Starting phenix.real_space_refine on Mon Sep 14 17:50:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mii_23852/09_2026/7mii_23852.map" } resolution = 2.7 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= 0.205 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 92 5.16 5 C 10284 2.51 5 N 2768 2.21 5 O 2928 1.98 5 F 12 1.80 5 H 16108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32208 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "B" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "C" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "E" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7968 Classifications: {'peptide': 497} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 472} Chain breaks: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN A 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Inner-chain residues flagged as termini: ['pdbres="GLN C 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {' MG': 1, 'UTP': 1, 'ZFY': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS A 243 " occ=0.75 residue: pdb=" N GLU B 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU B 155 " occ=0.75 residue: pdb=" N CYS B 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS B 243 " occ=0.75 residue: pdb=" N GLU C 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU C 155 " occ=0.75 residue: pdb=" N CYS C 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS C 243 " occ=0.75 residue: pdb=" N GLU E 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU E 155 " occ=0.75 residue: pdb=" N CYS E 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS E 243 " occ=0.75 Time building chain proxies: 5.16, per 1000 atoms: 0.16 Number of scatterers: 32208 At special positions: 0 Unit cell: (124.95, 133.35, 87.15, 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 92 16.00 P 12 15.00 Mg 4 11.99 F 12 9.00 O 2928 8.00 N 2768 7.00 C 10284 6.00 H 16108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 822.8 milliseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 49.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.917A pdb=" N ILE A 14 " --> pdb=" O ILE A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.743A pdb=" N THR A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 112 through 130 removed outlier: 7.149A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.076A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.453A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 removed outlier: 3.607A pdb=" N TYR A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 314 through 328 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.557A pdb=" N LEU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.940A pdb=" N GLN A 359 " --> pdb=" O HIS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.543A pdb=" N PHE A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'B' and resid 11 through 14 removed outlier: 3.916A pdb=" N ILE B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.743A pdb=" N THR B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 112 through 130 removed outlier: 7.149A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 169 removed outlier: 4.076A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 223 through 234 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.453A pdb=" N VAL B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 removed outlier: 3.607A pdb=" N TYR B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.557A pdb=" N LEU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.939A pdb=" N GLN B 359 " --> pdb=" O HIS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 392 Processing helix chain 'B' and resid 399 through 411 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.543A pdb=" N PHE B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 548 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'C' and resid 11 through 14 removed outlier: 3.917A pdb=" N ILE C 14 " --> pdb=" O ILE C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 14' Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.743A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.149A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 169 removed outlier: 4.075A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.453A pdb=" N VAL C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 removed outlier: 3.607A pdb=" N TYR C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.556A pdb=" N LEU C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 363 removed outlier: 3.939A pdb=" N GLN C 359 " --> pdb=" O HIS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 399 through 411 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.543A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'E' and resid 11 through 14 removed outlier: 3.916A pdb=" N ILE E 14 " --> pdb=" O ILE E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 11 through 14' Processing helix chain 'E' and resid 15 through 30 Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.743A pdb=" N THR E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 79 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 112 through 130 removed outlier: 7.149A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 156 through 169 removed outlier: 4.076A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 251 through 259 removed outlier: 4.453A pdb=" N VAL E 255 " --> pdb=" O TYR E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 271 removed outlier: 3.607A pdb=" N TYR E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 293 Processing helix chain 'E' and resid 314 through 328 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.557A pdb=" N LEU E 342 " --> pdb=" O ASP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 363 removed outlier: 3.939A pdb=" N GLN E 359 " --> pdb=" O HIS E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 392 Processing helix chain 'E' and resid 399 through 411 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 526 through 531 removed outlier: 3.543A pdb=" N PHE E 529 " --> pdb=" O HIS E 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 548 Processing helix chain 'E' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.745A pdb=" N LYS A 2 " --> pdb=" O CYS A 143 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE A 145 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 9 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N LEU A 213 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 177 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 215 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 179 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG A 217 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 218 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 336 removed outlier: 9.133A pdb=" N GLY A 366 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER A 300 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU A 368 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 367 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 398 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 369 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 523 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY A 397 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY A 501 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 512 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 499 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 514 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 497 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.745A pdb=" N LYS B 2 " --> pdb=" O CYS B 143 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 147 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 6 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 3 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 180 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU B 182 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY B 9 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 213 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN B 177 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL B 215 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS B 179 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG B 217 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER B 181 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 218 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA6, first strand: chain 'B' and resid 330 through 336 removed outlier: 9.133A pdb=" N GLY B 366 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER B 300 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU B 368 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 302 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 367 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL B 398 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 369 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL B 523 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 397 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 501 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 512 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 499 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 514 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 497 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.746A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY C 9 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 218 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AA9, first strand: chain 'C' and resid 330 through 336 removed outlier: 9.133A pdb=" N GLY C 366 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 398 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 369 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 501 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 512 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE C 499 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 514 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 497 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.746A pdb=" N LYS E 2 " --> pdb=" O CYS E 143 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 145 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 147 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 6 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY E 9 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N LEU E 213 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN E 177 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL E 215 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N HIS E 179 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG E 217 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER E 181 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER E 218 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'E' and resid 330 through 336 removed outlier: 9.132A pdb=" N GLY E 366 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 300 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU E 368 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA E 302 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE E 367 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL E 398 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 369 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE E 395 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 523 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY E 397 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE E 520 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY E 501 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE E 512 " --> pdb=" O PHE E 499 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE E 499 " --> pdb=" O ILE E 512 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 514 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU E 497 " --> pdb=" O LEU E 514 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2004 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: 6.80 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 3570 1.07 - 1.28: 15126 1.28 - 1.48: 6525 1.48 - 1.68: 7163 1.68 - 1.89: 152 Bond restraints: 32536 Sorted by residual: bond pdb=" N VAL E 215 " pdb=" H VAL E 215 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N SER C 219 " pdb=" H SER C 219 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" NH2 ARG B 453 " pdb="HH22 ARG B 453 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N CYS C 399 " pdb=" H CYS C 399 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" NE2 GLN A 502 " pdb="HE22 GLN A 502 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 ... (remaining 32531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.43: 58362 7.43 - 14.87: 522 14.87 - 22.30: 12 22.30 - 29.73: 4 29.73 - 37.17: 16 Bond angle restraints: 58916 Sorted by residual: angle pdb=" CA ILE A 80 " pdb=" CB ILE A 80 " pdb=" CG1 ILE A 80 " ideal model delta sigma weight residual 110.40 131.81 -21.41 1.70e+00 3.46e-01 1.59e+02 angle pdb=" CA ILE E 80 " pdb=" CB ILE E 80 " pdb=" CG1 ILE E 80 " ideal model delta sigma weight residual 110.40 131.81 -21.41 1.70e+00 3.46e-01 1.59e+02 angle pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " pdb=" CG1 ILE C 80 " ideal model delta sigma weight residual 110.40 131.78 -21.38 1.70e+00 3.46e-01 1.58e+02 angle pdb=" CA ILE B 80 " pdb=" CB ILE B 80 " pdb=" CG1 ILE B 80 " ideal model delta sigma weight residual 110.40 131.78 -21.38 1.70e+00 3.46e-01 1.58e+02 angle pdb=" CG1 ILE C 80 " pdb=" CB ILE C 80 " pdb=" HB ILE C 80 " ideal model delta sigma weight residual 109.00 71.83 37.17 3.00e+00 1.11e-01 1.53e+02 ... (remaining 58911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 13436 16.99 - 33.98: 1027 33.98 - 50.97: 369 50.97 - 67.96: 412 67.96 - 84.96: 80 Dihedral angle restraints: 15324 sinusoidal: 8600 harmonic: 6724 Sorted by residual: dihedral pdb=" C ARG A 217 " pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" CB ARG A 217 " ideal model delta harmonic sigma weight residual -122.60 -136.39 13.79 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" C ARG C 217 " pdb=" N ARG C 217 " pdb=" CA ARG C 217 " pdb=" CB ARG C 217 " ideal model delta harmonic sigma weight residual -122.60 -136.37 13.77 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" CA PRO A 115 " pdb=" C PRO A 115 " pdb=" N HIS A 116 " pdb=" CA HIS A 116 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 15321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 2243 0.194 - 0.388: 193 0.388 - 0.582: 24 0.582 - 0.776: 0 0.776 - 0.970: 4 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CB ILE A 80 " pdb=" CA ILE A 80 " pdb=" CG1 ILE A 80 " pdb=" CG2 ILE A 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CB ILE B 80 " pdb=" CA ILE B 80 " pdb=" CG1 ILE B 80 " pdb=" CG2 ILE B 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CB ILE E 80 " pdb=" CA ILE E 80 " pdb=" CG1 ILE E 80 " pdb=" CG2 ILE E 80 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 2461 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 285 " -0.153 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP A 285 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 285 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 285 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 285 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP A 285 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 285 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 285 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 285 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 285 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP A 285 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 285 " 0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP A 285 " 0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 285 " -0.084 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 285 " 0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP A 285 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 285 " 0.153 2.00e-02 2.50e+03 7.10e-02 2.02e+02 pdb=" CG TRP E 285 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 285 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 285 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 285 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP E 285 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP E 285 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 285 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 285 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP E 285 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP E 285 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP E 285 " -0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP E 285 " -0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 285 " 0.084 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 285 " -0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP E 285 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 285 " -0.153 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP B 285 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 285 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 285 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 285 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP B 285 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 285 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 285 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 285 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B 285 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 TRP B 285 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP B 285 " 0.156 2.00e-02 2.50e+03 pdb=" HE3 TRP B 285 " 0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 285 " -0.083 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 285 " 0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP B 285 " -0.059 2.00e-02 2.50e+03 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 436 1.89 - 2.56: 29315 2.56 - 3.24: 104153 3.24 - 3.92: 139960 3.92 - 4.60: 210992 Nonbonded interactions: 484856 Sorted by model distance: nonbonded pdb=" HG CYS C 399 " pdb=" HB2 GLN C 603 " model vdw 1.207 2.440 nonbonded pdb=" HG CYS A 399 " pdb=" HB2 GLN A 603 " model vdw 1.207 2.440 nonbonded pdb=" HG CYS B 399 " pdb=" HB2 GLN B 604 " model vdw 1.208 2.440 nonbonded pdb=" HG CYS E 399 " pdb=" HB2 GLN E 604 " model vdw 1.209 2.440 nonbonded pdb=" HE3 MET A 157 " pdb=" HE3 MET C 157 " model vdw 1.222 2.440 ... (remaining 484851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 556) selection = (chain 'B' and resid 1 through 556) selection = (chain 'C' and resid 1 through 556) selection = (chain 'E' and resid 1 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 1.870 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.530 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.013 0.134 16428 Z= 0.794 Angle : 2.063 21.408 22228 Z= 1.387 Chirality : 0.126 0.970 2464 Planarity : 0.014 0.112 2820 Dihedral : 15.263 84.956 6348 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.83 % Allowed : 4.13 % Favored : 94.04 % Cbeta Deviations : 1.95 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 1940 helix: -1.33 (0.14), residues: 892 sheet: -1.31 (0.24), residues: 372 loop : -1.10 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 205 TYR 0.155 0.024 TYR C 74 PHE 0.061 0.016 PHE A 409 TRP 0.109 0.032 TRP B 387 HIS 0.013 0.004 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.01342 / 0.79 (16428) covalent geometry : angle 2.06326 / 1.39 (22228) hydrogen bonds : bond 0.17148 / 11.49 ( 692) hydrogen bonds : angle 7.85813 / 5.61 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 495 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 333 ASN cc_start: 0.8168 (t0) cc_final: 0.7902 (t0) REVERT: A 392 LYS cc_start: 0.7850 (mttt) cc_final: 0.7595 (mttp) REVERT: A 402 MET cc_start: 0.7837 (ttp) cc_final: 0.7612 (ttp) REVERT: B 75 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 333 ASN cc_start: 0.8187 (t0) cc_final: 0.7912 (t0) REVERT: B 392 LYS cc_start: 0.7845 (mttt) cc_final: 0.7642 (mttp) REVERT: B 402 MET cc_start: 0.7827 (ttp) cc_final: 0.7592 (ttp) REVERT: B 454 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7641 (ttm110) REVERT: C 75 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8118 (mt-10) REVERT: C 333 ASN cc_start: 0.8137 (t0) cc_final: 0.7855 (t0) REVERT: C 392 LYS cc_start: 0.7865 (mttt) cc_final: 0.7651 (mttp) REVERT: C 454 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7614 (ttm110) REVERT: E 75 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8157 (mt-10) REVERT: E 392 LYS cc_start: 0.7838 (mttt) cc_final: 0.7625 (mttp) REVERT: E 402 MET cc_start: 0.7840 (ttp) cc_final: 0.7610 (ttp) REVERT: B 604 GLN cc_start: 0.7371 (pt0) cc_final: 0.7125 (pt0) REVERT: C 603 GLN cc_start: 0.7383 (pt0) cc_final: 0.7139 (pt0) outliers start: 32 outliers final: 4 residues processed: 523 average time/residue: 1.0848 time to fit residues: 642.4221 Evaluate side-chains 353 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain E residue 55 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS A 177 ASN A 329 ASN A 359 GLN A 494 GLN A 556 GLN B 96 HIS B 177 ASN B 329 ASN B 359 GLN B 494 GLN B 556 GLN C 96 HIS C 112 GLN C 177 ASN C 329 ASN C 359 GLN C 494 GLN C 556 GLN E 96 HIS E 112 GLN E 177 ASN E 240 GLN E 329 ASN E 359 GLN E 494 GLN E 556 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140106 restraints weight = 48798.814| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.53 r_work: 0.3417 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16428 Z= 0.161 Angle : 0.670 13.545 22228 Z= 0.345 Chirality : 0.078 1.515 2464 Planarity : 0.005 0.061 2820 Dihedral : 8.756 51.892 2420 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.95 % Allowed : 12.67 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.69 (0.18), residues: 1940 helix: 0.26 (0.17), residues: 904 sheet: -1.30 (0.24), residues: 392 loop : -0.66 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 164 TYR 0.016 0.002 TYR E 42 PHE 0.016 0.002 PHE A 163 TRP 0.012 0.002 TRP A 387 HIS 0.009 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16428) covalent geometry : angle 0.67040 / 0.35 (22228) hydrogen bonds : bond 0.04158 / 2.77 ( 692) hydrogen bonds : angle 5.49416 / 3.99 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 355 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 284 LYS cc_start: 0.7424 (mttt) cc_final: 0.6939 (mtpm) REVERT: A 392 LYS cc_start: 0.7436 (mttt) cc_final: 0.7137 (mttp) REVERT: A 454 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7846 (ttm170) REVERT: A 502 GLN cc_start: 0.6511 (pt0) cc_final: 0.6311 (pt0) REVERT: B 66 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 191 GLU cc_start: 0.6888 (tt0) cc_final: 0.6661 (tm-30) REVERT: B 228 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 246 ASP cc_start: 0.8500 (m-30) cc_final: 0.8235 (m-30) REVERT: B 284 LYS cc_start: 0.7442 (mttt) cc_final: 0.6894 (mtpm) REVERT: B 287 ASN cc_start: 0.8117 (m-40) cc_final: 0.7907 (m110) REVERT: B 392 LYS cc_start: 0.7498 (mttt) cc_final: 0.7211 (mttp) REVERT: C 66 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8278 (mt-10) REVERT: C 246 ASP cc_start: 0.8494 (m-30) cc_final: 0.8227 (m-30) REVERT: C 392 LYS cc_start: 0.7502 (mttt) cc_final: 0.7187 (mttp) REVERT: C 454 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7980 (ttm170) REVERT: E 246 ASP cc_start: 0.8499 (m-30) cc_final: 0.8227 (m-30) REVERT: E 392 LYS cc_start: 0.7446 (mttt) cc_final: 0.7142 (mttp) REVERT: E 454 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7724 (ttm170) REVERT: E 465 ARG cc_start: 0.7410 (ttt180) cc_final: 0.7007 (ttt-90) outliers start: 34 outliers final: 17 residues processed: 374 average time/residue: 1.0924 time to fit residues: 461.3263 Evaluate side-chains 325 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 308 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 329 ASN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130966 restraints weight = 49201.020| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.63 r_work: 0.3297 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16428 Z= 0.220 Angle : 0.680 14.985 22228 Z= 0.344 Chirality : 0.080 1.581 2464 Planarity : 0.005 0.057 2820 Dihedral : 9.197 52.364 2420 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.92 % Allowed : 13.02 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.64 (0.18), residues: 1940 helix: 0.30 (0.17), residues: 900 sheet: -1.08 (0.25), residues: 392 loop : -0.79 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 102 TYR 0.015 0.002 TYR B 42 PHE 0.016 0.002 PHE E 163 TRP 0.013 0.002 TRP E 387 HIS 0.005 0.002 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (16428) covalent geometry : angle 0.68042 / 0.34 (22228) hydrogen bonds : bond 0.04139 / 2.77 ( 692) hydrogen bonds : angle 5.29761 / 3.82 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8499 (mtm) cc_final: 0.7837 (mmt) REVERT: A 191 GLU cc_start: 0.6904 (tt0) cc_final: 0.6651 (tm-30) REVERT: A 284 LYS cc_start: 0.7483 (mttt) cc_final: 0.6929 (mtpm) REVERT: A 392 LYS cc_start: 0.7529 (mttt) cc_final: 0.7229 (mmtp) REVERT: A 448 MET cc_start: 0.7992 (ttp) cc_final: 0.7599 (ttp) REVERT: A 454 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7838 (ttm170) REVERT: A 502 GLN cc_start: 0.6648 (pt0) cc_final: 0.6427 (pt0) REVERT: B 228 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 232 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7146 (mtm) REVERT: B 284 LYS cc_start: 0.7435 (mttt) cc_final: 0.7215 (mmtp) REVERT: B 392 LYS cc_start: 0.7544 (mttt) cc_final: 0.7287 (mtmm) REVERT: C 109 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8081 (mmmt) REVERT: C 191 GLU cc_start: 0.6980 (tt0) cc_final: 0.6722 (tm-30) REVERT: C 228 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7415 (mm-30) REVERT: C 287 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7977 (t0) REVERT: C 392 LYS cc_start: 0.7504 (mttt) cc_final: 0.7244 (mtmm) REVERT: C 454 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7978 (ttm170) REVERT: E 109 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8053 (mmmt) REVERT: E 191 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: E 392 LYS cc_start: 0.7462 (mttt) cc_final: 0.7181 (mtmm) REVERT: E 454 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7712 (ttm170) REVERT: E 465 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7083 (ttt-90) REVERT: E 502 GLN cc_start: 0.6728 (pt0) cc_final: 0.6525 (pt0) outliers start: 51 outliers final: 25 residues processed: 377 average time/residue: 1.0928 time to fit residues: 466.6042 Evaluate side-chains 354 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 537 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 117 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 GLN A 179 HIS A 329 ASN B 122 GLN B 179 HIS B 329 ASN C 122 GLN C 179 HIS C 329 ASN E 122 GLN E 179 HIS E 185 GLN E 329 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131275 restraints weight = 49264.662| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.63 r_work: 0.3307 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.143 Angle : 0.595 14.893 22228 Z= 0.297 Chirality : 0.078 1.548 2464 Planarity : 0.005 0.044 2820 Dihedral : 8.701 49.745 2420 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.29 % Allowed : 13.88 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.34 (0.19), residues: 1940 helix: 0.59 (0.17), residues: 904 sheet: -0.93 (0.25), residues: 392 loop : -0.73 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 102 TYR 0.014 0.001 TYR E 42 PHE 0.013 0.001 PHE E 163 TRP 0.012 0.002 TRP E 387 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (16428) covalent geometry : angle 0.59461 / 0.30 (22228) hydrogen bonds : bond 0.03455 / 2.32 ( 692) hydrogen bonds : angle 4.96745 / 3.59 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 339 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8483 (mtm) cc_final: 0.7808 (mmt) REVERT: A 191 GLU cc_start: 0.6970 (tt0) cc_final: 0.6715 (tm-30) REVERT: A 284 LYS cc_start: 0.7598 (mttt) cc_final: 0.7395 (mmtp) REVERT: A 296 GLN cc_start: 0.7497 (mt0) cc_final: 0.6965 (mm110) REVERT: A 363 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7838 (ptmm) REVERT: A 392 LYS cc_start: 0.7470 (mttt) cc_final: 0.7042 (mmtp) REVERT: A 502 GLN cc_start: 0.6597 (pt0) cc_final: 0.6375 (pt0) REVERT: A 544 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 137 LYS cc_start: 0.7556 (pttt) cc_final: 0.7351 (pttp) REVERT: B 228 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7514 (mm-30) REVERT: B 392 LYS cc_start: 0.7455 (mttt) cc_final: 0.7173 (mtmm) REVERT: C 153 ASP cc_start: 0.7546 (p0) cc_final: 0.7221 (t0) REVERT: C 191 GLU cc_start: 0.6970 (tt0) cc_final: 0.6680 (tm-30) REVERT: C 228 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 300 SER cc_start: 0.8550 (m) cc_final: 0.8298 (t) REVERT: C 363 LYS cc_start: 0.8176 (ptmt) cc_final: 0.7808 (ptmm) REVERT: C 392 LYS cc_start: 0.7478 (mttt) cc_final: 0.7067 (mtmm) REVERT: C 454 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7941 (ttm170) REVERT: C 544 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8303 (mp) REVERT: E 191 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6351 (tm-30) REVERT: E 363 LYS cc_start: 0.8205 (ptmt) cc_final: 0.7979 (ptmm) REVERT: E 392 LYS cc_start: 0.7411 (mttt) cc_final: 0.6900 (mtmm) REVERT: E 454 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7715 (ttm170) REVERT: E 465 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7082 (ttt-90) REVERT: E 544 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8313 (mp) outliers start: 40 outliers final: 21 residues processed: 370 average time/residue: 1.1241 time to fit residues: 469.6146 Evaluate side-chains 352 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 ASN C 329 ASN E 185 GLN E 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.156776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129349 restraints weight = 49505.140| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.55 r_work: 0.3281 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16428 Z= 0.182 Angle : 0.612 15.009 22228 Z= 0.307 Chirality : 0.078 1.538 2464 Planarity : 0.005 0.052 2820 Dihedral : 9.076 55.297 2420 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.31 (0.18), residues: 1940 helix: 0.68 (0.17), residues: 888 sheet: -0.83 (0.25), residues: 368 loop : -0.86 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 164 TYR 0.013 0.002 TYR A 42 PHE 0.013 0.001 PHE A 163 TRP 0.011 0.002 TRP C 387 HIS 0.005 0.002 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (16428) covalent geometry : angle 0.61165 / 0.31 (22228) hydrogen bonds : bond 0.03581 / 2.40 ( 692) hydrogen bonds : angle 4.99724 / 3.60 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 0.749 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 157 MET cc_start: 0.8483 (mtm) cc_final: 0.7837 (mmt) REVERT: A 191 GLU cc_start: 0.6917 (tt0) cc_final: 0.6663 (tm-30) REVERT: A 202 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: A 296 GLN cc_start: 0.7509 (mt0) cc_final: 0.7013 (mm110) REVERT: A 300 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8324 (t) REVERT: A 392 LYS cc_start: 0.7500 (mttt) cc_final: 0.7194 (mppt) REVERT: A 481 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6851 (mtp85) REVERT: B 202 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7593 (ttp-170) REVERT: B 228 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 392 LYS cc_start: 0.7462 (mttt) cc_final: 0.7201 (mtmm) REVERT: B 465 ARG cc_start: 0.7735 (ttt-90) cc_final: 0.7405 (ttt-90) REVERT: B 481 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6806 (mtp85) REVERT: C 153 ASP cc_start: 0.7579 (p0) cc_final: 0.7292 (t0) REVERT: C 191 GLU cc_start: 0.6983 (tt0) cc_final: 0.6676 (tm-30) REVERT: C 228 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7466 (mm-30) REVERT: C 237 ASN cc_start: 0.7236 (m110) cc_final: 0.6987 (m110) REVERT: C 300 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8301 (t) REVERT: C 363 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7971 (ptmm) REVERT: C 392 LYS cc_start: 0.7519 (mttt) cc_final: 0.7198 (mppt) REVERT: C 448 MET cc_start: 0.7911 (ttp) cc_final: 0.7667 (ttp) REVERT: C 454 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7948 (ttm170) REVERT: C 465 ARG cc_start: 0.7743 (ttt-90) cc_final: 0.7525 (ttt-90) REVERT: C 481 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6897 (mtp85) REVERT: E 191 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6329 (tm-30) REVERT: E 300 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8307 (t) REVERT: E 363 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7977 (ptmm) REVERT: E 392 LYS cc_start: 0.7489 (mttt) cc_final: 0.7216 (mtmm) REVERT: E 454 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7828 (ttm170) REVERT: E 465 ARG cc_start: 0.7512 (ttt180) cc_final: 0.7155 (ttt-90) REVERT: E 481 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6857 (mtp85) REVERT: E 502 GLN cc_start: 0.6471 (pt0) cc_final: 0.6263 (pt0) outliers start: 49 outliers final: 24 residues processed: 367 average time/residue: 1.1543 time to fit residues: 477.6175 Evaluate side-chains 363 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 202 ARG Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 144 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 189 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 240 GLN C 329 ASN E 165 GLN E 185 GLN E 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.158683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130875 restraints weight = 49616.103| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.64 r_work: 0.3312 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.124 Angle : 0.567 15.031 22228 Z= 0.281 Chirality : 0.077 1.530 2464 Planarity : 0.005 0.038 2820 Dihedral : 7.848 48.857 2420 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.06 % Allowed : 15.25 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1940 helix: 1.00 (0.18), residues: 888 sheet: -0.70 (0.25), residues: 364 loop : -0.77 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 164 TYR 0.013 0.001 TYR A 42 PHE 0.012 0.001 PHE E 163 TRP 0.023 0.002 TRP E 387 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (16428) covalent geometry : angle 0.56746 / 0.28 (22228) hydrogen bonds : bond 0.03195 / 2.14 ( 692) hydrogen bonds : angle 4.79752 / 3.46 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 0.829 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 157 MET cc_start: 0.8505 (mtm) cc_final: 0.7838 (mmt) REVERT: A 191 GLU cc_start: 0.6967 (tt0) cc_final: 0.6619 (tm-30) REVERT: A 296 GLN cc_start: 0.7489 (mt0) cc_final: 0.7021 (mm110) REVERT: A 300 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8328 (t) REVERT: A 337 ILE cc_start: 0.8630 (mt) cc_final: 0.8408 (pt) REVERT: A 392 LYS cc_start: 0.7391 (mttt) cc_final: 0.7019 (mppt) REVERT: A 481 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6912 (mtp85) REVERT: B 228 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 296 GLN cc_start: 0.7513 (mt0) cc_final: 0.7124 (mm-40) REVERT: B 337 ILE cc_start: 0.8626 (mt) cc_final: 0.8397 (pt) REVERT: B 392 LYS cc_start: 0.7290 (mttt) cc_final: 0.6879 (mtmm) REVERT: B 448 MET cc_start: 0.7974 (ttp) cc_final: 0.7770 (ttp) REVERT: B 481 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6806 (mtp85) REVERT: C 153 ASP cc_start: 0.7428 (p0) cc_final: 0.7200 (t0) REVERT: C 191 GLU cc_start: 0.7026 (tt0) cc_final: 0.6717 (tm-30) REVERT: C 228 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7463 (mm-30) REVERT: C 296 GLN cc_start: 0.7548 (mt0) cc_final: 0.7104 (mm110) REVERT: C 300 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8318 (t) REVERT: C 363 LYS cc_start: 0.8166 (ptmt) cc_final: 0.7951 (ptmm) REVERT: C 392 LYS cc_start: 0.7314 (mttt) cc_final: 0.6902 (mppt) REVERT: C 448 MET cc_start: 0.7873 (ttp) cc_final: 0.7641 (ttp) REVERT: C 481 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6939 (mtp85) REVERT: E 202 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7603 (ttp-170) REVERT: E 283 PHE cc_start: 0.6589 (t80) cc_final: 0.6128 (t80) REVERT: E 287 ASN cc_start: 0.8347 (t0) cc_final: 0.7973 (m-40) REVERT: E 300 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8269 (t) REVERT: E 363 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7893 (ptmm) REVERT: E 392 LYS cc_start: 0.7136 (mttt) cc_final: 0.6686 (mtmm) REVERT: E 454 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7833 (ttm170) REVERT: E 465 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7137 (ttt-90) REVERT: E 481 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6858 (mtp85) outliers start: 36 outliers final: 20 residues processed: 366 average time/residue: 1.1455 time to fit residues: 471.8979 Evaluate side-chains 361 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 158 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 ASN C 240 GLN C 329 ASN E 165 GLN E 185 GLN E 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128886 restraints weight = 49651.536| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.64 r_work: 0.3282 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16428 Z= 0.177 Angle : 0.603 15.082 22228 Z= 0.301 Chirality : 0.078 1.530 2464 Planarity : 0.005 0.053 2820 Dihedral : 8.519 51.729 2420 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.06 % Allowed : 16.51 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.10 (0.18), residues: 1940 helix: 0.84 (0.17), residues: 888 sheet: -0.59 (0.26), residues: 356 loop : -0.83 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 465 TYR 0.012 0.002 TYR C 42 PHE 0.013 0.001 PHE C 163 TRP 0.021 0.002 TRP E 387 HIS 0.005 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (16428) covalent geometry : angle 0.60264 / 0.30 (22228) hydrogen bonds : bond 0.03443 / 2.31 ( 692) hydrogen bonds : angle 4.91330 / 3.53 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 340 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8525 (mtm) cc_final: 0.7860 (mmt) REVERT: A 191 GLU cc_start: 0.6838 (tt0) cc_final: 0.6489 (tm-30) REVERT: A 296 GLN cc_start: 0.7516 (mt0) cc_final: 0.7062 (mm110) REVERT: A 300 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (t) REVERT: A 392 LYS cc_start: 0.7450 (mttt) cc_final: 0.7156 (mppt) REVERT: A 481 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6907 (mtp85) REVERT: B 228 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7542 (mm-30) REVERT: B 296 GLN cc_start: 0.7542 (mt0) cc_final: 0.7163 (mm-40) REVERT: B 392 LYS cc_start: 0.7388 (mttt) cc_final: 0.7144 (mtmm) REVERT: B 481 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6718 (mtp85) REVERT: C 153 ASP cc_start: 0.7526 (p0) cc_final: 0.7271 (t0) REVERT: C 191 GLU cc_start: 0.7003 (tt0) cc_final: 0.6714 (tm-30) REVERT: C 228 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 296 GLN cc_start: 0.7564 (mt0) cc_final: 0.7120 (mm110) REVERT: C 300 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8310 (t) REVERT: C 363 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7924 (ptmm) REVERT: C 392 LYS cc_start: 0.7435 (mttt) cc_final: 0.7176 (mppt) REVERT: C 448 MET cc_start: 0.7884 (ttp) cc_final: 0.7635 (ttp) REVERT: C 481 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6953 (mtp85) REVERT: E 202 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: E 283 PHE cc_start: 0.6604 (t80) cc_final: 0.6211 (t80) REVERT: E 287 ASN cc_start: 0.8304 (t0) cc_final: 0.7957 (m-40) REVERT: E 296 GLN cc_start: 0.7537 (mt0) cc_final: 0.7065 (mm-40) REVERT: E 300 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8232 (t) REVERT: E 363 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7905 (ptmm) REVERT: E 392 LYS cc_start: 0.7231 (mttt) cc_final: 0.6962 (mtmm) REVERT: E 454 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7827 (ttm170) REVERT: E 465 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7146 (ttt-90) REVERT: E 481 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6973 (mtp85) outliers start: 36 outliers final: 23 residues processed: 360 average time/residue: 1.1198 time to fit residues: 453.2736 Evaluate side-chains 360 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 330 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN A 329 ASN B 329 ASN C 237 ASN C 240 GLN C 329 ASN E 198 GLN E 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127760 restraints weight = 49663.231| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.64 r_work: 0.3266 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16428 Z= 0.208 Angle : 0.625 15.129 22228 Z= 0.313 Chirality : 0.078 1.524 2464 Planarity : 0.005 0.052 2820 Dihedral : 9.021 54.751 2420 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.89 % Allowed : 17.03 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.30 (0.18), residues: 1940 helix: 0.64 (0.17), residues: 888 sheet: -0.62 (0.26), residues: 356 loop : -0.91 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 465 TYR 0.017 0.002 TYR E 74 PHE 0.013 0.002 PHE C 163 TRP 0.017 0.002 TRP E 387 HIS 0.005 0.002 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (16428) covalent geometry : angle 0.62477 / 0.31 (22228) hydrogen bonds : bond 0.03639 / 2.44 ( 692) hydrogen bonds : angle 5.03775 / 3.62 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8546 (mtm) cc_final: 0.7880 (mmt) REVERT: A 191 GLU cc_start: 0.6822 (tt0) cc_final: 0.6471 (tm-30) REVERT: A 283 PHE cc_start: 0.7110 (t80) cc_final: 0.6565 (t80) REVERT: A 296 GLN cc_start: 0.7560 (mt0) cc_final: 0.7118 (mm110) REVERT: A 300 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8278 (t) REVERT: A 392 LYS cc_start: 0.7448 (mttt) cc_final: 0.7205 (mppt) REVERT: A 481 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6898 (mtp85) REVERT: B 228 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7563 (mm-30) REVERT: B 296 GLN cc_start: 0.7512 (mt0) cc_final: 0.7081 (mm-40) REVERT: B 392 LYS cc_start: 0.7406 (mttt) cc_final: 0.7180 (mppt) REVERT: B 481 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6862 (mtp85) REVERT: B 502 GLN cc_start: 0.6356 (pt0) cc_final: 0.6132 (pt0) REVERT: C 153 ASP cc_start: 0.7548 (p0) cc_final: 0.7083 (t0) REVERT: C 191 GLU cc_start: 0.7058 (tt0) cc_final: 0.6740 (tm-30) REVERT: C 228 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 267 LYS cc_start: 0.8166 (tttm) cc_final: 0.7940 (tttp) REVERT: C 296 GLN cc_start: 0.7575 (mt0) cc_final: 0.7153 (mm110) REVERT: C 300 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8243 (t) REVERT: C 363 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7913 (ptmm) REVERT: C 392 LYS cc_start: 0.7398 (mttt) cc_final: 0.7147 (mppt) REVERT: C 481 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6945 (mtp85) REVERT: E 202 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7674 (ttp-170) REVERT: E 283 PHE cc_start: 0.6752 (t80) cc_final: 0.6448 (t80) REVERT: E 287 ASN cc_start: 0.8298 (t0) cc_final: 0.7939 (m-40) REVERT: E 296 GLN cc_start: 0.7539 (mt0) cc_final: 0.7054 (mm110) REVERT: E 300 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8266 (t) REVERT: E 363 LYS cc_start: 0.8294 (ptmt) cc_final: 0.8086 (ptmm) REVERT: E 392 LYS cc_start: 0.7226 (mttt) cc_final: 0.6962 (mtmm) REVERT: E 454 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7842 (ttm170) REVERT: E 465 ARG cc_start: 0.7572 (ttt180) cc_final: 0.7173 (ttt-90) REVERT: E 481 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6940 (mtp85) outliers start: 33 outliers final: 22 residues processed: 364 average time/residue: 1.1017 time to fit residues: 452.4636 Evaluate side-chains 367 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 ASN C 240 GLN C 329 ASN E 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.156459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128840 restraints weight = 49458.778| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.57 r_work: 0.3281 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.143 Angle : 0.577 15.152 22228 Z= 0.286 Chirality : 0.077 1.525 2464 Planarity : 0.005 0.039 2820 Dihedral : 7.992 49.156 2418 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.01 % Allowed : 17.43 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.07 (0.19), residues: 1940 helix: 0.88 (0.17), residues: 888 sheet: -0.59 (0.26), residues: 356 loop : -0.84 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 465 TYR 0.012 0.001 TYR A 42 PHE 0.012 0.001 PHE C 163 TRP 0.018 0.002 TRP E 387 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (16428) covalent geometry : angle 0.57706 / 0.29 (22228) hydrogen bonds : bond 0.03251 / 2.18 ( 692) hydrogen bonds : angle 4.84613 / 3.50 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 347 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8474 (mtm) cc_final: 0.7850 (mmt) REVERT: A 191 GLU cc_start: 0.6810 (tt0) cc_final: 0.6462 (tm-30) REVERT: A 296 GLN cc_start: 0.7542 (mt0) cc_final: 0.7108 (mm110) REVERT: A 300 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8234 (t) REVERT: A 392 LYS cc_start: 0.7398 (mttt) cc_final: 0.7141 (mppt) REVERT: A 481 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6931 (mtp85) REVERT: B 228 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 296 GLN cc_start: 0.7557 (mt0) cc_final: 0.7133 (mm-40) REVERT: B 392 LYS cc_start: 0.7331 (mttt) cc_final: 0.7085 (mppt) REVERT: B 448 MET cc_start: 0.7970 (ttp) cc_final: 0.7725 (ttp) REVERT: B 481 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6889 (mtp85) REVERT: B 502 GLN cc_start: 0.6359 (pt0) cc_final: 0.6119 (pt0) REVERT: C 16 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8928 (ttmm) REVERT: C 153 ASP cc_start: 0.7531 (p0) cc_final: 0.7111 (t0) REVERT: C 191 GLU cc_start: 0.7014 (tt0) cc_final: 0.6702 (tm-30) REVERT: C 228 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 267 LYS cc_start: 0.8167 (tttm) cc_final: 0.7930 (tttp) REVERT: C 296 GLN cc_start: 0.7571 (mt0) cc_final: 0.7142 (mm110) REVERT: C 300 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8296 (t) REVERT: C 363 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7900 (ptmm) REVERT: C 392 LYS cc_start: 0.7394 (mttt) cc_final: 0.7142 (mppt) REVERT: C 481 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6988 (mtp85) REVERT: E 153 ASP cc_start: 0.7632 (p0) cc_final: 0.7206 (t0) REVERT: E 202 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7574 (ttp-170) REVERT: E 283 PHE cc_start: 0.6789 (t80) cc_final: 0.6359 (t80) REVERT: E 287 ASN cc_start: 0.8302 (t0) cc_final: 0.7957 (m-40) REVERT: E 296 GLN cc_start: 0.7587 (mt0) cc_final: 0.7078 (mm110) REVERT: E 300 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (t) REVERT: E 363 LYS cc_start: 0.8183 (ptmt) cc_final: 0.7936 (ptmm) REVERT: E 392 LYS cc_start: 0.7221 (mttt) cc_final: 0.6962 (mtmm) REVERT: E 454 ARG cc_start: 0.8089 (ttm110) cc_final: 0.7860 (ttm170) REVERT: E 465 ARG cc_start: 0.7528 (ttt180) cc_final: 0.7268 (ttt-90) REVERT: E 481 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6951 (mtp85) outliers start: 35 outliers final: 19 residues processed: 363 average time/residue: 1.1179 time to fit residues: 458.4632 Evaluate side-chains 368 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 240 GLN A 329 ASN B 329 ASN B 383 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN C 329 ASN E 185 GLN E 198 GLN E 329 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130186 restraints weight = 49750.349| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.57 r_work: 0.3283 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.127 Angle : 0.565 15.208 22228 Z= 0.279 Chirality : 0.077 1.531 2464 Planarity : 0.004 0.038 2820 Dihedral : 7.424 46.332 2416 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 18.06 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.08 (0.19), residues: 1940 helix: 1.06 (0.17), residues: 888 sheet: -0.56 (0.26), residues: 356 loop : -0.83 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 465 TYR 0.013 0.001 TYR C 42 PHE 0.011 0.001 PHE C 163 TRP 0.016 0.002 TRP E 387 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16428) covalent geometry : angle 0.56489 / 0.28 (22228) hydrogen bonds : bond 0.03114 / 2.10 ( 692) hydrogen bonds : angle 4.74066 / 3.42 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 356 time to evaluate : 0.702 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 157 MET cc_start: 0.8467 (mtm) cc_final: 0.7850 (mmt) REVERT: A 191 GLU cc_start: 0.6821 (tt0) cc_final: 0.6463 (tm-30) REVERT: A 296 GLN cc_start: 0.7594 (mt0) cc_final: 0.7173 (mm110) REVERT: A 300 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 392 LYS cc_start: 0.7291 (mttt) cc_final: 0.7051 (mppt) REVERT: A 393 ILE cc_start: 0.7773 (mt) cc_final: 0.7558 (mm) REVERT: A 481 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6958 (mtp85) REVERT: B 137 LYS cc_start: 0.7768 (pttp) cc_final: 0.7396 (ptpt) REVERT: B 228 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7633 (mm-30) REVERT: B 296 GLN cc_start: 0.7592 (mt0) cc_final: 0.7169 (mm-40) REVERT: B 392 LYS cc_start: 0.7234 (mttt) cc_final: 0.6979 (mppt) REVERT: B 448 MET cc_start: 0.7964 (ttp) cc_final: 0.7763 (ttp) REVERT: B 481 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6900 (mtp85) REVERT: B 502 GLN cc_start: 0.6342 (pt0) cc_final: 0.6094 (pt0) REVERT: C 16 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8935 (ttmm) REVERT: C 153 ASP cc_start: 0.7482 (p0) cc_final: 0.7182 (t0) REVERT: C 191 GLU cc_start: 0.6991 (tt0) cc_final: 0.6742 (tm-30) REVERT: C 228 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7493 (mm-30) REVERT: C 267 LYS cc_start: 0.8168 (tttm) cc_final: 0.7935 (tttp) REVERT: C 296 GLN cc_start: 0.7587 (mt0) cc_final: 0.7152 (mm110) REVERT: C 300 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8278 (t) REVERT: C 363 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7885 (ptmm) REVERT: C 392 LYS cc_start: 0.7293 (mttt) cc_final: 0.7048 (mppt) REVERT: C 481 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7014 (mtp85) REVERT: E 153 ASP cc_start: 0.7493 (p0) cc_final: 0.7182 (t0) REVERT: E 202 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7557 (ttp-170) REVERT: E 283 PHE cc_start: 0.6675 (t80) cc_final: 0.6344 (t80) REVERT: E 287 ASN cc_start: 0.8280 (t0) cc_final: 0.7988 (m-40) REVERT: E 296 GLN cc_start: 0.7634 (mt0) cc_final: 0.7111 (mm110) REVERT: E 300 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8258 (t) REVERT: E 363 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7737 (ptmm) REVERT: E 392 LYS cc_start: 0.7209 (mttt) cc_final: 0.6964 (mtmm) REVERT: E 454 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7859 (ttm170) REVERT: E 465 ARG cc_start: 0.7573 (ttt180) cc_final: 0.7288 (ttt-90) REVERT: E 481 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6967 (mtp85) outliers start: 30 outliers final: 18 residues processed: 370 average time/residue: 1.0998 time to fit residues: 460.0929 Evaluate side-chains 376 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 350 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 481 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 481 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 55 HIS Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 498 SER Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 521 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 192 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 150 optimal weight: 0.0670 chunk 116 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 329 ASN B 329 ASN C 165 GLN C 240 GLN C 329 ASN E 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130526 restraints weight = 49553.120| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.58 r_work: 0.3292 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16428 Z= 0.122 Angle : 0.559 15.202 22228 Z= 0.276 Chirality : 0.077 1.536 2464 Planarity : 0.004 0.037 2820 Dihedral : 7.292 45.353 2416 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 18.81 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.16 (0.19), residues: 1940 helix: 1.16 (0.18), residues: 888 sheet: -0.53 (0.26), residues: 356 loop : -0.82 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 465 TYR 0.013 0.001 TYR A 74 PHE 0.011 0.001 PHE B 163 TRP 0.023 0.002 TRP E 387 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (16428) covalent geometry : angle 0.55920 / 0.28 (22228) hydrogen bonds : bond 0.03072 / 2.07 ( 692) hydrogen bonds : angle 4.70021 / 3.40 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11499.19 seconds wall clock time: 194 minutes 42.81 seconds (11682.81 seconds total)