: 1.69 (0.18), residues: 2124 helix: 2.47 (0.18), residues: 856 sheet: 1.15 (0.27), residues: 340 loop : -0.16 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 385 TYR 0.012 0.001 TYR C 478 PHE 0.015 0.002 PHE A 61 TRP 0.006 0.002 TRP C 339 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (17008) covalent geometry : angle 0.53361 / 0.27 (23164) hydrogen bonds : bond 0.03939 / 2.67 ( 760) hydrogen bonds : angle 4.58735 / 3.28 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 0.952 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: A 309 LYS cc_start: 0.7758 (tttp) cc_final: 0.7283 (ttmt) REVERT: A 468 THR cc_start: 0.8060 (p) cc_final: 0.7703 (t) REVERT: A 469 GLN cc_start: 0.8182 (mt0) cc_final: 0.7705 (mm-40) REVERT: B 145 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7764 (ttp-170) REVERT: B 274 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6933 (mtp180) REVERT: B 275 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8215 (tpt-90) REVERT: B 312 GLU cc_start: 0.7091 (tp30) cc_final: 0.6674 (tp30) REVERT: B 385 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.7195 (mmm-85) REVERT: B 413 ASN cc_start: 0.8186 (t0) cc_final: 0.7903 (t0) REVERT: B 468 THR cc_start: 0.8058 (p) cc_final: 0.7735 (m) REVERT: B 469 GLN cc_start: 0.8125 (mt0) cc_final: 0.7502 (mm110) REVERT: C 413 ASN cc_start: 0.8149 (t0) cc_final: 0.7853 (t0) REVERT: C 468 THR cc_start: 0.8043 (p) cc_final: 0.7690 (t) REVERT: C 469 GLN cc_start: 0.8123 (mt0) cc_final: 0.7736 (mm-40) REVERT: D 334 LYS cc_start: 0.8284 (tttp) cc_final: 0.7908 (tttp) REVERT: D 413 ASN cc_start: 0.8088 (t0) cc_final: 0.7782 (t0) REVERT: D 468 THR cc_start: 0.8051 (p) cc_final: 0.7732 (m) REVERT: D 469 GLN cc_start: 0.8064 (mt0) cc_final: 0.7639 (mm110) outliers start: 19 outliers final: 12 residues processed: 289 average time/residue: 1.4055 time to fit residues: 452.0900 Evaluate side-chains 289 residues out of total 1752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 276 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 275 ARG Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 238 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 127 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 192 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS B 41 HIS D 41 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.134804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.101381 restraints weight = 51657.159| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.49 r_work: 0.2871 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17008 Z= 0.106 Angle : 0.492 6.421 23164 Z= 0.246 Chirality : 0.043 0.143 2608 Planarity : 0.004 0.034 3044 Dihedral : 6.211 57.422 2504 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.97 % Allowed : 12.27 % Favored : 86.76 % 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: 1.85 (0.18), residues: 2124 helix: 2.67 (0.18), residues: 856 sheet: 1.06 (0.27), residues: 340 loop : -0.07 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.012 0.001 TYR C 478 PHE 0.010 0.001 PHE B 61 TRP 0.006 0.001 TRP A 339 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (17008) covalent geometry : angle 0.49241 / 0.25 (23164) hydrogen bonds : bond 0.03395 / 2.30 ( 760) hydrogen bonds : angle 4.43764 / 3.18 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11975.40 seconds wall clock time: 203 minutes 0.74 seconds (12180.74 seconds total)